Carrel name: journal-virusGenes-cord Creating study carrel named journal-virusGenes-cord Initializing database file: cache/cord-005207-02wmt2e9.json key: cord-005207-02wmt2e9 authors: Lee, Hee-Kyung; Yeo, Sang-Geon title: Cloning and Sequence Analysis of the Nucleocapsid Gene of Porcine Epidemic Diarrhea Virus Chinju99 date: 2003 journal: Virus Genes DOI: 10.1023/a:1023447732567 sha: doc_id: 5207 cord_uid: 02wmt2e9 file: cache/cord-005252-m02inmc4.json key: cord-005252-m02inmc4 authors: Kwon, Hyuk Moo; Jackwood, Mark W. title: Molecular cloning and sequence comparison of the S1 glycoprotein of the Gray and JMK strains of avian infectious bronchitis virus date: 1995 journal: Virus Genes DOI: 10.1007/bf01702878 sha: doc_id: 5252 cord_uid: m02inmc4 file: cache/cord-257122-h3zi8k8g.json key: cord-257122-h3zi8k8g authors: Lin, Chao-Nan; Chang, Ruey-Yi; Su, Bi-Ling; Chueh, Ling-Ling title: Full genome analysis of a novel type II feline coronavirus NTU156 date: 2012-12-14 journal: Virus Genes DOI: 10.1007/s11262-012-0864-0 sha: doc_id: 257122 cord_uid: h3zi8k8g file: cache/cord-266634-bww62vx8.json key: cord-266634-bww62vx8 authors: Gopinath, M.; Shaila, M. S. title: Evidence for N(7) guanine methyl transferase activity encoded within the modular domain of RNA-dependent RNA polymerase L of a Morbillivirus date: 2015-10-07 journal: Virus Genes DOI: 10.1007/s11262-015-1252-3 sha: doc_id: 266634 cord_uid: bww62vx8 file: cache/cord-284675-7zv449sc.json key: cord-284675-7zv449sc authors: Yew, Tan Do; Bejo, Mohd Hair; Ideris, Aini; Omar, Abdul Rahman; Meng, Goh Yong title: Base Usage and Dinucleotide Frequency of Infectious Bursal Disease Virus date: 2004 journal: Virus Genes DOI: 10.1023/b:viru.0000012262.89898.c7 sha: doc_id: 284675 cord_uid: 7zv449sc file: cache/cord-012091-3bo88tux.json key: cord-012091-3bo88tux authors: Ibrahim, Madiha Salah; Watanabe, Yohei; Ellakany, H. F.; Yamagishi, Aki; Sapsutthipas, Sompong; Toyoda, Tetsuya; Abd El-Hamied, H. S.; Ikuta, Kazuyoshi title: Host-specific genetic variation of highly pathogenic avian influenza viruses (H5N1) date: 2011-02-17 journal: Virus Genes DOI: 10.1007/s11262-011-0583-y sha: doc_id: 12091 cord_uid: 3bo88tux file: cache/cord-288239-ca5uthvd.json key: cord-288239-ca5uthvd authors: Jeoung, Hye-Young; Lim, Ji-Ae; Jeong, Wooseog; Oem, Jae-Ku; An, Dong-Jun title: Three clusters of bovine kobuvirus isolated in Korea, 2008–2010 date: 2011-03-12 journal: Virus Genes DOI: 10.1007/s11262-011-0593-9 sha: doc_id: 288239 cord_uid: ca5uthvd file: cache/cord-259398-s8qsjkj2.json key: cord-259398-s8qsjkj2 authors: Chouljenko, Vladimir N.; Kousoulas, Konstantin G.; Lin, Xiaoqing; Storz, Johannes title: Nucleotide and Predicted Amino Acid Sequences of All Genes Encoded by the 3′ Genomic Portion (9.5 kb) of Respiratory Bovine Coronaviruses and Comparisons Among Respiratory and Enteric Coronaviruses date: 1998 journal: Virus Genes DOI: 10.1023/a:1008048916808 sha: doc_id: 259398 cord_uid: s8qsjkj2 file: cache/cord-282126-gmjnbnx5.json key: cord-282126-gmjnbnx5 authors: Yang, Limin; Li, Jing; Bi, Yuhai; Xu, Lei; Liu, Wenjun title: Development and application of a reverse transcription loop-mediated isothermal amplification method for rapid detection of Duck hepatitis A virus type 1 date: 2012-08-07 journal: Virus Genes DOI: 10.1007/s11262-012-0798-6 sha: doc_id: 282126 cord_uid: gmjnbnx5 file: cache/cord-302584-fwdpzv85.json key: cord-302584-fwdpzv85 authors: Zhu, Ying; Liu, Mo; Zhao, Weiguang; Zhang, Jianlin; Zhang, Xue; Wang, Ke; Gu, Chunfang; Wu, Kailang; Li, Yan; Zheng, Congyi; Xiao, Gengfu; Yan, Huimin; Zhang, Jiamin; Guo, Deyin; Tien, Po; Wu, Jianguo title: Isolation of Virus from a SARS Patient and Genome-wide Analysis of Genetic Mutations Related to Pathogenesis and Epidemiology from 47 SARS-CoV Isolates date: 2005-01-01 journal: Virus Genes DOI: 10.1007/s11262-004-4586-9 sha: doc_id: 302584 cord_uid: fwdpzv85 file: cache/cord-307580-nokd5kmx.json key: cord-307580-nokd5kmx authors: Yang, Guang; Che, Xibing; Gofman, Rose; Ben-Shalom, Yossi; Piestun, Dan; Gafny, Ron; Mawassi, Munir; Bar-Joseph, Moshe title: D-RNA Molecules Associated with Subisolates of the VT Strain of Citrus Tristeza Virus which Induce Different Seedling-Yellows Reactions date: 1999 journal: Virus Genes DOI: 10.1023/a:1008105004407 sha: doc_id: 307580 cord_uid: nokd5kmx file: cache/cord-311712-lkvt9slp.json key: cord-311712-lkvt9slp authors: Barrett, John W.; Sun, Yunming; Nazarian, Steven H.; Belsito, Tara A.; Brunetti, Craig R.; McFadden, Grant title: Optimization of Codon Usage of Poxvirus Genes allows for Improved Transient Expression in Mammalian Cells date: 2006 journal: Virus Genes DOI: 10.1007/s11262-005-0035-7 sha: doc_id: 311712 cord_uid: lkvt9slp file: cache/cord-268627-nnx46nwf.json key: cord-268627-nnx46nwf authors: Ren, Xiaofeng; Li, Pengchong title: Development of reverse transcription loop-mediated isothermal amplification for rapid detection of porcine epidemic diarrhea virus date: 2011-02-01 journal: Virus Genes DOI: 10.1007/s11262-011-0570-3 sha: doc_id: 268627 cord_uid: nnx46nwf file: cache/cord-322475-i29t7ce8.json key: cord-322475-i29t7ce8 authors: Chen, Xi; Yang, Jinxian; Yu, Fusong; Ge, Junqing; Lin, Tianlong; Song, Tieying title: Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) samples from field cases in Fujian, China date: 2012-07-29 journal: Virus Genes DOI: 10.1007/s11262-012-0794-x sha: doc_id: 322475 cord_uid: i29t7ce8 file: cache/cord-348896-a2mjj5dt.json key: cord-348896-a2mjj5dt authors: Abid, Nabil Ben Salem; Chupin, Sergei A.; Bjadovskaya, Olga P.; Andreeva, Olga G.; Aouni, Mahjoub; Buesa, Javier; Baybikov, Taufik Z.; Prokhvatilova, Larisa B. title: Molecular study of porcine transmissible gastroenteritis virus after serial animal passages revealed point mutations in S protein date: 2010-12-28 journal: Virus Genes DOI: 10.1007/s11262-010-0562-8 sha: doc_id: 348896 cord_uid: a2mjj5dt file: cache/cord-283168-kl1hoa1x.json key: cord-283168-kl1hoa1x authors: Farkas, Tibor; Fey, Brittney; Hargitt, Edwin; Parcells, Mark; Ladman, Brian; Murgia, Maria; Saif, Yehia title: Molecular detection of novel picornaviruses in chickens and turkeys date: 2011-12-13 journal: Virus Genes DOI: 10.1007/s11262-011-0695-4 sha: doc_id: 283168 cord_uid: kl1hoa1x file: cache/cord-311204-fc12f845.json key: cord-311204-fc12f845 authors: Zhou, Ling; Tang, Qinghai; Shi, Lijun; Kong, Miaomiao; Liang, Lin; Mao, Qianqian; Bu, Bin; Yao, Lunguang; Zhao, Kai; Cui, Shangjin; Leal, Élcio title: Full-length genomic characterization and molecular evolution of canine parvovirus in China date: 2016-04-02 journal: Virus Genes DOI: 10.1007/s11262-016-1309-y sha: doc_id: 311204 cord_uid: fc12f845 file: cache/cord-269720-o81j3d1j.json key: cord-269720-o81j3d1j authors: Page, Kevin W.; Britton, Paul; Boursnell, Michael E. G. title: Sequence analysis of the leader RNA of two porcine coronaviruses: Transmissible gastroenteritis virus and porcine respiratory coronavirus date: 1990 journal: Virus Genes DOI: 10.1007/bf00570024 sha: doc_id: 269720 cord_uid: o81j3d1j file: cache/cord-269340-o9jdt86j.json key: cord-269340-o9jdt86j authors: Callison, Scott Andrew; Jackwood, Mark W.; Hilt, Deborah Ann title: Infectious Bronchitis Virus S2 Gene Sequence Variability May Affect S1 Subunit Specific Antibody Binding date: 1999 journal: Virus Genes DOI: 10.1023/a:1008179208217 sha: doc_id: 269340 cord_uid: o9jdt86j file: cache/cord-011794-ejoufvvj.json key: cord-011794-ejoufvvj authors: Binder, Florian; Reiche, Sven; Roman-Sosa, Gleyder; Saathoff, Marion; Ryll, René; Trimpert, Jakob; Kunec, Dusan; Höper, Dirk; Ulrich, Rainer G. title: Isolation and characterization of new Puumala orthohantavirus strains from Germany date: 2020-04-23 journal: Virus Genes DOI: 10.1007/s11262-020-01755-3 sha: doc_id: 11794 cord_uid: ejoufvvj file: cache/cord-295554-0pzjyrdf.json key: cord-295554-0pzjyrdf authors: Lima, Francisco Esmaile de Sales; Campos, Fabrício Souza; Kunert Filho, Hiran Castagnino; Batista, Helena Beatriz de Carvalho Ruthner; Carnielli Júnior, Pedro; Cibulski, Samuel Paulo; Spilki, Fernando Rosado; Roehe, Paulo Michel; Franco, Ana Cláudia title: Detection of Alphacoronavirus in velvety free-tailed bats (Molossus molossus) and Brazilian free-tailed bats (Tadarida brasiliensis) from urban area of Southern Brazil date: 2013-03-16 journal: Virus Genes DOI: 10.1007/s11262-013-0899-x sha: doc_id: 295554 cord_uid: 0pzjyrdf file: cache/cord-303672-ujp78213.json key: cord-303672-ujp78213 authors: Gu, Wen-yuan; Li, Yan; Liu, Bao-jing; Wang, Jing; Yuan, Guang-fu; Chen, Shao-jie; Zuo, Yu-Zhu; Fan, Jing-Hui title: Short hairpin RNAs targeting M and N genes reduce replication of porcine deltacoronavirus in ST cells date: 2019-08-28 journal: Virus Genes DOI: 10.1007/s11262-019-01701-y sha: doc_id: 303672 cord_uid: ujp78213 file: cache/cord-265095-lf5j4ic7.json key: cord-265095-lf5j4ic7 authors: Ten Dam, Edwin B.; Pleij, Cornelius W. A.; Bosch, Leendert title: RNA pseudoknots: Translational frameshifting and readthrough on viral RNAs date: 1990 journal: Virus Genes DOI: 10.1007/bf00678404 sha: doc_id: 265095 cord_uid: lf5j4ic7 file: cache/cord-331919-6kistim2.json key: cord-331919-6kistim2 authors: Song, Daesub; Park, Bongkyun title: Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines date: 2012-01-22 journal: Virus Genes DOI: 10.1007/s11262-012-0713-1 sha: doc_id: 331919 cord_uid: 6kistim2 file: cache/cord-254291-y8xvh6hs.json key: cord-254291-y8xvh6hs authors: Yamanaka, Miles; Crisp, Tracey; Brown, Rhonda; Dale, Beverly title: Nucleotide Sequence of the Inter-Structural Gene Region of Feline Infectious Peritonitis Virus date: 1998 journal: Virus Genes DOI: 10.1023/a:1008099209942 sha: doc_id: 254291 cord_uid: y8xvh6hs file: cache/cord-303834-yqysedne.json key: cord-303834-yqysedne authors: Ducatez, Mariette F.; Liais, Etienne; Croville, Guillaume; Guérin, Jean-Luc title: Full genome sequence of guinea fowl coronavirus associated with fulminating disease date: 2015-02-25 journal: Virus Genes DOI: 10.1007/s11262-015-1183-z sha: doc_id: 303834 cord_uid: yqysedne file: cache/cord-263489-i4tkdgy4.json key: cord-263489-i4tkdgy4 authors: Suo, Siqingaowa; Wang, Xue; Zarlenga, Dante; Bu, Ri-e; Ren, Yudong; Ren, Xiaofeng title: Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential date: 2015-05-27 journal: Virus Genes DOI: 10.1007/s11262-015-1208-7 sha: doc_id: 263489 cord_uid: i4tkdgy4 file: cache/cord-299573-vq6ckqtd.json key: cord-299573-vq6ckqtd authors: Lee, Meong-Hun; Jeoung, Hye-Young; Park, Hye-Ran; Lim, Ji-Ae; Song, Jae-Young; An, Dong-Jun title: Phylogenetic analysis of porcine astrovirus in domestic pigs and wild boars in South Korea date: 2012-09-11 journal: Virus Genes DOI: 10.1007/s11262-012-0816-8 sha: doc_id: 299573 cord_uid: vq6ckqtd file: cache/cord-346643-os2kyvvf.json key: cord-346643-os2kyvvf authors: Wang, Li; Dai, Xianjin; Song, Han; Yuan, Peng; Yang, Zhou; Dong, Wei; Song, Zhenhui title: Inhibition of porcine transmissible gastroenteritis virus infection in porcine kidney cells using short hairpin RNAs targeting the membrane gene date: 2016-11-15 journal: Virus Genes DOI: 10.1007/s11262-016-1409-8 sha: doc_id: 346643 cord_uid: os2kyvvf file: cache/cord-333914-c150ki1n.json key: cord-333914-c150ki1n authors: Koba, Ryota; Suzuki, Satori; Sato, Go; Sato, Shingo; Suzuki, Kazuo; Maruyama, Soichi; Tohya, Yukinobu title: Identification and characterization of a novel bat polyomavirus in Japan date: 2020-08-20 journal: Virus Genes DOI: 10.1007/s11262-020-01789-7 sha: doc_id: 333914 cord_uid: c150ki1n file: cache/cord-328518-umvk59dc.json key: cord-328518-umvk59dc authors: Lee, Dana N.; Angiel, Meagan title: Two novel adenoviruses found in Cave Myotis bats (Myotis velifer) in Oklahoma date: 2019-12-03 journal: Virus Genes DOI: 10.1007/s11262-019-01719-2 sha: doc_id: 328518 cord_uid: umvk59dc file: cache/cord-005253-8qja4j9h.json key: cord-005253-8qja4j9h authors: Li, Weike; Li, Tiansong; Liu, Yuxiu; Gao, Yuwei; Yang, Songtao; Feng, Na; Sun, Heting; Wang, Shengle; Wang, Lei; Bu, Zhigao; Xia, Xianzhu title: Genetic characterization of an isolate of canine distemper virus from a Tibetan Mastiff in China date: 2014-04-02 journal: Virus Genes DOI: 10.1007/s11262-014-1062-z sha: doc_id: 5253 cord_uid: 8qja4j9h file: cache/cord-272693-432ixb7g.json key: cord-272693-432ixb7g authors: Phillips, J. E.; Jackwood, M. W.; McKinley, E. T.; Thor, S. W.; Hilt, D. A.; Acevedol, N. D.; Williams, S. M.; Kissinger, J. C.; Paterson, A. H.; Robertson, J. S.; Lemke, C. title: Changes in nonstructural protein 3 are associated with attenuation in avian coronavirus infectious bronchitis virus date: 2011-09-10 journal: Virus Genes DOI: 10.1007/s11262-011-0668-7 sha: doc_id: 272693 cord_uid: 432ixb7g file: cache/cord-287748-co9j3uig.json key: cord-287748-co9j3uig authors: Kobayashi, Tomoya; Murakami, Shin; Yamamoto, Terumasa; Mineshita, Ko; Sakuyama, Muneki; Sasaki, Reiko; Maeda, Ken; Horimoto, Taisuke title: Detection of bat hepatitis E virus RNA in microbats in Japan date: 2018-05-29 journal: Virus Genes DOI: 10.1007/s11262-018-1577-9 sha: doc_id: 287748 cord_uid: co9j3uig file: cache/cord-344558-1jgqofbr.json key: cord-344558-1jgqofbr authors: Kocherhans, Rolf; Bridgen, Anne; Ackermann, Mathias; Tobler, Kurt title: Completion of the Porcine Epidemic Diarrhoea Coronavirus (PEDV) Genome Sequence date: 2001 journal: Virus Genes DOI: 10.1023/a:1011831902219 sha: doc_id: 344558 cord_uid: 1jgqofbr file: cache/cord-310298-26x2p9wc.json key: cord-310298-26x2p9wc authors: Tao, Pan; Dai, Li; Luo, Mengcheng; Tang, Fangqiang; Tien, Po; Pan, Zishu title: Analysis of synonymous codon usage in classical swine fever virus date: 2008-10-29 journal: Virus Genes DOI: 10.1007/s11262-008-0296-z sha: doc_id: 310298 cord_uid: 26x2p9wc file: cache/cord-279863-5kxgu4t9.json key: cord-279863-5kxgu4t9 authors: Oem, Jae-Ku; An, Dong-Jun title: Phylogenetic analysis of bovine astrovirus in Korean cattle date: 2013-11-23 journal: Virus Genes DOI: 10.1007/s11262-013-1013-0 sha: doc_id: 279863 cord_uid: 5kxgu4t9 file: cache/cord-340438-9q3ic0ye.json key: cord-340438-9q3ic0ye authors: Zhang, Jianqiang; Yim-Im, Wannarat; Chen, Qi; Zheng, Ying; Schumacher, Loni; Huang, Haiyan; Gauger, Phillip; Harmon, Karen; Li, Ganwu title: Identification of porcine epidemic diarrhea virus variant with a large spike gene deletion from a clinical swine sample in the United States date: 2018-02-21 journal: Virus Genes DOI: 10.1007/s11262-018-1542-7 sha: doc_id: 340438 cord_uid: 9q3ic0ye file: cache/cord-296791-h8ftslps.json key: cord-296791-h8ftslps authors: Junwei, Ge; Baoxian, Li; Lijie, Tang; Yijing, Li title: Cloning and sequence analysis of the N gene of porcine epidemic diarrhea virus LJB/03 date: 2006-10-01 journal: Virus Genes DOI: 10.1007/s11262-005-0059-z sha: doc_id: 296791 cord_uid: h8ftslps file: cache/cord-025704-icedihm2.json key: cord-025704-icedihm2 authors: Pawestri, Hana A.; Nugraha, Arie A.; Han, Alvin X.; Pratiwi, Eka; Parker, Edyth; Richard, Mathilde; van der Vliet, Stefan; Fouchier, Ron A. M.; Muljono, David H.; de Jong, Menno D.; Setiawaty, Vivi; Eggink, Dirk title: Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008–2015 date: 2020-06-01 journal: Virus Genes DOI: 10.1007/s11262-020-01765-1 sha: doc_id: 25704 cord_uid: icedihm2 Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named journal-virusGenes-cord === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51879 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50050 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50407 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50194 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50569 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51210 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49657 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50658 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50771 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49659 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49934 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51410 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51462 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50017 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49811 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50254 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49692 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51459 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49755 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50281 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51342 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50654 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51427 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51450 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49809 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50320 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51421 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50197 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51928 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 52537 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-254291-y8xvh6hs author: Yamanaka, Miles title: Nucleotide Sequence of the Inter-Structural Gene Region of Feline Infectious Peritonitis Virus date: 1998 pages: extension: .txt txt: ./txt/cord-254291-y8xvh6hs.txt cache: ./cache/cord-254291-y8xvh6hs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254291-y8xvh6hs.txt' === file2bib.sh === id: cord-299573-vq6ckqtd author: Lee, Meong-Hun title: Phylogenetic analysis of porcine astrovirus in domestic pigs and wild boars in South Korea date: 2012-09-11 pages: extension: .txt txt: ./txt/cord-299573-vq6ckqtd.txt cache: ./cache/cord-299573-vq6ckqtd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-299573-vq6ckqtd.txt' === file2bib.sh === id: cord-269340-o9jdt86j author: Callison, Scott Andrew title: Infectious Bronchitis Virus S2 Gene Sequence Variability May Affect S1 Subunit Specific Antibody Binding date: 1999 pages: extension: .txt txt: ./txt/cord-269340-o9jdt86j.txt cache: ./cache/cord-269340-o9jdt86j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269340-o9jdt86j.txt' === file2bib.sh === id: cord-005207-02wmt2e9 author: Lee, Hee-Kyung title: Cloning and Sequence Analysis of the Nucleocapsid Gene of Porcine Epidemic Diarrhea Virus Chinju99 date: 2003 pages: extension: .txt txt: ./txt/cord-005207-02wmt2e9.txt cache: ./cache/cord-005207-02wmt2e9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005207-02wmt2e9.txt' === file2bib.sh === id: cord-005253-8qja4j9h author: Li, Weike title: Genetic characterization of an isolate of canine distemper virus from a Tibetan Mastiff in China date: 2014-04-02 pages: extension: .txt txt: ./txt/cord-005253-8qja4j9h.txt cache: ./cache/cord-005253-8qja4j9h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005253-8qja4j9h.txt' === file2bib.sh === id: cord-263489-i4tkdgy4 author: Suo, Siqingaowa title: Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential date: 2015-05-27 pages: extension: .txt txt: ./txt/cord-263489-i4tkdgy4.txt cache: ./cache/cord-263489-i4tkdgy4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263489-i4tkdgy4.txt' === file2bib.sh === id: cord-311204-fc12f845 author: Zhou, Ling title: Full-length genomic characterization and molecular evolution of canine parvovirus in China date: 2016-04-02 pages: extension: .txt txt: ./txt/cord-311204-fc12f845.txt cache: ./cache/cord-311204-fc12f845.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311204-fc12f845.txt' === file2bib.sh === id: cord-268627-nnx46nwf author: Ren, Xiaofeng title: Development of reverse transcription loop-mediated isothermal amplification for rapid detection of porcine epidemic diarrhea virus date: 2011-02-01 pages: extension: .txt txt: ./txt/cord-268627-nnx46nwf.txt cache: ./cache/cord-268627-nnx46nwf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268627-nnx46nwf.txt' === file2bib.sh === id: cord-012091-3bo88tux author: Ibrahim, Madiha Salah title: Host-specific genetic variation of highly pathogenic avian influenza viruses (H5N1) date: 2011-02-17 pages: extension: .txt txt: ./txt/cord-012091-3bo88tux.txt cache: ./cache/cord-012091-3bo88tux.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012091-3bo88tux.txt' === file2bib.sh === id: cord-310298-26x2p9wc author: Tao, Pan title: Analysis of synonymous codon usage in classical swine fever virus date: 2008-10-29 pages: extension: .txt txt: ./txt/cord-310298-26x2p9wc.txt cache: ./cache/cord-310298-26x2p9wc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310298-26x2p9wc.txt' Que is empty; done journal-virusGenes-cord === reduce.pl bib === id = cord-005207-02wmt2e9 author = Lee, Hee-Kyung title = Cloning and Sequence Analysis of the Nucleocapsid Gene of Porcine Epidemic Diarrhea Virus Chinju99 date = 2003 pages = extension = .txt mime = text/plain words = 2171 sentences = 118 flesch = 63 summary = The nucleocapsid (N) gene of the porcine epidemic diarrhea virus (PEDV) Chinju99 which was previously isolated in Chinju, Korea was cloned and sequenced to establish the information for the development of genetically engineered diagnostic reagents. The nucleotide sequence encoding the entire N gene open reading frame (ORF) of Chinju99 was 1326 bases long and encoded a protein of 441 amino acids with predicted M (r) of 49 kDa. It consisted of 405 adenine (30.5%), 293 cytosine (22.1%), 334 guanines (25.2%) and 294 thymines (22.2%) residues. In the present study, a DNA clone was constructed for the full-length N gene open reading frame (ORF) of PEDV isolated in Chinju, Korea. The complete sequences of nucleotides and deduced amino acids of the N gene were determined, and further analyzed with those of other PEDVs for the information in the production of genetically engineered diagnostic reagents. cache = ./cache/cord-005207-02wmt2e9.txt txt = ./txt/cord-005207-02wmt2e9.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-012091-3bo88tux author = Ibrahim, Madiha Salah title = Host-specific genetic variation of highly pathogenic avian influenza viruses (H5N1) date = 2011-02-17 pages = extension = .txt mime = text/plain words = 2486 sentences = 132 flesch = 52 summary = The complete genome sequences of two isolates A/chicken/Egypt/CL6/07 (CL6/07) and A/duck/Egypt/D2br10/07 (D2br10/07) of highly pathogenic avian influenza virus (HPAI) H5N1 isolated at the beginning of 2007 outbreak in Egypt were determined and compared with all Egyptian HPAI H5N1 sequences available in the GenBank. For 2007 and 2008, the CL6/07 and D2br10/07-specific amino acids were detected in GenBank available sequences but they could not be species-correlated due to the low number of duck reference sequences, except the Lys140 (H5 Table 1 ). In our analysis, comparative genetic characterization of the eight RNA segments of CL6/07 and D2br10/07 together with 2006-2010 GenBank Egyptian reference sequences showed that both viruses had nucleotide as well as amino acid differences that appeared to be specific for each, except for the M gene that was highly conserved. Highly pathogenic avian influenza virus subtype H5N1 in Africa: a comprehensive phylogenetic analysis and molecular characterization of isolates cache = ./cache/cord-012091-3bo88tux.txt txt = ./txt/cord-012091-3bo88tux.txt === reduce.pl bib === === reduce.pl bib === id = cord-268627-nnx46nwf author = Ren, Xiaofeng title = Development of reverse transcription loop-mediated isothermal amplification for rapid detection of porcine epidemic diarrhea virus date = 2011-02-01 pages = extension = .txt mime = text/plain words = 2775 sentences = 156 flesch = 58 summary = In this study, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed for detection of porcine epidemic diarrhea virus (PEDV). The results showed that the optimal reaction condition for RT-LAMP amplifying PEDV N gene was achieved at 63°C for 50 min. The total RNAs were extracted from the culture supernatants of PEDV, TGEV, PRV, PRRSV, and IBV using the RNA extraction kit (KeyGen Biotech, China) and the genomic DNA of PrV was extracted from virus-infected Vero cell culture using the DNA extraction kit (Omega, Norcross, USA) according to the manufacturer's instructions. As shown in Fig. 2a , the DNA products of the RT-LAMP at different temperatures showed multiple of characteristic ladder bands; however, the intensity of DNAs determined by Gel Analyzer software from the reactions at 63°C was stronger than that at other reaction temperatures, which was judged as the optimal temperature for RT-LAMP amplifying PEDV N gene. The sensitivity of the RT-LAMP assay was first compared with the conventional RT-PCR amplifying the tenfold serial dilutions of RNA templates of PEDV. cache = ./cache/cord-268627-nnx46nwf.txt txt = ./txt/cord-268627-nnx46nwf.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-311204-fc12f845 author = Zhou, Ling title = Full-length genomic characterization and molecular evolution of canine parvovirus in China date = 2016-04-02 pages = extension = .txt mime = text/plain words = 2229 sentences = 138 flesch = 65 summary = Canine parvovirus type 2 (CPV-2) can cause acute haemorrhagic enteritis in dogs and myocarditis in puppies. Some faecal samples were negative for the CPV-2 antigen based on a colloidal gold test strip but were positive based on PCR, and a viral strain was isolated from one such sample. Identification of CPV-2 with cell culture and IPMA Feline kidney cell line F81 was obtained from the American Type Culture Collection, USA and was used to isolate viruses from clinical samples and to observe cytopathic effects associated with viral replication. Cloning the full-length genomic sequence of CPV-2 DNA and RNA were extracted from the homogenized samples (faeces from infected dogs) with the TIANamp Virus DNA/RNA Kit (Beijing TIANGEN Biotech Company, Beijing, China) according to the manufacturer's protocol. One viral strain was isolated from the faeces of dogs that tested negative in the colloidal gold test strip but positive with PCR. cache = ./cache/cord-311204-fc12f845.txt txt = ./txt/cord-311204-fc12f845.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-254291-y8xvh6hs author = Yamanaka, Miles title = Nucleotide Sequence of the Inter-Structural Gene Region of Feline Infectious Peritonitis Virus date = 1998 pages = extension = .txt mime = text/plain words = 832 sentences = 48 flesch = 67 summary = The sequence of the region located between the S and M glycoprotein genes of the 79-1146 strain of feline infectious peritonitis virus (FIPV) is presented. The inter-structural gene region encodes 3 open reading frames (ORFs), termed ORFs 3a, 3b and 4, with nucleotide sequences conforming to the minimum conserved transcription signal upstream of each. The FIPV interstructural gene region is identical in length when compared to the Insavc-1 strain of canine coronavirus (CCV) but differs from various strains of transmissible gastroenteritis virus (TGEV) by the presence of deletions and insertions. This inter-structural gene region has been examined in the related coronaviruses transmissible gastroenteritis virus (TGEV) and canine coronavirus (CCV) (2±6). The arrangement of the open reading frames (ORFs) in the inter-structural gene region has been described for the FIPV genome (1,7), but detailed sequence has not been presented. The sequence identity between FIPV 79-1146 and the Purdue strain of TGEV in the inter-structural gene region is 90.7%. cache = ./cache/cord-254291-y8xvh6hs.txt txt = ./txt/cord-254291-y8xvh6hs.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-299573-vq6ckqtd author = Lee, Meong-Hun title = Phylogenetic analysis of porcine astrovirus in domestic pigs and wild boars in South Korea date = 2012-09-11 pages = extension = .txt mime = text/plain words = 1963 sentences = 103 flesch = 60 summary = In this study, 25/129 (19.4 %) domestic pig and 1/146 (0.7 %) wild boar fecal samples tested in South Korea were positive for PAstV. Bayesian inference (BI) tree analysis for RNA-dependent RNA polymerase (RdRp) and capsid (ORF2) gene sequences, including Mamastrovirus and Avastrovirus, revealed a relatively geographically divergent lineage. It was also observed that PAstV infections are widespread in South Korea regardless of the disease state in domestic pigs and in wild boars as well. It was, therefore, the aim of this study to investigate the genetic groups of Korean PAstV in domestic pigs and wild boars and to identify the incidence of co-infection with other porcine enteric viruses as well. A study of the molecular epidemiology and genetic diversity of human astrovirus in South Korea from 2002 to 2007 revealed genotype 1 to be the most prevalent, accounting for 72.19 % of strains, followed by genotypes 8 Korean PAstVs are shown in bold prints, and strains isolates from Korean and Hungarian wild boar are marked with a star and an arrow, respectively. cache = ./cache/cord-299573-vq6ckqtd.txt txt = ./txt/cord-299573-vq6ckqtd.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-269340-o9jdt86j author = Callison, Scott Andrew title = Infectious Bronchitis Virus S2 Gene Sequence Variability May Affect S1 Subunit Specific Antibody Binding date = 1999 pages = extension = .txt mime = text/plain words = 2116 sentences = 110 flesch = 60 summary = The S2 gene of several strains of infectious bronchitis virus (IBV) belonging to the Arkansas, Connecticut, and Florida serotypes was sequenced. Thus, we are interested in examining the S2 gene and its deduced amino acid sequence of IBV strains in an attempt to determine if it plays a role in the binding of S1 subunit speci®c antibodies to the virus. We also selected Connecticut 46 and Florida 18288 for S2 gene sequencing because these strains are known to share 96.6% deduced amino acid identity for their S1 subunits, yet remain serologically distinct (14, 15) . In the alignment, members of the U.S. serotypes Arkansas, Mass, Connecticut, Florida, and foreign S2 Gene Sequence Variability serogroups B and C, fall into the same groupings as observed when deduced amino acid sequence data for the S1 subunit is used for phylogenetic analysis (Fig. 3) . One change in the GAV 92 S2 deduced amino acid sequence ( position 50 E?G) led to a 180 ¯i p in the secondary structure prediction of the S2 subunit. cache = ./cache/cord-269340-o9jdt86j.txt txt = ./txt/cord-269340-o9jdt86j.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-310298-26x2p9wc author = Tao, Pan title = Analysis of synonymous codon usage in classical swine fever virus date = 2008-10-29 pages = extension = .txt mime = text/plain words = 3416 sentences = 184 flesch = 56 summary = Using the complete genome sequences of 35 classical swine fever viruses (CSFV) representing all three genotypes and all three kinds of virulence, we analyzed synonymous codon usage and the relative dinucleotide abundance in CSFV. The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in CSFV. As shown in Table 4 , the first axis value in COA of each selected genome, which contains most of the variation in synonymous codon usage bias between these genomes, is closely correlated with the GC composition at the first, second, and third codon position. Mean values of 35 CSFVs relative dinucleotide ratios ± S.D Table 3 Summary of correlation analysis between the first two axes in COA and sixteen dinucleotides in the selected viruses , indicating that the overall extent of codon usage bias in CSFV genomes is low. cache = ./cache/cord-310298-26x2p9wc.txt txt = ./txt/cord-310298-26x2p9wc.txt === reduce.pl bib === === reduce.pl bib === id = cord-263489-i4tkdgy4 author = Suo, Siqingaowa title = Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential date = 2015-05-27 pages = extension = .txt mime = text/plain words = 2211 sentences = 130 flesch = 65 summary = title: Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential Herein, we use similar technology and advance previous work by using the rS-AD as an immobilizing target to select phages from a peptide display library, with diagnostic potential for TGEV. Our results indicate that phages bearing peptide ligands that bind rS-AD can be used to develop a phage-mediated ELISA with high sensitivity and specificity to distinguish TGEV from other common swine viruses. To compare the sensitivities of phage-mediated ELISA to antibody-mediated ELISA, TGEV serially diluted in 0.1 M NaHCO 3 (pH 8.6) was coated onto duplicate ELISA plates overnight at 4°C followed by blocking with 5 % skim milk for 3 h at rt. Predicted amino acid sequences were generated for ten selected phages In summary, we identified peptides that specifically bind to TGEV and can form the basis of new diagnostic tests where the sensitivity of phTGEV-SAD15 was 0.1 lg of TGEV. cache = ./cache/cord-263489-i4tkdgy4.txt txt = ./txt/cord-263489-i4tkdgy4.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-005253-8qja4j9h author = Li, Weike title = Genetic characterization of an isolate of canine distemper virus from a Tibetan Mastiff in China date = 2014-04-02 pages = extension = .txt mime = text/plain words = 3386 sentences = 135 flesch = 58 summary = This analysis shows that an N-glycosylation site at aa 108-110 within the F protein of CDV-TM-CC is specific for the wild-type strains (5804P, A75/17, and 164071) and the Asia-1 group strains, and may be another important factor for the poor immune response. Consistent with the results for the H protein, the homology of the deduced CDV-TM-CC amino acid sequence of the N protein to the Asia-1 strains (CYN07-hV, HLJ1-06, and Hebei) was high with 98.7-98.9 % identity, as shown in Fig. 4 . Analysis of the 1-135 aa signal peptide region of the F protein of CDV-TM-CC demonstrated the same set of amino acid variations in comparison with the Onderstepoort strain as for the other Asia-1 strains (CYN07-hV, HLJ1-06, and Hebei): 8 S/ 8 K, 11 T/ 11 P, 19 (Fig. 6) . cache = ./cache/cord-005253-8qja4j9h.txt txt = ./txt/cord-005253-8qja4j9h.txt === reduce.pl bib === ===== Reducing email addresses cord-269340-o9jdt86j Creating transaction Updating adr table ===== Reducing keywords cord-257122-h3zi8k8g cord-005252-m02inmc4 cord-005207-02wmt2e9 cord-266634-bww62vx8 cord-284675-7zv449sc cord-012091-3bo88tux cord-288239-ca5uthvd cord-259398-s8qsjkj2 cord-282126-gmjnbnx5 cord-311712-lkvt9slp cord-307580-nokd5kmx cord-302584-fwdpzv85 cord-322475-i29t7ce8 cord-268627-nnx46nwf cord-283168-kl1hoa1x cord-311204-fc12f845 cord-348896-a2mjj5dt cord-269720-o81j3d1j cord-011794-ejoufvvj cord-295554-0pzjyrdf cord-265095-lf5j4ic7 cord-299573-vq6ckqtd cord-303672-ujp78213 cord-254291-y8xvh6hs cord-303834-yqysedne cord-263489-i4tkdgy4 cord-331919-6kistim2 cord-346643-os2kyvvf cord-333914-c150ki1n cord-005253-8qja4j9h cord-287748-co9j3uig cord-340438-9q3ic0ye cord-296791-h8ftslps cord-025704-icedihm2 cord-344558-1jgqofbr cord-279863-5kxgu4t9 cord-272693-432ixb7g cord-310298-26x2p9wc cord-269340-o9jdt86j cord-328518-umvk59dc Creating transaction Updating wrd table ===== Reducing urls cord-282126-gmjnbnx5 cord-284675-7zv449sc cord-311712-lkvt9slp cord-268627-nnx46nwf cord-346643-os2kyvvf cord-283168-kl1hoa1x cord-311204-fc12f845 cord-011794-ejoufvvj cord-005253-8qja4j9h cord-272693-432ixb7g cord-344558-1jgqofbr cord-296791-h8ftslps cord-310298-26x2p9wc Creating transaction Updating url table ===== Reducing named entities cord-005207-02wmt2e9 cord-257122-h3zi8k8g cord-005252-m02inmc4 cord-259398-s8qsjkj2 cord-282126-gmjnbnx5 cord-311712-lkvt9slp cord-311204-fc12f845 cord-012091-3bo88tux cord-348896-a2mjj5dt cord-011794-ejoufvvj cord-307580-nokd5kmx cord-268627-nnx46nwf cord-269720-o81j3d1j cord-284675-7zv449sc cord-322475-i29t7ce8 cord-283168-kl1hoa1x cord-288239-ca5uthvd cord-295554-0pzjyrdf cord-269340-o9jdt86j cord-266634-bww62vx8 cord-302584-fwdpzv85 cord-303672-ujp78213 cord-331919-6kistim2 cord-265095-lf5j4ic7 cord-254291-y8xvh6hs cord-299573-vq6ckqtd cord-303834-yqysedne cord-263489-i4tkdgy4 cord-346643-os2kyvvf cord-333914-c150ki1n cord-005253-8qja4j9h cord-272693-432ixb7g cord-328518-umvk59dc cord-287748-co9j3uig cord-344558-1jgqofbr cord-310298-26x2p9wc cord-340438-9q3ic0ye cord-279863-5kxgu4t9 cord-296791-h8ftslps cord-025704-icedihm2 Creating transaction Updating ent table ===== Reducing parts of speech parallel: Warning: No more processes: Decreasing number of running jobs to 39. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-005252-m02inmc4 cord-257122-h3zi8k8g cord-005207-02wmt2e9 cord-266634-bww62vx8 cord-012091-3bo88tux cord-284675-7zv449sc cord-288239-ca5uthvd cord-311712-lkvt9slp cord-259398-s8qsjkj2 cord-307580-nokd5kmx cord-282126-gmjnbnx5 cord-322475-i29t7ce8 cord-302584-fwdpzv85 cord-268627-nnx46nwf cord-348896-a2mjj5dt cord-283168-kl1hoa1x cord-011794-ejoufvvj cord-269720-o81j3d1j cord-311204-fc12f845 cord-269340-o9jdt86j cord-303672-ujp78213 cord-331919-6kistim2 cord-254291-y8xvh6hs cord-303834-yqysedne cord-295554-0pzjyrdf cord-005253-8qja4j9h cord-287748-co9j3uig cord-333914-c150ki1n cord-328518-umvk59dc cord-272693-432ixb7g cord-299573-vq6ckqtd cord-263489-i4tkdgy4 cord-346643-os2kyvvf cord-279863-5kxgu4t9 cord-340438-9q3ic0ye cord-310298-26x2p9wc cord-344558-1jgqofbr cord-296791-h8ftslps cord-265095-lf5j4ic7 cord-025704-icedihm2 Creating transaction Updating pos table Building ./etc/reader.txt cord-025704-icedihm2 cord-011794-ejoufvvj cord-328518-umvk59dc cord-311712-lkvt9slp cord-310298-26x2p9wc cord-269340-o9jdt86j number of items: 40 sum of words: 23,585 average size in words: 2,358 average readability score: 60 nouns: virus; viruses; sequence; sequences; protein; gene; strains; amino; cells; acid; genome; analysis; codon; strain; genes; study; region; samples; °; species; usage; cell; infection; coronavirus; proteins; isolates; dna; type; host; influenza; structure; primers; bats; results; number; differences; site; min; sites; replication; coronaviruses; regions; nucleotides; disease; data; polymerase; group; changes; reaction; detection verbs: using; show; found; containing; includes; based; isolated; detected; indicating; compared; infected; reported; determined; identifying; suggesting; observed; following; predicted; resulted; encoded; described; associated; collected; according; revealed; performed; caused; binding; known; obtained; analyzed; located; sequenced; related; conserved; expressed; representing; occur; examined; develop; strains; involving; appeared; amplifying; provide; cloned; selected; formed; mediated; given adjectives: viral; different; nucleotide; porcine; human; specific; high; genetic; positive; avian; similar; antigenic; phylogenetic; structural; non; first; potential; molecular; genomic; several; new; present; important; available; complete; pathogenic; infectious; clinical; large; major; full; novel; attenuated; low; respiratory; many; small; single; possible; bovine; infected; secondary; like; virulent; recombinant; key; wild; higher; old; effective adverbs: also; however; respectively; highly; well; previously; nt; therefore; recently; closely; first; approximately; moreover; downstream; still; upstream; genetically; furthermore; together; interestingly; directly; even; subsequently; rather; generally; single; significantly; less; similarly; now; mainly; relatively; probably; newly; currently; usually; clearly; yet; successfully; long; indeed; double; particularly; likely; least; frequently; potentially; often; much; later pronouns: we; it; its; their; our; i; they; them; us; his; he; you; one; themselves; your; ourself; itself; her; ch/; ay278741 proper nouns: RNA; PEDV; TGEV; PCR; Fig; RT; S; M; C; H5N1; T; IBV; SARS; N; PUUV; ORF; LAMP; China; CDV; aa; GC; Ark; USA; GenBank; Table; CoV; Virus; TM; CSFV; IBDV; ELISA; SY; S2; II; PRCV; S1; G; Genes; K; bp; ®; CC; Korea; Indonesia; HPAI; A; D; s11262; RBCV; DOI keywords: rna; tgev; pedv; bat; lamp; h5n1; dna; codon; whu; vp5; virus; v29; trk22; tmk22; south; sars; rbcv; puuv; prcv; pig; pcr; pca; p55; osnabrück; ntu156; myotis; mass; korea; indonesia; indel; ibv; ibdv; hpai; germany; ga98; fr/2011; florida; fipv; ebcv; ctv; csfv; cpv-2; cov; cl6/07; chk148; chinju99; cell; cdv; cattle; brazil one topic; one dimension: virus file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089008/ titles(s): Cloning and Sequence Analysis of the Nucleocapsid Gene of Porcine Epidemic Diarrhea Virus Chinju99 three topics; one dimension: virus; codon; virus file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7262163/, https://www.ncbi.nlm.nih.gov/pubmed/14739650/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7329759/ titles(s): Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008–2015 | Base Usage and Dinucleotide Frequency of Infectious Bursal Disease Virus | Isolation and characterization of new Puumala orthohantavirus strains from Germany five topics; three dimensions: virus pedv protein; codon strains usage; tgev cells rna; virus pedv sequence; h5n1 viruses influenza file(s): https://www.ncbi.nlm.nih.gov/pubmed/2402881/, https://www.ncbi.nlm.nih.gov/pubmed/14739650/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7329759/, https://www.ncbi.nlm.nih.gov/pubmed/21909766/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112484/ titles(s): RNA pseudoknots: Translational frameshifting and readthrough on viral RNAs | Base Usage and Dinucleotide Frequency of Infectious Bursal Disease Virus | Isolation and characterization of new Puumala orthohantavirus strains from Germany | Changes in nonstructural protein 3 are associated with attenuation in avian coronavirus infectious bronchitis virus | Host-specific genetic variation of highly pathogenic avian influenza viruses (H5N1) Type: cord title: journal-virusGenes-cord date: 2021-05-30 time: 16:05 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: facet_journal:"Virus Genes" ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-348896-a2mjj5dt author: Abid, Nabil Ben Salem title: Molecular study of porcine transmissible gastroenteritis virus after serial animal passages revealed point mutations in S protein date: 2010-12-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine respiratory coronavirus is related genetically to porcine transmissible gastroenteritis virus with a large deletion in S protein. The respiratory virus is a mutated form that may be a consequence of the gastroenteritis virus’s evolution. Intensive passages of the virus in its natural host may enhance the appearance of mutations and therefore may contribute to any attenuated form of the virus. The objective of this study was to characterize the porcine transmissible gastroenteritis virus TMK22 strain after passages in piglets from 1992 until 2007. A typical experimental infection, molecular characterization, and serological analysis were also carried out to further characterize and to evaluate any significant difference between strains. The sequence analysis showed two amino acid deletions and loss of an N-glycosylation site in transmissible gastroenteritis virus S protein after passages in piglets. Although these deletions were positioned at the beginning of the antigenic site B of S protein, no clinical differences were observed in piglets infected experimentally either with the native virus or the mutated one. Serological tests did not show any antibody reactivity difference between the two strains. In this article, we report that the S protein deletion did not affect the virus’s pathogenicity. The variety of the virus’s evolutionary forms may be a result, not only of the multiple passages in natural hosts, but also of other factors, such as different pathogens co-infection, nutrition, immunity, and others. Further studies need to be carried out to characterize the mutated strain. url: https://www.ncbi.nlm.nih.gov/pubmed/21188626/ doi: 10.1007/s11262-010-0562-8 id: cord-311712-lkvt9slp author: Barrett, John W. title: Optimization of Codon Usage of Poxvirus Genes allows for Improved Transient Expression in Mammalian Cells date: 2006 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Transient expression of viral genes from certain poxviruses in uninfected mammalian cells can sometimes be unexpectedly inefficient. The reasons for poor expression levels can be due to a number of features of the gene cassette, such as cryptic splice sites, polymerase II termination sequences or motifs that lead to mRNA instability. Here we suggest that in some cases the problem of low protein expression in transfected mammalian cells may be due to inefficient codon usage. We have observed that for many poxvirus genes from the yatapoxvirus genus this deficiency can be overcome by synthesis of the gene with codon sequences optimized for expression in primate cells. This led us to examine colon usage across 2-dozen sequenced members of the Poxviridae. We conclude that codon usage is surprisingly divergent across the different Poxviridae genera but is much more conserved within a single genus. Thus, Poxviridae genera can be divided into distinct groups based on their observed codon bias. When viewed in this context, successful transient expression of transfected poxvirus genes in uninfected mammalian cells can be more accurately predicted based on codon bias. As a corollary, for specific poxvirus genes with less favorable codon usage, codon optimization can result in profoundly increased transient expression levels following transfection of uninfected mammalian cell lines. url: https://www.ncbi.nlm.nih.gov/pubmed/16791414/ doi: 10.1007/s11262-005-0035-7 id: cord-011794-ejoufvvj author: Binder, Florian title: Isolation and characterization of new Puumala orthohantavirus strains from Germany date: 2020-04-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Orthohantaviruses are re-emerging rodent-borne pathogens distributed all over the world. Here, we report the isolation of a Puumala orthohantavirus (PUUV) strain from bank voles caught in a highly endemic region around the city Osnabrück, north-west Germany. Coding and non-coding sequences of all three segments (S, M, and L) were determined from original lung tissue, after isolation and after additional passaging in VeroE6 cells and a bank vole-derived kidney cell line. Different single amino acid substitutions were observed in the RNA-dependent RNA polymerase (RdRP) of the two stable PUUV isolates. The PUUV strain from VeroE6 cells showed a lower titer when propagated on bank vole cells compared to VeroE6 cells. Additionally, glycoprotein precursor (GPC)-derived virus-like particles of a German PUUV sequence allowed the generation of monoclonal antibodies that allowed the reliable detection of the isolated PUUV strain in the immunofluorescence assay. In conclusion, this is the first isolation of a PUUV strain from Central Europe and the generation of glycoprotein-specific monoclonal antibodies for this PUUV isolate. The obtained virus isolate and GPC-specific antibodies are instrumental tools for future reservoir host studies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11262-020-01755-3) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7329759/ doi: 10.1007/s11262-020-01755-3 id: cord-269340-o9jdt86j author: Callison, Scott Andrew title: Infectious Bronchitis Virus S2 Gene Sequence Variability May Affect S1 Subunit Specific Antibody Binding date: 1999 words: 2116.0 sentences: 110.0 pages: flesch: 60.0 cache: ./cache/cord-269340-o9jdt86j.txt txt: ./txt/cord-269340-o9jdt86j.txt summary: The S2 gene of several strains of infectious bronchitis virus (IBV) belonging to the Arkansas, Connecticut, and Florida serotypes was sequenced. Thus, we are interested in examining the S2 gene and its deduced amino acid sequence of IBV strains in an attempt to determine if it plays a role in the binding of S1 subunit speci®c antibodies to the virus. We also selected Connecticut 46 and Florida 18288 for S2 gene sequencing because these strains are known to share 96.6% deduced amino acid identity for their S1 subunits, yet remain serologically distinct (14, 15) . In the alignment, members of the U.S. serotypes Arkansas, Mass, Connecticut, Florida, and foreign S2 Gene Sequence Variability serogroups B and C, fall into the same groupings as observed when deduced amino acid sequence data for the S1 subunit is used for phylogenetic analysis (Fig. 3) . One change in the GAV 92 S2 deduced amino acid sequence ( position 50 E?G) led to a 180 ¯i p in the secondary structure prediction of the S2 subunit. abstract: The S2 gene of several strains of infectious bronchitis virus (IBV) belonging to the Arkansas, Connecticut, and Florida serotypes was sequenced. Phylogenetic analysis of the S2 gene nucleotide and deduced amino acid sequence data resulted in groups of strains that were the same as groupings observed when S1 sequence data was used. Thus, it appears that S2 subunits are conserved within a serotype but not between serotypes. Although the sequence differences were small, we found that only a few amino acid differences were responsible for different secondary structure predictions for the S2 subunit. It is likely that these changes create different interactions between the S1 and S2 subunits, which could affect the conformation of the S1 subunit where serotype specific epitopes are located. Based on this sequence data, we hypothesize that the S2 subunit can affect specific antibody binding to the S1 subunit of the IBV spike glycoprotein. url: https://www.ncbi.nlm.nih.gov/pubmed/10541018/ doi: 10.1023/a:1008179208217 id: cord-322475-i29t7ce8 author: Chen, Xi title: Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) samples from field cases in Fujian, China date: 2012-07-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The outbreak of porcine epidemic diarrhea virus (PEDV) has been a big problem of swine industry in China in recent years. In this study, we investigated molecular diversity, phylogenetic relationships, and protein characterization of Fujian field samples with other PEDV reference strains. Sequence analysis of the S1 and sM genes showed that each sample had unique characteristics, and the sample P55 may be differentiated from the others by the unique deletions and insertions of sM gene. Phylogenetic analysis based on S1 or sM gene, which have high levels of variations, indicated that each sample was related to the specific reference strain, and this finding was consistent with the protein characterization prediction analysis. The study is useful to better understand the prevalence of PEDV and its prevention and control in Fujian. url: https://doi.org/10.1007/s11262-012-0794-x doi: 10.1007/s11262-012-0794-x id: cord-259398-s8qsjkj2 author: Chouljenko, Vladimir N. title: Nucleotide and Predicted Amino Acid Sequences of All Genes Encoded by the 3′ Genomic Portion (9.5 kb) of Respiratory Bovine Coronaviruses and Comparisons Among Respiratory and Enteric Coronaviruses date: 1998 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The 3′-ends of the genomes (9538 bp) of two wild-type respiratory bovine coronavirus (RBCV) isolates LSU and OK were obtained by cDNA sequencing. In addition, the 3′-end of the genome (9545) of the wild-type enteric bovine coronavirus (EBCV) strain LY-138 was assembled from available sequences and by cDNA sequencing of unknown genomic regions. Comparative analyses of RBCV and EBCV nucleotide and deduced amino acid sequences revealed that RBCV-specific nucleotide and amino acid differences were disproportionally concentrated within the S gene and the genomic region between the S and E genes. Comparisons among virulent and avirulent BCV strains revealed that virulence-specific nucleotide and amino acid changes were located within the S and E genes, and the 32 kDa open reading frame. url: https://www.ncbi.nlm.nih.gov/pubmed/9778786/ doi: 10.1023/a:1008048916808 id: cord-303834-yqysedne author: Ducatez, Mariette F. title: Full genome sequence of guinea fowl coronavirus associated with fulminating disease date: 2015-02-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Guinea fowl coronavirus (GfCoV), a recently characterized avian coronavirus, was identified from outbreaks of fulminating disease (peracute enteritis) in guinea fowl in France. The full-length genomic sequence was determined to better understand its genetic relationship with avian coronaviruses. The full-length coding genome sequence was 26,985 nucleotides long with 11 open reading frames and no hemagglutinin–esterase gene: a genome organization identical to that of turkey coronavirus [5′ untranslated region (UTR)—replicase (ORFs 1a, 1ab)—spike (S) protein—ORF3 (ORFs 3a, 3b)—small envelop (E or 3c) protein—membrane (M) protein—ORF5 (ORFs 4b, 4c, 5a, 5b)—nucleocapsid (N) protein (ORFs N and 6b)—3′ UTR]. This is the first complete genome sequence of a GfCoV and confirms that the new virus belongs to group gammacoronaviruses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11262-015-1183-z) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/25712772/ doi: 10.1007/s11262-015-1183-z id: cord-283168-kl1hoa1x author: Farkas, Tibor title: Molecular detection of novel picornaviruses in chickens and turkeys date: 2011-12-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Fecal specimens, including swabs and litter extracts, collected from chickens, domestic ducks, turkeys, and Canadian geese were tested using degenerate primers targeting regions encoding for conserved amino acid motifs (YGDD and DY(T/S)(R/K/G)WDST) in calicivirus RNA-dependent RNA polymerases. Similar motifs are also present in other RNA viruses. Two fecal specimens and 18 litter extracts collected from chickens and turkeys yielded RT-PCR products. BLAST search and phylogenetic analysis revealed that all amplicons represented picornaviruses that clustered into two major groups. Four chicken and one turkey samples yielded 250 bp amplicons with 84–91% nucleotide identity to the recently described turkey hepatitis viruses, while 280 and 283 bp amplicons obtained from 11 chicken and 4 turkey samples represented novel picornaviruses with the closest nucleotide identity to kobuviruses (54–61%) and turdiviruses (47–54%). Analysis of 2.2–3.2 kb extended genome sequences including the partial P2 (2C) and complete P3 (3A, 3B (VPg), 3C(pro), and 3D(pol)) regions of selected strains indicated that viruses yielding the 280/283 bp amplicons represent a putative new genus of Picornaviridae. The 3′-non-translated region (NTR) of the turkey hepatitis-like viruses described in this study was significantly longer (641–654 nt) than that of any of the other piconaviruses and included a putative short open reading frame (ORF). In summary, we report the molecular detection of novel picornaviruses that appear to be endemic in both chickens and turkeys. url: https://doi.org/10.1007/s11262-011-0695-4 doi: 10.1007/s11262-011-0695-4 id: cord-266634-bww62vx8 author: Gopinath, M. title: Evidence for N(7) guanine methyl transferase activity encoded within the modular domain of RNA-dependent RNA polymerase L of a Morbillivirus date: 2015-10-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Post-transcriptional modification of viral mRNA is essential for the translation of viral proteins by cellular translation machinery. Due to the cytoplasmic replication of Paramyxoviruses, the viral-encoded RNA-dependent RNA polymerase (RdRP) is thought to possess all activities required for mRNA capping and methylation. In the present work, using partially purified recombinant RNA polymerase complex of rinderpest virus expressed in insect cells, we demonstrate the in vitro methylation of capped mRNA. Further, we show that a recombinant C-terminal fragment (1717–2183 aa) of L protein is capable of methylating capped mRNA, suggesting that the various post-transcriptional activities of the L protein are located in independently folding domains. url: https://doi.org/10.1007/s11262-015-1252-3 doi: 10.1007/s11262-015-1252-3 id: cord-303672-ujp78213 author: Gu, Wen-yuan title: Short hairpin RNAs targeting M and N genes reduce replication of porcine deltacoronavirus in ST cells date: 2019-08-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine deltacoronavirus (PDCoV) is a recently identified coronavirus that causes intestinal diseases in neonatal piglets with diarrhea, vomiting, dehydration, and post-infection mortality of 50–100%. Currently, there are no effective treatments or vaccines available to control PDCoV. To study the potential of RNA interference (RNAi) as a strategy against PDCoV infection, two short hairpin RNA (shRNA)-expressing plasmids (pGenesil-M and pGenesil-N) that targeted the M and N genes of PDCoV were constructed and transfected separately into swine testicular (ST) cells, which were then infected with PDCoV strain HB-BD. The potential of the plasmids to inhibit PDCoV replication was evaluated by cytopathic effect, virus titers, and real-time quantitative RT-PCR assay. The cytopathogenicity assays demonstrated that pGenesil-M and pGenesil-N protected ST cells against pathological changes with high specificity and efficacy. The 50% tissue culture infective dose showed that the PDCoV titers in ST cells treated with pGenesil-M and pGenesil-N were reduced 13.2- and 32.4-fold, respectively. Real-time quantitative RT-PCR also confirmed that the amount of viral RNA in cell cultures pre-transfected with pGenesil-M and pGenesil-N was reduced by 45.8 and 56.1%, respectively. This is believed to be the first report to show that shRNAs targeting the M and N genes of PDCoV exert antiviral effects in vitro, which suggests that RNAi is a promising new strategy against PDCoV infection. url: https://doi.org/10.1007/s11262-019-01701-y doi: 10.1007/s11262-019-01701-y id: cord-012091-3bo88tux author: Ibrahim, Madiha Salah title: Host-specific genetic variation of highly pathogenic avian influenza viruses (H5N1) date: 2011-02-17 words: 2486.0 sentences: 132.0 pages: flesch: 52.0 cache: ./cache/cord-012091-3bo88tux.txt txt: ./txt/cord-012091-3bo88tux.txt summary: The complete genome sequences of two isolates A/chicken/Egypt/CL6/07 (CL6/07) and A/duck/Egypt/D2br10/07 (D2br10/07) of highly pathogenic avian influenza virus (HPAI) H5N1 isolated at the beginning of 2007 outbreak in Egypt were determined and compared with all Egyptian HPAI H5N1 sequences available in the GenBank. For 2007 and 2008, the CL6/07 and D2br10/07-specific amino acids were detected in GenBank available sequences but they could not be species-correlated due to the low number of duck reference sequences, except the Lys140 (H5 Table 1 ). In our analysis, comparative genetic characterization of the eight RNA segments of CL6/07 and D2br10/07 together with 2006-2010 GenBank Egyptian reference sequences showed that both viruses had nucleotide as well as amino acid differences that appeared to be specific for each, except for the M gene that was highly conserved. Highly pathogenic avian influenza virus subtype H5N1 in Africa: a comprehensive phylogenetic analysis and molecular characterization of isolates abstract: The complete genome sequences of two isolates A/chicken/Egypt/CL6/07 (CL6/07) and A/duck/Egypt/D2br10/07 (D2br10/07) of highly pathogenic avian influenza virus (HPAI) H5N1 isolated at the beginning of 2007 outbreak in Egypt were determined and compared with all Egyptian HPAI H5N1 sequences available in the GenBank. Sequence analysis utilizing the RNA from the original tissue homogenate showed amino acid substitutions in seven of the viral segments in both samples. Interestingly, these changes were different between the CL6/07 and D2br10/07 when compared to other Egyptian isolates. Moreover, phylogenetic analysis showed independent sub-clustering of the two viruses within the Egyptian sequences signifying a possible differential adaptation in the two hosts. Further, pre-amplification analysis of H5N1 might be necessary for accurate data interpretation and identification of distinct factor(s) influencing the evolution of the virus in different poultry species. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112484/ doi: 10.1007/s11262-011-0583-y id: cord-288239-ca5uthvd author: Jeoung, Hye-Young title: Three clusters of bovine kobuvirus isolated in Korea, 2008–2010 date: 2011-03-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Fecal samples (n = 107) were collected from cattle with ascertained or suspected diarrheal disease on Korean farms during 2008–2010. Of these, 37 samples tested positive for bovine kobuvirus. The 37 positive samples came from 32 cattle that exhibited diarrhea and five cattle that were non-diarrhetic. The majority of the virus-positive feces samples were from calves under 1 month of age (n = 25). Nine of the 37 cattle infected with bovine kobuvirus were confirmed to have a co-infection with other viruses including bovine rotavirus (n = 3), bovine coronavirus (n = 1), bovine viral diarrhea virus (n = 1), and both bovine coronavirus and bovine viral diarrhea virus (n = 4). A neighbor-joining tree grouped 36 of the Korean kobuvirus strains (with the exception of the KB8 strain) into three clusters (G1, G3, and G4), while strains derived from Thailand and Japan (except the U1 strain) were included in the G2 cluster. The results indicated that Korean bovine kobuvirus has diverse lineages regardless of disease status and species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11262-011-0593-9) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/21399921/ doi: 10.1007/s11262-011-0593-9 id: cord-296791-h8ftslps author: Junwei, Ge title: Cloning and sequence analysis of the N gene of porcine epidemic diarrhea virus LJB/03 date: 2006-10-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The nucleocapsid (N) gene of the porcine epidemic diarrhea virus (PEDV) strain LJB/03 which was previously isolated in Heilongjiang province, China, was cloned, sequenced and compared with published sequences of other avian and mammalian coronavirus. The nucleotide sequence encoding the entire N gene open reading frame (ORF) of LJB/03 was 1326 bases long and encoded a protein of 441 amino acids with predicted Mr of 49 kDa. It consisted of 405 adenines (30.5%), 294 cytosines (22.1%), 329 guanines (24.8%) and 298 thymines (22.5%) residues. Sequence comparison with other PEDV strains selected from GenBank revealed that the LJB/03 N gene has a high sequence homology to those of other PEDV isolates, 97.4% with JS2004, 95.6% with chinju99, 96.6% with Br1/87, and 96.8% with CV777. The encoded protein shared 96.4% amino acid identities compared with CV777, 96.1% with Brl/87, 98% with JS2004, 96.90% with chinju99, respectively. The amino acid sequence contained seven potential protein kinase C phosphorylation sites, nine Casein kinase II phosphorylation sites, one Tyrosine kinase phosphorylation site, two cAMP- and cGMP-dependent protein kinase phosphorylation sites. url: https://www.ncbi.nlm.nih.gov/pubmed/16972037/ doi: 10.1007/s11262-005-0059-z id: cord-333914-c150ki1n author: Koba, Ryota title: Identification and characterization of a novel bat polyomavirus in Japan date: 2020-08-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A novel polyomavirus (PyV) was identified in the intestinal contents of Japanese eastern bent-wing bats (Miniopterus fuliginosus) via metagenomic analysis. We subsequently sequenced the full genome of the virus, which has been tentatively named Miniopterus fuliginosus polyomavirus (MfPyV). The nucleotide sequence identity of the genome with those of other bat PyVs was less than 80%. Phylogenetic analysis revealed that MfPyV belonged to the same cluster as PyVs detected in Miniopterus schreibersii. This study has identified the presence of a novel PyV in Japanese bats and provided genetic information about the virus. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11262-020-01789-7) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32816186/ doi: 10.1007/s11262-020-01789-7 id: cord-287748-co9j3uig author: Kobayashi, Tomoya title: Detection of bat hepatitis E virus RNA in microbats in Japan date: 2018-05-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Several recent studies have reported that various bat species harbor bat hepatitis E viruses (BatHEV) belonging to the family Hepeviridae, which also contains human hepatitis E virus (HEV). The distribution and ecology of BatHEV are not well known. Here, we collected and screened 81 bat fecal samples from nine bat species in Japan to detect BatHEV RNA by RT-PCR using HEV-specific primers, and detected three positive samples. Sequence and phylogenetic analyses indicated that these three viruses were BatHEVs belonging to genus Orthohepevirus D like other BatHEV strains reported earlier in various countries. These data support the first detection of BatHEVs in Japanese microbats, indicating their wide geographical distribution among multiple bat species. url: https://www.ncbi.nlm.nih.gov/pubmed/29845506/ doi: 10.1007/s11262-018-1577-9 id: cord-344558-1jgqofbr author: Kocherhans, Rolf title: Completion of the Porcine Epidemic Diarrhoea Coronavirus (PEDV) Genome Sequence date: 2001 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The sequence of the replicase gene of porcine epidemic diarrhoea virus (PEDV) has been determined. This completes the sequence of the entire genome of strain CV777, which was found to be 28,033 nucleotides (nt) in length (excluding the poly A-tail). A cloning strategy, which involves primers based on conserved regions in the predicted ORF1 products from other coronaviruses whose genome sequence has been determined, was used to amplify the equivalent, but as yet unknown, sequence of PEDV. Primary sequences derived from these products were used to design additional primers resulting in the amplification and sequencing of the entire ORF1 of PEDV. Analysis of the nucleotide sequences revealed a small open reading frame (ORF) located near the 5′ end (no 99–137), and two large, slightly overlapping ORFs, ORF1a (nt 297–12650) and ORF1b (nt 12605–20641). The ORF1a and ORF1b sequences overlapped at a potential ribosomal frame shift site. The amino acid sequence analysis suggested the presence of several functional motifs within the putative ORF1 protein. By analogy to other coronavirus replicase gene products, three protease and one growth factor-like motif were seen in ORF1a, and one polymerase domain, one metal ion-binding domain, and one helicase motif could be assigned within ORF1b. Comparative amino acid sequence alignments revealed that PEDV is most closely related to human coronavirus (HCoV)-229E and transmissible gastroenteritis virus (TGEV) and less related to murine hepatitis virus (MHV) and infectious bronchitis virus (IBV). These results thus confirm and extend the findings from sequence analysis of the structural genes of PEDV. url: https://www.ncbi.nlm.nih.gov/pubmed/11724265/ doi: 10.1023/a:1011831902219 id: cord-005252-m02inmc4 author: Kwon, Hyuk Moo title: Molecular cloning and sequence comparison of the S1 glycoprotein of the Gray and JMK strains of avian infectious bronchitis virus date: 1995 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The nucleotide sequences of S1 glycoprotein genes of the Gray and JMK strains of avian infectious bronchitis virus (IBV) were determined and compared with published sequences for IBV. The IBV Gray and JMK strains had 99% nucleotide sequence similarity. The overall nucleotide sequence similarity of the Gray and JMK strains compared with other IBV strains was between 82.0% and 87.4%. The similarity of the predicted amino acid sequence for the S1 glycoproteins of the Gray and JMK strains was 98.8%. Six of the 10 differences in the amino acid sequence were found between residues 99 and 127, suggesting a possible role for that region in the tissue trophisms of the viruses. The S1 glycoprotein of the Gray and JMK strains had 79.5%–84.6% amino acid similarity with the published sequence of other IBV strains. Serine instead of phenylalanine was observed in the protease cleavage site between the S1 and S2 glycoprotein subunits for the Gray and JMK strains, which was similar to the published sequence for the Ark99 and SE17 strains. The significance of that amino acid change is not known. Based on the nucleotide sequence of the Gray and JMK strains, theBsmAI restriction enzyme was selected by computer analysis and was used in restriction fragment length polymorphism analysis to differentiate the two strains. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089256/ doi: 10.1007/bf01702878 id: cord-328518-umvk59dc author: Lee, Dana N. title: Two novel adenoviruses found in Cave Myotis bats (Myotis velifer) in Oklahoma date: 2019-12-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Bats are carriers of potentially zoonotic viruses, therefore it is crucial to identify viruses currently found in bats to better understand how they are maintained in bat populations and evaluate risks for transmission to other species. Adenoviruses have been previously detected in bats throughout the world, but sampling is still limited. In this study, 30 pooled-guano samples were collected from a cave roost of Myotis velifer in Oklahoma. A portion of the DNA polymerase gene from Adenoviridae was amplified successfully in 18 M. velifer samples; however, DNA sequence was obtained from only 6 of these M. velifer samples. One was collected in October 2016, one in March 2017, and 4 in July 2017. The October and March samples contained viral DNA that was 3.1% different from each other but 33% different than the novel viral sequence found in the July 2017 samples. Phylogenetic analysis of these fragments confirmed our isolates were from the genus Mastadenovirus and had genetic diversity ranging from 20 to 50% when compared to other bat adenoviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/31797220/ doi: 10.1007/s11262-019-01719-2 id: cord-005207-02wmt2e9 author: Lee, Hee-Kyung title: Cloning and Sequence Analysis of the Nucleocapsid Gene of Porcine Epidemic Diarrhea Virus Chinju99 date: 2003 words: 2171.0 sentences: 118.0 pages: flesch: 63.0 cache: ./cache/cord-005207-02wmt2e9.txt txt: ./txt/cord-005207-02wmt2e9.txt summary: The nucleocapsid (N) gene of the porcine epidemic diarrhea virus (PEDV) Chinju99 which was previously isolated in Chinju, Korea was cloned and sequenced to establish the information for the development of genetically engineered diagnostic reagents. The nucleotide sequence encoding the entire N gene open reading frame (ORF) of Chinju99 was 1326 bases long and encoded a protein of 441 amino acids with predicted M (r) of 49 kDa. It consisted of 405 adenine (30.5%), 293 cytosine (22.1%), 334 guanines (25.2%) and 294 thymines (22.2%) residues. In the present study, a DNA clone was constructed for the full-length N gene open reading frame (ORF) of PEDV isolated in Chinju, Korea. The complete sequences of nucleotides and deduced amino acids of the N gene were determined, and further analyzed with those of other PEDVs for the information in the production of genetically engineered diagnostic reagents. abstract: The nucleocapsid (N) gene of the porcine epidemic diarrhea virus (PEDV) Chinju99 which was previously isolated in Chinju, Korea was cloned and sequenced to establish the information for the development of genetically engineered diagnostic reagents. Also, sequences of the nucleotides and deduced amino acids of the Chinju99 N gene were analyzed by alignment with those of CV777 and Br1/87. The nucleotide sequence encoding the entire N gene open reading frame (ORF) of Chinju99 was 1326 bases long and encoded a protein of 441 amino acids with predicted M (r) of 49 kDa. It consisted of 405 adenine (30.5%), 293 cytosine (22.1%), 334 guanines (25.2%) and 294 thymines (22.2%) residues. The Chinju99 N ORF nucleotide sequence was 96.5% and 96.4% homologous with that of the CV777 and Br1/87, respectively. The Chinju99 N protein revealed 96.8% amino acid identity with that of Br1/87 and CV777, respectively. The amino acid sequence contained seven potential sites for threonine (T)- or serine (S)-linked phosphorylation by each protein kinase C and casein kinase II. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089008/ doi: 10.1023/a:1023447732567 id: cord-299573-vq6ckqtd author: Lee, Meong-Hun title: Phylogenetic analysis of porcine astrovirus in domestic pigs and wild boars in South Korea date: 2012-09-11 words: 1963.0 sentences: 103.0 pages: flesch: 60.0 cache: ./cache/cord-299573-vq6ckqtd.txt txt: ./txt/cord-299573-vq6ckqtd.txt summary: In this study, 25/129 (19.4 %) domestic pig and 1/146 (0.7 %) wild boar fecal samples tested in South Korea were positive for PAstV. Bayesian inference (BI) tree analysis for RNA-dependent RNA polymerase (RdRp) and capsid (ORF2) gene sequences, including Mamastrovirus and Avastrovirus, revealed a relatively geographically divergent lineage. It was also observed that PAstV infections are widespread in South Korea regardless of the disease state in domestic pigs and in wild boars as well. It was, therefore, the aim of this study to investigate the genetic groups of Korean PAstV in domestic pigs and wild boars and to identify the incidence of co-infection with other porcine enteric viruses as well. A study of the molecular epidemiology and genetic diversity of human astrovirus in South Korea from 2002 to 2007 revealed genotype 1 to be the most prevalent, accounting for 72.19 % of strains, followed by genotypes 8 Korean PAstVs are shown in bold prints, and strains isolates from Korean and Hungarian wild boar are marked with a star and an arrow, respectively. abstract: Porcine astrovirus (PAstV) belongs to genetically divergent lineages within the genus Mamastrovirus. In this study, 25/129 (19.4 %) domestic pig and 1/146 (0.7 %) wild boar fecal samples tested in South Korea were positive for PAstV. Positive samples were mainly from pigs under 6 weeks old. Bayesian inference (BI) tree analysis for RNA-dependent RNA polymerase (RdRp) and capsid (ORF2) gene sequences, including Mamastrovirus and Avastrovirus, revealed a relatively geographically divergent lineage. The PAstVs of Hungary and America belong to lineage PAstV 4; those of Japan belong to PAstV 1; and those of Canada belong to PAstV 1, 2, 3, and 5, but not to 4. This study revealed that the PAstVs of Korea belong predominantly to lineage PAstV 4 and secondarily to PAstV 2. It was also observed that PAstV infections are widespread in South Korea regardless of the disease state in domestic pigs and in wild boars as well. url: https://doi.org/10.1007/s11262-012-0816-8 doi: 10.1007/s11262-012-0816-8 id: cord-005253-8qja4j9h author: Li, Weike title: Genetic characterization of an isolate of canine distemper virus from a Tibetan Mastiff in China date: 2014-04-02 words: 3386.0 sentences: 135.0 pages: flesch: 58.0 cache: ./cache/cord-005253-8qja4j9h.txt txt: ./txt/cord-005253-8qja4j9h.txt summary: This analysis shows that an N-glycosylation site at aa 108-110 within the F protein of CDV-TM-CC is specific for the wild-type strains (5804P, A75/17, and 164071) and the Asia-1 group strains, and may be another important factor for the poor immune response. Consistent with the results for the H protein, the homology of the deduced CDV-TM-CC amino acid sequence of the N protein to the Asia-1 strains (CYN07-hV, HLJ1-06, and Hebei) was high with 98.7-98.9 % identity, as shown in Fig. 4 . Analysis of the 1-135 aa signal peptide region of the F protein of CDV-TM-CC demonstrated the same set of amino acid variations in comparison with the Onderstepoort strain as for the other Asia-1 strains (CYN07-hV, HLJ1-06, and Hebei): 8 S/ 8 K, 11 T/ 11 P, 19 (Fig. 6) . abstract: Canine distemper (CD) is a highly contagious, often fatal, multisystemic, and incurable disease in dogs and other carnivores, which is caused by canine distemper virus (CDV). Although vaccines have been used as the principal means of controlling the disease, CD has been reported in vaccinated animals. The hemoagglutinin (H) protein is one of the most important antigens for inducing protective immunity against CD, and antigenic variation of recent CDV strains may explain vaccination failure. In this study, a new CDV isolate (TM-CC) was obtained from a Tibetan Mastiff that died of distemper, and its genome was characterized. Phylogenetic analysis of the H gene revealed that the CDV-TM-CC strain is unique among 20 other CDV strains and can be classified into the Asia-1 group with the Chinese strains, Hebei and HLJ1-06, and the Japanese strain, CYN07-hV. The H gene of CDV-TM-CC shows low identity (90.4 % nt and 88.9 % aa) with the H gene of the classical Onderstepoort vaccine strain, which may explain the inability of the Tibetan Mastiff to mount a protective immune response. We also performed a comprehensive phylogenetic analysis of the N, P, and F protein sequences, as well as potential N-glycosylation sites and cysteine residues. This analysis shows that an N-glycosylation site at aa 108-110 within the F protein of CDV-TM-CC is specific for the wild-type strains (5804P, A75/17, and 164071) and the Asia-1 group strains, and may be another important factor for the poor immune response. These results provide important information for the design of CD vaccines in the China region and elsewhere. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089258/ doi: 10.1007/s11262-014-1062-z id: cord-295554-0pzjyrdf author: Lima, Francisco Esmaile de Sales title: Detection of Alphacoronavirus in velvety free-tailed bats (Molossus molossus) and Brazilian free-tailed bats (Tadarida brasiliensis) from urban area of Southern Brazil date: 2013-03-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A survey was carried out in search for bat coronaviruses in an urban maternity roost of about 500 specimens of two species of insectivorous bats, Molossus molossus and Tadarida brasiliensis, in Southern Brazil. Twenty-nine out of 150 pooled fecal samples tested positive by reverse transcription-PCR contained fragments of the RNA-dependent RNA polymerase gene of coronavirus-related viruses. The sequences clustered along with bat alphacoronaviruses, forming a subcluster within this group. Our findings point to the need for risk assessment and continued surveillance of coronavirus infections of bats in Brazil. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11262-013-0899-x) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/23504146/ doi: 10.1007/s11262-013-0899-x id: cord-257122-h3zi8k8g author: Lin, Chao-Nan title: Full genome analysis of a novel type II feline coronavirus NTU156 date: 2012-12-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infections by type II feline coronaviruses (FCoVs) have been shown to be significantly correlated with fatal feline infectious peritonitis (FIP). Despite nearly six decades having passed since its first emergence, different studies have shown that type II FCoV represents only a small portion of the total FCoV seropositivity in cats; hence, there is very limited knowledge of the evolution of type II FCoV. To elucidate the correlation between viral emergence and FIP, a local isolate (NTU156) that was derived from a FIP cat was analyzed along with other worldwide strains. Containing an in-frame deletion of 442 nucleotides in open reading frame 3c, the complete genome size of NTU156 (28,897 nucleotides) appears to be the smallest among the known type II feline coronaviruses. Bootscan analysis revealed that NTU156 evolved from two crossover events between type I FCoV and canine coronavirus, with recombination sites located in the RNA-dependent RNA polymerase and M genes. With an exchange of nearly one-third of the genome with other members of alphacoronaviruses, the new emerging virus could gain new antigenicity, posing a threat to cats that either have been infected with a type I virus before or never have been infected with FCoV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11262-012-0864-0) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s11262-012-0864-0 doi: 10.1007/s11262-012-0864-0 id: cord-279863-5kxgu4t9 author: Oem, Jae-Ku title: Phylogenetic analysis of bovine astrovirus in Korean cattle date: 2013-11-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Bovine astrovirus (BAstV) belongs to a genetically divergent lineage within the genus Mamastrovirus. The present study showed that BAstV was associated with the gastroenteric tracts of cattle in nine positive fecal samples from 115 cattle, whereas no positive samples were found in the brain tissues of 14 downer cattle. Interestingly, the positive diarrheal samples were obtained mainly from calves aged 14 days–3 months. Bayesian inference tree analysis of the partial ORF1ab and capsid (ORF2) gene sequences of BAstVs identified four divergent groups. Eleven BAstVs, four porcine astroviruses, and two deer astroviruses (DAstVs; CcAstV-1 and -2) belonged to group 1; group 2 contained two BAstVs (BAstK08–51 and BAstK10–96) with another two in group 3 (BAstK08–2 and BAstK08–53); and group 4 comprised the BAstV-NeuroS1 strain derived from a cattle brain tissue sample and an ovine astrovirus. The same divergent groups were obtained when the pairwise alignments were produced using both amino acid and nucleotide sequences. The Korean BAstVs isolated from infected cattle had a nationwide distribution and they belonged to groups 1, 2, and 3. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11262-013-1013-0) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s11262-013-1013-0 doi: 10.1007/s11262-013-1013-0 id: cord-269720-o81j3d1j author: Page, Kevin W. title: Sequence analysis of the leader RNA of two porcine coronaviruses: Transmissible gastroenteritis virus and porcine respiratory coronavirus date: 1990 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The leader RNA sequence was determined for two pig coronaviruses, tranmissible gastroenteritis virus (TGEV), and porcine respiratory coronavirus (PRCV). Primer extension, of a synthetic oligonucleotide complementary to the 5′ end of the nucleoprotein gene of TGEV was used to produce a single-stranded DNA copy of the leader RNA from the nucleoprotein mRNA species from TGEV and PRCV, the sequences of which were determined by Maxam and Gilbert cleavage. Northern blot analysis, using a synthetic oligonucleotide complementary to the leader RNA, showed that the leader RNA sequence was present on all of the subgenomic mRNA species. The porcine coronavirus leader RNA sequences were compared to each other and to published coronavirus leader RNA sequences. Sequence homologies and secondary structure similarities were identified that may play a role in the biological function of these RNA sequences. url: https://www.ncbi.nlm.nih.gov/pubmed/1962975/ doi: 10.1007/bf00570024 id: cord-025704-icedihm2 author: Pawestri, Hana A. title: Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008–2015 date: 2020-06-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Since the initial detection in 2003, Indonesia has reported 200 human cases of highly pathogenic avian influenza H5N1 (HPAI H5N1), associated with an exceptionally high case fatality rate (84%) compared to other geographical regions affected by other genetic clades of the virus. However, there is limited information on the genetic diversity of HPAI H5N1 viruses, especially those isolated from humans in Indonesia. In this study, the genetic and antigenic characteristics of 35 HPAI H5N1 viruses isolated from humans were analyzed. Full genome sequences were analyzed for the presence of substitutions in the receptor binding site, and polymerase complex, as markers for virulence or human adaptation, as well as antiviral drug resistance substitutions. Only a few substitutions associated with human adaptation were observed, a remarkably low prevalence of the human adaptive substitution PB2-E627K, which is common during human infection with other H5N1 clades and a known virulence marker for avian influenza viruses during human infections. In addition, the antigenic profile of these Indonesian HPAI H5N1 viruses was determined using serological analysis and antigenic cartography. Antigenic characterization showed two distinct antigenic clusters, as observed previously for avian isolates. These two antigenic clusters were not clearly associated with time of virus isolation. This study provides better insight in genetic diversity of H5N1 viruses during human infection and the presence of human adaptive markers. These findings highlight the importance of evaluating virus genetics for HPAI H5N1 viruses to estimate the risk to human health and the need for increased efforts to monitor the evolution of H5N1 viruses across Indonesia. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11262-020-01765-1) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7262163/ doi: 10.1007/s11262-020-01765-1 id: cord-272693-432ixb7g author: Phillips, J. E. title: Changes in nonstructural protein 3 are associated with attenuation in avian coronavirus infectious bronchitis virus date: 2011-09-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Full-length genome sequencing of pathogenic and attenuated (for chickens) avian coronavirus infectious bronchitis virus (IBV) strains of the same serotype was conducted to identify genetic differences between the pathotypes. Analysis of the consensus full-length genome for three different IBV serotypes (Ark, GA98, and Mass41) showed that passage in embryonated eggs, to attenuate the viruses for chickens, resulted in 34.75–43.66% of all the amino acid changes occurring in nsp 3 within a virus type, whereas changes in the spike glycoprotein, thought to be the most variable protein in IBV, ranged from 5.8 to 13.4% of all changes. The attenuated viruses did not cause any clinical signs of disease and had lower replication rates than the pathogenic viruses of the same serotype in chickens. However, both attenuated and pathogenic viruses of the same serotype replicated similarly in embryonated eggs, suggesting that mutations in nsp 3, which is involved in replication of the virus, might play an important role in the reduced replication observed in chickens leading to the attenuated phenotype. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11262-011-0668-7) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/21909766/ doi: 10.1007/s11262-011-0668-7 id: cord-268627-nnx46nwf author: Ren, Xiaofeng title: Development of reverse transcription loop-mediated isothermal amplification for rapid detection of porcine epidemic diarrhea virus date: 2011-02-01 words: 2775.0 sentences: 156.0 pages: flesch: 58.0 cache: ./cache/cord-268627-nnx46nwf.txt txt: ./txt/cord-268627-nnx46nwf.txt summary: In this study, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed for detection of porcine epidemic diarrhea virus (PEDV). The results showed that the optimal reaction condition for RT-LAMP amplifying PEDV N gene was achieved at 63°C for 50 min. The total RNAs were extracted from the culture supernatants of PEDV, TGEV, PRV, PRRSV, and IBV using the RNA extraction kit (KeyGen Biotech, China) and the genomic DNA of PrV was extracted from virus-infected Vero cell culture using the DNA extraction kit (Omega, Norcross, USA) according to the manufacturer''s instructions. As shown in Fig. 2a , the DNA products of the RT-LAMP at different temperatures showed multiple of characteristic ladder bands; however, the intensity of DNAs determined by Gel Analyzer software from the reactions at 63°C was stronger than that at other reaction temperatures, which was judged as the optimal temperature for RT-LAMP amplifying PEDV N gene. The sensitivity of the RT-LAMP assay was first compared with the conventional RT-PCR amplifying the tenfold serial dilutions of RNA templates of PEDV. abstract: In this study, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed for detection of porcine epidemic diarrhea virus (PEDV). Six primers were designed to amplify the nucleocapsid (N) gene of PEDV. The optimization, sensitivity, and specificity of the RT-LAMP were investigated. The results showed that the optimal reaction condition for RT-LAMP amplifying PEDV N gene was achieved at 63°C for 50 min. The RT-LAMP assay was more sensitive than gel-based RT-PCR and enzyme-linked immunosorbent assay. It was capable of detecting PEDV from clinical samples and differentiating PEDV from Porcine transmissible gastroenteritis virus, Porcine rotavirus, Porcine pseudorabies virus, Porcine reproductive and respiratory syndrome virus, and Avian infectious bronchitis virus. url: https://www.ncbi.nlm.nih.gov/pubmed/21286798/ doi: 10.1007/s11262-011-0570-3 id: cord-331919-6kistim2 author: Song, Daesub title: Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines date: 2012-01-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The porcine epidemic diarrhoea virus (PEDV), a member of the Coronaviridae family, causes acute diarrhoea and dehydration in pigs. Although it was first identified in Europe, it has become increasingly problematic in many Asian countries, including Korea, China, Japan, the Philippines, and Thailand. The economic impacts of the PEDV are substantial, given that it results in significant morbidity and mortality in neonatal piglets and is associated with increased costs related to vaccination and disinfection. Recently, progress has been made in understanding the molecular epidemiology of PEDV, thereby leading to the development of new vaccines. In the current review, we first describe the molecular and genetic characteristics of the PEDV. Then we discuss its molecular epidemiology and diagnosis, what vaccines are available, and how PEDV can be treated. url: https://www.ncbi.nlm.nih.gov/pubmed/22270324/ doi: 10.1007/s11262-012-0713-1 id: cord-263489-i4tkdgy4 author: Suo, Siqingaowa title: Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential date: 2015-05-27 words: 2211.0 sentences: 130.0 pages: flesch: 65.0 cache: ./cache/cord-263489-i4tkdgy4.txt txt: ./txt/cord-263489-i4tkdgy4.txt summary: title: Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential Herein, we use similar technology and advance previous work by using the rS-AD as an immobilizing target to select phages from a peptide display library, with diagnostic potential for TGEV. Our results indicate that phages bearing peptide ligands that bind rS-AD can be used to develop a phage-mediated ELISA with high sensitivity and specificity to distinguish TGEV from other common swine viruses. To compare the sensitivities of phage-mediated ELISA to antibody-mediated ELISA, TGEV serially diluted in 0.1 M NaHCO 3 (pH 8.6) was coated onto duplicate ELISA plates overnight at 4°C followed by blocking with 5 % skim milk for 3 h at rt. Predicted amino acid sequences were generated for ten selected phages In summary, we identified peptides that specifically bind to TGEV and can form the basis of new diagnostic tests where the sensitivity of phTGEV-SAD15 was 0.1 lg of TGEV. abstract: The spike (S) protein of porcine transmissible gastroenteritis virus (TGEV) is located within the viral envelope and is the only structural protein that possesses epitopes capable of inducing virus-neutralizing antibodies. Among the four N-terminal antigenic sites A, B, C, and D, site A and to a lesser extent site D (S-AD) induce key neutralizing antibodies. Recently, we expressed S-AD (rS-AD) in recombinant form. In the current study, we used the rS-AD as an immobilized target to identify peptides from a phage-display library with application for diagnosis. Among the 9 phages selected that specifically bound to rS-AD, the phage bearing the peptide TLNMHLFPFHTG bound with the highest affinity and was subsequently used to develop a phage-based ELISA for TGEV. When compared with conventional antibody-based ELISA, phage-mediated ELISA was more sensitive; however, it did not perform better than semi-quantitative RT-PCR, though phage-mediated ELISA was quicker and easier to set up. url: https://www.ncbi.nlm.nih.gov/pubmed/26013256/ doi: 10.1007/s11262-015-1208-7 id: cord-310298-26x2p9wc author: Tao, Pan title: Analysis of synonymous codon usage in classical swine fever virus date: 2008-10-29 words: 3416.0 sentences: 184.0 pages: flesch: 56.0 cache: ./cache/cord-310298-26x2p9wc.txt txt: ./txt/cord-310298-26x2p9wc.txt summary: Using the complete genome sequences of 35 classical swine fever viruses (CSFV) representing all three genotypes and all three kinds of virulence, we analyzed synonymous codon usage and the relative dinucleotide abundance in CSFV. The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in CSFV. As shown in Table 4 , the first axis value in COA of each selected genome, which contains most of the variation in synonymous codon usage bias between these genomes, is closely correlated with the GC composition at the first, second, and third codon position. Mean values of 35 CSFVs relative dinucleotide ratios ± S.D Table 3 Summary of correlation analysis between the first two axes in COA and sixteen dinucleotides in the selected viruses , indicating that the overall extent of codon usage bias in CSFV genomes is low. abstract: Using the complete genome sequences of 35 classical swine fever viruses (CSFV) representing all three genotypes and all three kinds of virulence, we analyzed synonymous codon usage and the relative dinucleotide abundance in CSFV. The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in CSFV. Furthermore, we observed that the relative abundance of dinucleotides in CSFV is independent of the overall base composition but is still the result of differential mutational pressure, which also shapes codon usage. In addition, other factors, such as the subgenotypes and aromaticity, also influence the codon usage variation among the genomes of CSFV. This study represents the most comprehensive analysis to date of CSFV codon usage patterns and provides a basic understanding of the mechanisms for codon usage bias. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11262-008-0296-z) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s11262-008-0296-z doi: 10.1007/s11262-008-0296-z id: cord-265095-lf5j4ic7 author: Ten Dam, Edwin B. title: RNA pseudoknots: Translational frameshifting and readthrough on viral RNAs date: 1990 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Ribosomal frameshifting on retroviral RNAs has been proposed to be mediated by slippage of two adjacent tRNAs into the — 1 direction at a specific heptanucleotide sequence. Here we report a computer-aided analysis of the structure around the established or putative frameshift sites in a number of retroviral, coronaviral, toroviral, and luteoviral RNAs and two dsRNA yeast viruses. In almost all cases a stable hairpin was predicted four to nine nucleotides downstream of the shifty heptanucleotide. More than half of the resulting hairpin loops give rise to potential pseudoknotting with sequences downstream of this hairpin. Especially in the case of the shifty heptanucleotides U UUA AAC and G GGA AAC, stable downstream pseudoknots are present. Indications were also found for the presence of pseudoknots downstream of amber stop condons at readthrough sites in some retroviral RNAs. url: https://www.ncbi.nlm.nih.gov/pubmed/2402881/ doi: 10.1007/bf00678404 id: cord-346643-os2kyvvf author: Wang, Li title: Inhibition of porcine transmissible gastroenteritis virus infection in porcine kidney cells using short hairpin RNAs targeting the membrane gene date: 2016-11-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The membrane (M) protein is the most abundant component of the porcine transmissible gastroenteritis virus (TGEV) particle. To exploit the possibility of using RNA interference (RNAi) as a strategy against TGEV infection, three plasmids (pRNAT-1, pRNAT-2, and pRNAT-3) expressing short hairpin RNAs were designed to target three different coding regions of the M gene of TGEV. The plasmids were constructed and transiently transfected into a porcine kidney cells, PK-15, to determine whether these constructs inhibited TGEV production. The analysis of cytopathic effects demonstrated that pRNAT-2 and pRNAT-3 could protect PK-15 cells against pathological changes specifically and efficiently. Additionally, indirect immunofluorescence and 50% tissue culture infectious dose (TCID(50)) assays showed that pRNAT-2 and pRNAT-3 inhibited the multiplication of the virus at the protein level effectively. Quantitative real-time PCR further confirmed that the amounts of viral RNAs in cell cultures pre-transfected with the three plasmids were reduced by 13, 68, and 70%, respectively. This is the first report showing that RNAi targeting of the M gene. Our results could promote studies of the specific function of viral genes associated with TGEV infection and might provide a theoretical basis for potential therapeutic applications. url: https://doi.org/10.1007/s11262-016-1409-8 doi: 10.1007/s11262-016-1409-8 id: cord-254291-y8xvh6hs author: Yamanaka, Miles title: Nucleotide Sequence of the Inter-Structural Gene Region of Feline Infectious Peritonitis Virus date: 1998 words: 832.0 sentences: 48.0 pages: flesch: 67.0 cache: ./cache/cord-254291-y8xvh6hs.txt txt: ./txt/cord-254291-y8xvh6hs.txt summary: The sequence of the region located between the S and M glycoprotein genes of the 79-1146 strain of feline infectious peritonitis virus (FIPV) is presented. The inter-structural gene region encodes 3 open reading frames (ORFs), termed ORFs 3a, 3b and 4, with nucleotide sequences conforming to the minimum conserved transcription signal upstream of each. The FIPV interstructural gene region is identical in length when compared to the Insavc-1 strain of canine coronavirus (CCV) but differs from various strains of transmissible gastroenteritis virus (TGEV) by the presence of deletions and insertions. This inter-structural gene region has been examined in the related coronaviruses transmissible gastroenteritis virus (TGEV) and canine coronavirus (CCV) (2±6). The arrangement of the open reading frames (ORFs) in the inter-structural gene region has been described for the FIPV genome (1,7), but detailed sequence has not been presented. The sequence identity between FIPV 79-1146 and the Purdue strain of TGEV in the inter-structural gene region is 90.7%. abstract: The sequence of the region located between the S and M glycoprotein genes of the 79-1146 strain of feline infectious peritonitis virus (FIPV) is presented. The inter-structural gene region encodes 3 open reading frames (ORFs), termed ORFs 3a, 3b and 4, with nucleotide sequences conforming to the minimum conserved transcription signal upstream of each. An additional ORF, 3x, partially overlaps the 3′ end of ORF 3a. The FIPV interstructural gene region is identical in length when compared to the Insavc-1 strain of canine coronavirus (CCV) but differs from various strains of transmissible gastroenteritis virus (TGEV) by the presence of deletions and insertions. The sizes of ORF 3a and 4 are conserved in FIPV, TGEV and CCV. However, as with CCV, the FIPV ORF 3b is truncated in comparison with TGEV. url: https://www.ncbi.nlm.nih.gov/pubmed/9654687/ doi: 10.1023/a:1008099209942 id: cord-307580-nokd5kmx author: Yang, Guang title: D-RNA Molecules Associated with Subisolates of the VT Strain of Citrus Tristeza Virus which Induce Different Seedling-Yellows Reactions date: 1999 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Citrus tristeza virus (CTV) strains were previously catalogued as seedling-yellows (SY) and non-SY (nSY) types, according to their yellowing and stunting effects on indicator seedlings. Among subisolates of the VT strain, which were selected from chronically infected Alemow plants, there was a correlation between the presence of 2.4-, 2.7- and 4.5-kb D-RNAs, and SY and nSY reactions, respectively. Similarly, plants infected with Mor-T subisolates, which cause SY, contained D-RNAs of 2.6 to 2.8 kb, while nSY subisolates from recovered sour orange tissue contained a major D-RNA of 5.1 kb. Plants harboring the 2.7-kb D-RNA were protected against challenge inoculation with a subisolate harboring the 4.5-kb D-RNA. This study suggests that the nSY reaction results either from the absence of SY gene(s) in the genomes of certain CTV strains or through the suppression of the effects of SY gene(s) by D-RNAs with 5′ parts larger than 4000 nt. url: https://www.ncbi.nlm.nih.gov/pubmed/10499445/ doi: 10.1023/a:1008105004407 id: cord-282126-gmjnbnx5 author: Yang, Limin title: Development and application of a reverse transcription loop-mediated isothermal amplification method for rapid detection of Duck hepatitis A virus type 1 date: 2012-08-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We developed and evaluated a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detecting Duck hepatitis A virus type 1 (DHAV-1). The amplification could be finished in 1 h under isothermal conditions at 63 °C by employing a set of four primers targeting the 2C gene of DHAV-1. The RT-LAMP assay showed higher sensitivity than the RT-PCR with a detection limit of 0.1 ELD(50) 0.1 ml(−1) of DHAV-1. The RT-LAMP assay was highly specific; no cross-reactivity was observed from the samples of other related viruses, bacteria, allantoic fluid of normal chicken embryos, or the livers of uninfected ducks. Thirty clinical samples were subjected to detection by RT-LAMP, RT-PCR, and virus isolation, which obtained completely consistent, positive results. As a simple, rapid, and accurate detection method, this RT-LAMP assay has important potential applications in the clinical diagnosis of DHAV-1. url: https://doi.org/10.1007/s11262-012-0798-6 doi: 10.1007/s11262-012-0798-6 id: cord-284675-7zv449sc author: Yew, Tan Do title: Base Usage and Dinucleotide Frequency of Infectious Bursal Disease Virus date: 2004 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Base usage and dinucleotide frequency have been extensively studied in many eukaryotic organisms and bacteria, but not for viruses. In this paper, a comprehensive analysis of these aspects for infectious bursal disease virus (IBDV) was presented. The analysis of base usage indicated that all of the IBDV genes possess equivalent overall nucleotide distributions. However when the base usage at each codon positions was analysed by using cluster analysis, the VP5 open reading frame (ORF) formed a different cluster isolated from the other genes. The unusual base usage of VP5 ORF may indicate that the gene was originated by the virus “overprinting strategy”, a strategy in which virus may create novel gene by utilizing the unused reading frames of its existing genes. Meanwhile, the GC content of the IBDV genes and the chicken's coding sequences was comparable; suggesting the virus imitation of the host to increase its translational efficiency. The analysis of dinucleotide frequency indicated that IBDV genome had dinucleotide bias: the frequencies of CpG and TpA were lower and the TpG was higher than the expected. Classical methylation pathway, a process where CpG converted to TpG, may explain the significant correlation between the CpG deficiency and TpG abundance. “Principal component analysis of the dinucleotide frequencies” (DF-PCA) was used to analyse the overall dinucleotide frequencies of IBDV genome. DF-PCA on the hypervariable region and polyprotein (VPX-VP4-VP3) gene showed that the very virulent IBDV (vvIBDV) was segregated from other strains; which meant vvIBDV had a unique dinucleotide pattern. In summary, the study of base usage and dinucleotide frequency had unravelled many overlooked genomic properties of the virus. url: https://www.ncbi.nlm.nih.gov/pubmed/14739650/ doi: 10.1023/b:viru.0000012262.89898.c7 id: cord-340438-9q3ic0ye author: Zhang, Jianqiang title: Identification of porcine epidemic diarrhea virus variant with a large spike gene deletion from a clinical swine sample in the United States date: 2018-02-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Two genetically different porcine epidemic diarrhea virus (PEDV) strains have been identified in the USA: US prototype (also called non-S INDEL) and S INDEL PEDVs. In February 2017, a PEDV variant (USA/OK10240-8/2017) was identified in a rectal swab from a sow farm in Oklahoma, USA. Complete genome sequence analyses indicated this PEDV variant was genetically similar to US non-S INDEL strain but had a continuous 600-nt (200-aa) deletion in the N-terminal domain of the spike gene compared to non-S INDEL PEDVs. This is the first report of detecting PEDV bearing large spike gene deletion in clinical swine samples in the USA. url: https://www.ncbi.nlm.nih.gov/pubmed/29468451/ doi: 10.1007/s11262-018-1542-7 id: cord-311204-fc12f845 author: Zhou, Ling title: Full-length genomic characterization and molecular evolution of canine parvovirus in China date: 2016-04-02 words: 2229.0 sentences: 138.0 pages: flesch: 65.0 cache: ./cache/cord-311204-fc12f845.txt txt: ./txt/cord-311204-fc12f845.txt summary: Canine parvovirus type 2 (CPV-2) can cause acute haemorrhagic enteritis in dogs and myocarditis in puppies. Some faecal samples were negative for the CPV-2 antigen based on a colloidal gold test strip but were positive based on PCR, and a viral strain was isolated from one such sample. Identification of CPV-2 with cell culture and IPMA Feline kidney cell line F81 was obtained from the American Type Culture Collection, USA and was used to isolate viruses from clinical samples and to observe cytopathic effects associated with viral replication. Cloning the full-length genomic sequence of CPV-2 DNA and RNA were extracted from the homogenized samples (faeces from infected dogs) with the TIANamp Virus DNA/RNA Kit (Beijing TIANGEN Biotech Company, Beijing, China) according to the manufacturer''s protocol. One viral strain was isolated from the faeces of dogs that tested negative in the colloidal gold test strip but positive with PCR. abstract: Canine parvovirus type 2 (CPV-2) can cause acute haemorrhagic enteritis in dogs and myocarditis in puppies. This disease has become one of the most serious infectious diseases of dogs. During 2014 in China, there were many cases of acute infectious diarrhoea in dogs. Some faecal samples were negative for the CPV-2 antigen based on a colloidal gold test strip but were positive based on PCR, and a viral strain was isolated from one such sample. The cytopathic effect on susceptible cells and the results of the immunoperoxidase monolayer assay, PCR, and sequencing indicated that the pathogen was CPV-2. The strain was named CPV-NY-14, and the full-length genome was sequenced and analysed. A maximum likelihood tree was constructed using the full-length genome and all available CPV-2 genomes. New strains have replaced the original strain in Taiwan and Italy, although the CPV-2a strain is still predominant there. However, CPV-2a still causes many cases of acute infectious diarrhoea in dogs in China. url: https://doi.org/10.1007/s11262-016-1309-y doi: 10.1007/s11262-016-1309-y id: cord-302584-fwdpzv85 author: Zhu, Ying title: Isolation of Virus from a SARS Patient and Genome-wide Analysis of Genetic Mutations Related to Pathogenesis and Epidemiology from 47 SARS-CoV Isolates date: 2005-01-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Severe acute respiratory syndrome (SARS) caused by SARS-associated coronavirus (SARS-CoV) is a fatal disease. Prevention of future outbreaks is essential and requires understanding pathogenesis and evolution of the virus. We have isolated a SARS-CoV in China and analyzed 47 SARS-CoV genomes with the aims to reveal the evolution trends of the virus and provide insights into understanding pathogenesis and SARS epidemic. Specimen from a SARS patient was inoculated into cell culture. The presence of SARS-CoV was determined by RT-PCR and confirmed by electron microscopy. Virus was isolated followed by the determination of its genome sequences, which were then analyzed by comparing with other 46 SARS-CoV genomes. Genetic mutations with potential implications to pathogenesis and the epidemic were characterized. This viral genome consists of 29,728 nucleotides with overall organization in agreement with that of published isolates. A total of 348 positions were mutated on 47 viral genomes. Among them 22 had mutations in more than three genomes. Hot spots of nucleotide variations and unique trends of mutations were identified on the viral genomes. Mutation rates were different from gene to gene and were correlated well with periodical or geographic characteristics of the epidemic. url: https://www.ncbi.nlm.nih.gov/pubmed/15744567/ doi: 10.1007/s11262-004-4586-9 ==== make-pages.sh questions [ERIC WAS HERE] ==== make-pages.sh search /data-disk/reader-compute/reader-cord/bin/make-pages.sh: line 77: /data-disk/reader-compute/reader-cord/tmp/search.htm: No such file or directory Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/tsv2htm-search.py", line 51, in with open( TEMPLATE, 'r' ) as handle : htm = handle.read() FileNotFoundError: [Errno 2] No such file or directory: '/data-disk/reader-compute/reader-cord/tmp/search.htm' ==== make-pages.sh topic modeling corpus Zipping study carrel