# ent

id: cord-005207-02wmt2e9
type: CHEMICAL
entity:
  N gene of PEDV The DNA was cloned into pTZ19R vector DNA Fig 1 and subjected to sequencing The nucleotide


id: cord-005252-m02inmc4
type: CELL_TYPE
entity:
  G T T G T T A G C G A G C T M 4 1 G T T T G C T A G C G A G C T A 9 9 T T A A T A G C C A 7 T S E I T T T A A T A G C T PPI T T G C T A G C A C C T G


id: cord-005252-m02inmc4
type: PROTEIN
entity:
  T A C T A C C A A A G C G C C T T C A G A C C A C C T A A T G G T T G G C A T T T A C A T G G A G G 2 0 0 J M K C B e


id: cord-005252-m02inmc4
type: PROTEIN
entity:
  T G C G C A A G C T G G C T C T T M 4 1 T G C G A A G C C G G C T C T T A 9 9 T G C G A G T A G G A C T G S E I C CT G G C A T G PPI T G C G G G C T G G A C T G 300 J M K C B e


id: cord-005252-m02inmc4
type: PROTEIN
entity:
  C A A G A C T T A T T C A G T G T C G T G T G A M 4 1 C A C G A T T A T C A G TG T C G T G T G A A 9 9 C C C A A C A C T T G G C A C T C G S E I C A C A G A C G T T C G G C A C T C PPI C C C A A A A T T G G C A C T C G G


id: cord-005252-m02inmc4
type: CELL_TYPE
entity:
  G C T T C T G T A G C C A T G A T T G C A C C A C A T A G T G G T A T G T C G T G G T C T G T C C A 3 5 0 J M K B e


id: cord-005252-m02inmc4
type: PROTEIN
entity:
  T A T C G G T C A T C A G T A G A G M 4 1 T A T CG G T C A T C A G T A G A G A 9 9 C A C T A A C T C SEI T G G C T A A C T A PPI C A C C A A C T T A 4 0 0 J M K B e


id: cord-005252-m02inmc4
type: CELL_TYPE
entity:
  T G T T A T A G A C M 4 1 T G T T A C T A G A C A 9 9 A T C T T A T C A T SEI A A T C CT PPl A T C C T A A C T C A


id: cord-005252-m02inmc4
type: PROTEIN
entity:
  C A T T G G T C T A A G G C T G C T A A A G M 4 1 A A T A T A T G G T C A T A A G G C T G C b Ab_AG A 9 9 A G C T A A A G G T T A SEI A G C T T C A A A G T T T A P P I A G C C A A A C G T T A G


id: cord-005252-m02inmc4
type: CELL_TYPE
entity:
  T T A C A A G G C C A A A T C C G C A T T T C T G C T A T G A G A A G C G T T A A T A G T C G T C C 5 0 0 J M K C C A T B e


id: cord-005252-m02inmc4
type: PROTEIN
entity:
  C G C A G A G G C A C T M 4 1 C G C A G A G G C A C T A 9 9 G G A C T A C A A G SEI T C T G T A A T G T A T A


id: cord-005252-m02inmc4
type: PROTEIN
entity:
  G A T T G T T A C M 4 1 A T T G T T A C A 9 9 G A G A T T C SEI G A T T T A G C C PPI G A G A T T C G A 650 J M K B e


id: cord-005252-m02inmc4
type: PROTEIN
entity:
  T A C A C C A T C T M 4 1 T A C A C C C A T C T A 9 9 T C A CT T G A G T C C SEI T A C C A G T T PPI T CA C CT T G A G T C C A C C A G 7 0 0 J M K B e


id: cord-005252-m02inmc4
type: CELL_TYPE
entity:
  T T A G C G C A A C C C T A T C G A M 4 1 T A G C G C A A C C C T A TC G A A 9 9 A G T C CA T G S E I T T CC A T C T G T T T PPI A GT C C A T G G 1 0 0 0 J M K B e


id: cord-005252-m02inmc4
type: DNA
entity:
  C A A A C T C A A A G T M 4 1 A C A A A C T C A A G T A 9 9 T C A G T S E I G T A G T PPI T C A G T 1 0 5 0 J M K T B e


id: cord-005252-m02inmc4
type: DNA
entity:
  C A M 4 1 C G C A 9 9 C T A A C C A T A T C A T T T SE C G CT C PP2 C T A A C C A T A T C A T T T G A G 4 0 0 J M K B e


id: cord-259398-s8qsjkj2
type: DNA
entity:
  1008048916808 sha 2005dff40b722e725ed082da6ccab655fc479cb5 doc_id 259398 cord_uid s8qsjkj2 The 3 ends


id: cord-259398-s8qsjkj2
type: CHEMICAL
entity:
  N genes Primer pair 5F5 3B3 ampli ed a cDNA fragment containing the 3 H end of S 4 9 kDa 4 8 kDa 12 7 kDa E M and the 5 H end of N genes Primer pair B5 H B3 H ampli ed the 3 H end of the spike gene primer pair 5F24 A3 H ampli ed a cDNA that coded for the carboxy terminal portion of the S1 subunit primer pair A5 H 3B11 ampli ed a cDNA fragment that coded for the amino terminus of S and primer pair 5F16 3B10 ampli ed the 32 kDa


id: cord-011794-ejoufvvj
type: PROTEIN
entity:
  antibodies 2E10 1 1 5F12 1 1 3B12 1 200 5B8 1 1 5H1 1 1 4G10 1 100 1B12 1 2 1G9 1 100 8G4 1 50 1H7 1 1 2H11 1 5 or N protein


id: cord-348896-a2mjj5dt
type: WORK_OF_ART
entity:
  Viral Infections of the Gastrointestinal Tract Viral Diarrhea of Man and Animals Diseases of Swine Diseases of Swine


id: cord-269720-o81j3d1j
type: CELL_LINE
entity:
  X20 SSC X1 SSC 0 15 M NaCI 0 015 M trisodium citrate pH 7 0 for 18 hr and baked at 80 for 2 hr The membrane was boiled in 50 mM Tris HCl pH 8 0 for 5 min to remove glyoxal groups from the RNA


id: cord-284675-7zv449sc
type: DNA
entity:
  D00499 D00867 D00868 D00869 D49706 D83985 L42284 M64285 M66722 M97346 X03993 X54858 X84034 X89570 X92760 X95883 Y14955 Y14956 Y14957 Y14962 Y14963 Y18612 Y18682 Z25481


id: cord-322475-i29t7ce8
type: ORG
entity:
  Project Management for Agricultural Science and Technology Achievements Transformation Fund 2010GB2C400209 Science and Technology Major Project of Fujian


id: cord-283168-kl1hoa1x
type: CHEMICAL
entity:
  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


id: cord-283168-kl1hoa1x
type: CHEMICAL
entity:
  Cardiovirus Aphtovirus Hepatovirus Parechovirus Erbovirus Kobuvirus Teschovirus Sapelovirus Senecavirus Tremovirus and Avihepatovirus 1 Several other picornaviruses


id: cord-266634-bww62vx8
type: CHEMICAL
entity:
  bromophenol blue position Fig 2a lane 1 while a reaction lacking the guanylyl transferase enzyme showed only the GTP lane 2 This


id: cord-302584-fwdpzv85
type: PERSON
entity:
  Wang Ke Gu Chunfang Wu Kailang Li Yan Zheng Congyi Xiao Gengfu Yan Huimin Zhang Jiamin Guo Deyin Tien Po Wu Jianguo


id: cord-269340-o9jdt86j
type: PROTEIN
entity:
  cord 269340 o9jdt86j authors Callison Scott Andrew Jackwood Mark W Hilt Deborah Ann title Infectious Bronchitis Virus S2 Gene Sequence


id: cord-299573-vq6ckqtd
type: DNA
entity:
  PEDV T1 GTGGTTTTGGTYRTAAATGC 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 and T2 CACTAACCAACGTGGARCTA 855 874


id: cord-303834-yqysedne
type: DNA
entity:
  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


id: cord-346643-os2kyvvf
type: DNA
entity:
  membrane gene date 2016 11 15 journal Virus Genes DOI 10 1007 s11262 016 1409 8 sha 8375539936b6724e16526afef18b9902fdbf97b6 doc_id 346643 cord_uid os2kyvvf The membrane M protein


id: cord-272693-432ixb7g
type: DNA
entity:
  5 0 untranslated region UTR polyproteins 1a and 1ab spike 3a 3b envelope membrane 4b 5a 5b nucleocapsid and 3 0 UTR


id: cord-272693-432ixb7g
type: CHEMICAL
entity:
  MgCl 2 5 mM 109 RNA PCR buffer 19 dNTP mixture 1 mM RNase inhibitor 1 units ll reverse transcriptase 0 25 units ll 5 0 degenerate primer 2 5 lM and RNA 5 75 ll reaction then 10 ll per sample


id: cord-287748-co9j3uig
type: CELL_LINE
entity:
  mammalian cell lines Madin Darby canine kidney MDCK African green monkey VeroE6 human A549 Madin Darby bovine kidney MDBK


id: cord-310298-26x2p9wc
type: DNA
entity:
  CSFV genomes 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 representing 6 subgenotypes 1 1 1 2 2 1 2 2 2 3 and 3 4


id: cord-340438-9q3ic0ye
type: PROTEIN
entity:
  amino acid residues 1 219 499 638 636 789 and 1371 1377 19 20 21 22 The aminopeptidase N protein APN


id: cord-025704-icedihm2
type: DNA
entity:
  Uni12M primer AGC RAA AGC AGG 27 using SuperScript III Reverse Transcriptase Invitrogen Carlsbad CA USA


id: cord-025704-icedihm2
type: ORG
entity:
  Phy CLIP World Health Organization World Organisation for Animal HF Agriculture Organization HNEWG 2014


id: cord-025704-icedihm2
type: ORG
entity:
  World Health Organization World Organisation for Animal HF Agriculture Organization HEWG Nomenclature


# bib

id: cord-005207-02wmt2e9
title: Cloning and Sequence Analysis of the Nucleocapsid Gene of Porcine Epidemic Diarrhea Virus Chinju99
author: Lee, Hee-Kyung
date: 2003
txt: ./txt/cord-005207-02wmt2e9.txt
cache: ./cache/cord-005207-02wmt2e9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089008/
doi: 10.1023/a:1023447732567
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.


id: cord-005252-m02inmc4
author: Kwon, Hyuk Moo
date: 1995
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089256/
doi: 10.1007/bf01702878
title:
  Molecular cloning and sequence comparison of the S1 glycoprotein of the Gray and JMK strains of avian infectious bronchitis virus

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.


id: cord-005253-8qja4j9h
title: Genetic characterization of an isolate of canine distemper virus from a Tibetan Mastiff in China
author: Li, Weike
date: 2014-04-02
txt: ./txt/cord-005253-8qja4j9h.txt
cache: ./cache/cord-005253-8qja4j9h.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089258/
doi: 10.1007/s11262-014-1062-z
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.


id: cord-011794-ejoufvvj
title: Isolation and characterization of new Puumala orthohantavirus strains from Germany
author: Binder, Florian
date: 2020-04-23
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7329759/
doi: 10.1007/s11262-020-01755-3
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.


id: cord-012091-3bo88tux
title: Host-specific genetic variation of highly pathogenic avian influenza viruses (H5N1)
author: Ibrahim, Madiha Salah
date: 2011-02-17
txt: ./txt/cord-012091-3bo88tux.txt
cache: ./cache/cord-012091-3bo88tux.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112484/
doi: 10.1007/s11262-011-0583-y
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.


id: cord-025704-icedihm2
author: Pawestri, Hana A.
date: 2020-06-01
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7262163/
doi: 10.1007/s11262-020-01765-1
title:
  Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008–2015

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.


id: cord-254291-y8xvh6hs
title: Nucleotide Sequence of the Inter-Structural Gene Region of Feline Infectious Peritonitis Virus
author: Yamanaka, Miles
date: 1998
txt: ./txt/cord-254291-y8xvh6hs.txt
cache: ./cache/cord-254291-y8xvh6hs.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/9654687/
doi: 10.1023/a:1008099209942
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.


id: cord-257122-h3zi8k8g
title: Full genome analysis of a novel type II feline coronavirus NTU156
author: Lin, Chao-Nan
date: 2012-12-14
url: https://doi.org/10.1007/s11262-012-0864-0
doi: 10.1007/s11262-012-0864-0
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.


id: cord-259398-s8qsjkj2
author: Chouljenko, Vladimir N.
date: 1998
url: https://www.ncbi.nlm.nih.gov/pubmed/9778786/
doi: 10.1023/a:1008048916808
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

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.


id: cord-263489-i4tkdgy4
author: Suo, Siqingaowa
date: 2015-05-27
txt: ./txt/cord-263489-i4tkdgy4.txt
cache: ./cache/cord-263489-i4tkdgy4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26013256/
doi: 10.1007/s11262-015-1208-7
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.

title:
  Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential

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.


id: cord-265095-lf5j4ic7
title: RNA pseudoknots: Translational frameshifting and readthrough on viral RNAs
author: Ten Dam, Edwin B.
date: 1990
url: https://www.ncbi.nlm.nih.gov/pubmed/2402881/
doi: 10.1007/bf00678404
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.


id: cord-266634-bww62vx8
author: Gopinath, M.
date: 2015-10-07
url: https://doi.org/10.1007/s11262-015-1252-3
doi: 10.1007/s11262-015-1252-3
title:
  Evidence for N(7) guanine methyl transferase activity encoded within the modular domain of RNA-dependent RNA polymerase L of a Morbillivirus

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.


id: cord-268627-nnx46nwf
author: Ren, Xiaofeng
date: 2011-02-01
txt: ./txt/cord-268627-nnx46nwf.txt
cache: ./cache/cord-268627-nnx46nwf.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/21286798/
doi: 10.1007/s11262-011-0570-3
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.

title:
  Development of reverse transcription loop-mediated isothermal amplification for rapid detection of porcine epidemic diarrhea virus

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.


id: cord-269340-o9jdt86j
author: Callison, Scott Andrew
date: 1999
txt: ./txt/cord-269340-o9jdt86j.txt
cache: ./cache/cord-269340-o9jdt86j.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/10541018/
doi: 10.1023/a:1008179208217
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.

title:
  Infectious Bronchitis Virus S2 Gene Sequence Variability May Affect S1 Subunit Specific Antibody Binding

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.


id: cord-269720-o81j3d1j
author: Page, Kevin W.
date: 1990
url: https://www.ncbi.nlm.nih.gov/pubmed/1962975/
doi: 10.1007/bf00570024
title:
  Sequence analysis of the leader RNA of two porcine coronaviruses: Transmissible gastroenteritis virus and porcine respiratory coronavirus

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.


id: cord-272693-432ixb7g
author: Phillips, J. E.
date: 2011-09-10
url: https://www.ncbi.nlm.nih.gov/pubmed/21909766/
doi: 10.1007/s11262-011-0668-7
title:
  Changes in nonstructural protein 3 are associated with attenuation in avian coronavirus infectious bronchitis virus

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.


id: cord-279863-5kxgu4t9
title: Phylogenetic analysis of bovine astrovirus in Korean cattle
author: Oem, Jae-Ku
date: 2013-11-23
url: https://doi.org/10.1007/s11262-013-1013-0
doi: 10.1007/s11262-013-1013-0
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.


id: cord-282126-gmjnbnx5
author: Yang, Limin
date: 2012-08-07
url: https://doi.org/10.1007/s11262-012-0798-6
doi: 10.1007/s11262-012-0798-6
title:
  Development and application of a reverse transcription loop-mediated isothermal amplification method for rapid detection of Duck hepatitis A virus type 1

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.


id: cord-283168-kl1hoa1x
title: Molecular detection of novel picornaviruses in chickens and turkeys
author: Farkas, Tibor
date: 2011-12-13
url: https://doi.org/10.1007/s11262-011-0695-4
doi: 10.1007/s11262-011-0695-4
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.


id: cord-284675-7zv449sc
title: Base Usage and Dinucleotide Frequency of Infectious Bursal Disease Virus
author: Yew, Tan Do
date: 2004
url: https://www.ncbi.nlm.nih.gov/pubmed/14739650/
doi: 10.1023/b:viru.0000012262.89898.c7
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.


id: cord-287748-co9j3uig
title: Detection of bat hepatitis E virus RNA in microbats in Japan
author: Kobayashi, Tomoya
date: 2018-05-29
url: https://www.ncbi.nlm.nih.gov/pubmed/29845506/
doi: 10.1007/s11262-018-1577-9
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.


id: cord-288239-ca5uthvd
title: Three clusters of bovine kobuvirus isolated in Korea, 2008–2010
author: Jeoung, Hye-Young
date: 2011-03-12
url: https://www.ncbi.nlm.nih.gov/pubmed/21399921/
doi: 10.1007/s11262-011-0593-9
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.


id: cord-295554-0pzjyrdf
author: Lima, Francisco Esmaile de Sales
date: 2013-03-16
url: https://www.ncbi.nlm.nih.gov/pubmed/23504146/
doi: 10.1007/s11262-013-0899-x
title:
  Detection of Alphacoronavirus in velvety free-tailed bats (Molossus molossus) and Brazilian free-tailed bats (Tadarida brasiliensis) from urban area of Southern Brazil

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.


id: cord-296791-h8ftslps
title: Cloning and sequence analysis of the N gene of porcine epidemic diarrhea virus LJB/03
author: Junwei, Ge
date: 2006-10-01
url: https://www.ncbi.nlm.nih.gov/pubmed/16972037/
doi: 10.1007/s11262-005-0059-z
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.


id: cord-299573-vq6ckqtd
title: Phylogenetic analysis of porcine astrovirus in domestic pigs and wild boars in South Korea
author: Lee, Meong-Hun
date: 2012-09-11
txt: ./txt/cord-299573-vq6ckqtd.txt
cache: ./cache/cord-299573-vq6ckqtd.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s11262-012-0816-8
doi: 10.1007/s11262-012-0816-8
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.


id: cord-302584-fwdpzv85
author: Zhu, Ying
date: 2005-01-01
url: https://www.ncbi.nlm.nih.gov/pubmed/15744567/
doi: 10.1007/s11262-004-4586-9
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

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.


id: cord-303672-ujp78213
author: Gu, Wen-yuan
date: 2019-08-28
url: https://doi.org/10.1007/s11262-019-01701-y
doi: 10.1007/s11262-019-01701-y
title:
  Short hairpin RNAs targeting M and N genes reduce replication of porcine deltacoronavirus in ST cells

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.


id: cord-303834-yqysedne
title: Full genome sequence of guinea fowl coronavirus associated with fulminating disease
author: Ducatez, Mariette F.
date: 2015-02-25
url: https://www.ncbi.nlm.nih.gov/pubmed/25712772/
doi: 10.1007/s11262-015-1183-z
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.


id: cord-307580-nokd5kmx
author: Yang, Guang
date: 1999
url: https://www.ncbi.nlm.nih.gov/pubmed/10499445/
doi: 10.1023/a:1008105004407
title:
  D-RNA Molecules Associated with Subisolates of the VT Strain of Citrus Tristeza Virus which Induce Different Seedling-Yellows Reactions

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.


id: cord-310298-26x2p9wc
title: Analysis of synonymous codon usage in classical swine fever virus
author: Tao, Pan
date: 2008-10-29
txt: ./txt/cord-310298-26x2p9wc.txt
cache: ./cache/cord-310298-26x2p9wc.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s11262-008-0296-z
doi: 10.1007/s11262-008-0296-z
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.


id: cord-311204-fc12f845
title: Full-length genomic characterization and molecular evolution of canine parvovirus in China
author: Zhou, Ling
date: 2016-04-02
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url: https://doi.org/10.1007/s11262-016-1309-y
doi: 10.1007/s11262-016-1309-y
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.


id: cord-311712-lkvt9slp
author: Barrett, John W.
date: 2006
url: https://www.ncbi.nlm.nih.gov/pubmed/16791414/
doi: 10.1007/s11262-005-0035-7
title:
  Optimization of Codon Usage of Poxvirus Genes allows for Improved Transient Expression in Mammalian Cells

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.


id: cord-322475-i29t7ce8
author: Chen, Xi
date: 2012-07-29
url: https://doi.org/10.1007/s11262-012-0794-x
doi: 10.1007/s11262-012-0794-x
title:
  Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) samples from field cases in Fujian, China

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.


id: cord-328518-umvk59dc
title: Two novel adenoviruses found in Cave Myotis bats (Myotis velifer) in Oklahoma
author: Lee, Dana N.
date: 2019-12-03
url: https://www.ncbi.nlm.nih.gov/pubmed/31797220/
doi: 10.1007/s11262-019-01719-2
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.


id: cord-331919-6kistim2
author: Song, Daesub
date: 2012-01-22
url: https://www.ncbi.nlm.nih.gov/pubmed/22270324/
doi: 10.1007/s11262-012-0713-1
title:
  Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines

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.


id: cord-333914-c150ki1n
title: Identification and characterization of a novel bat polyomavirus in Japan
author: Koba, Ryota
date: 2020-08-20
url: https://www.ncbi.nlm.nih.gov/pubmed/32816186/
doi: 10.1007/s11262-020-01789-7
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.


id: cord-340438-9q3ic0ye
author: Zhang, Jianqiang
date: 2018-02-21
url: https://www.ncbi.nlm.nih.gov/pubmed/29468451/
doi: 10.1007/s11262-018-1542-7
title:
  Identification of porcine epidemic diarrhea virus variant with a large spike gene deletion from a clinical swine sample in the United States

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.


id: cord-344558-1jgqofbr
title: Completion of the Porcine Epidemic Diarrhoea Coronavirus (PEDV) Genome Sequence
author: Kocherhans, Rolf
date: 2001
url: https://www.ncbi.nlm.nih.gov/pubmed/11724265/
doi: 10.1023/a:1011831902219
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.


id: cord-346643-os2kyvvf
author: Wang, Li
date: 2016-11-15
url: https://doi.org/10.1007/s11262-016-1409-8
doi: 10.1007/s11262-016-1409-8
title:
  Inhibition of porcine transmissible gastroenteritis virus infection in porcine kidney cells using short hairpin RNAs targeting the membrane gene

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.


id: cord-348896-a2mjj5dt
author: Abid, Nabil Ben Salem
date: 2010-12-28
url: https://www.ncbi.nlm.nih.gov/pubmed/21188626/
doi: 10.1007/s11262-010-0562-8
title:
  Molecular study of porcine transmissible gastroenteritis virus after serial animal passages revealed point mutations in S protein

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.


