cord-005207-02wmt2e9	2003	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.
cord-005252-m02inmc4	1995	
cord-005253-8qja4j9h	2014	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) .
cord-011794-ejoufvvj	2020	
cord-012091-3bo88tux	2011	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
cord-025704-icedihm2	2020	
cord-254291-y8xvh6hs	1998	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%.
cord-257122-h3zi8k8g	2012	
cord-259398-s8qsjkj2	1998	
cord-263489-i4tkdgy4	2015	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.
cord-265095-lf5j4ic7	1990	
cord-266634-bww62vx8	2015	
cord-268627-nnx46nwf	2011	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.
cord-269340-o9jdt86j	1999	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.
cord-269720-o81j3d1j	1990	
cord-272693-432ixb7g	2011	
cord-279863-5kxgu4t9	2013	
cord-282126-gmjnbnx5	2012	
cord-283168-kl1hoa1x	2011	
cord-284675-7zv449sc	2004	
cord-287748-co9j3uig	2018	
cord-288239-ca5uthvd	2011	
cord-295554-0pzjyrdf	2013	
cord-296791-h8ftslps	2006	
cord-299573-vq6ckqtd	2012	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.
cord-302584-fwdpzv85	2005	
cord-303672-ujp78213	2019	
cord-303834-yqysedne	2015	
cord-307580-nokd5kmx	1999	
cord-310298-26x2p9wc	2008	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.
cord-311204-fc12f845	2016	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.
cord-311712-lkvt9slp	2006	
cord-322475-i29t7ce8	2012	
cord-328518-umvk59dc	2019	
cord-331919-6kistim2	2012	
cord-333914-c150ki1n	2020	
cord-340438-9q3ic0ye	2018	
cord-344558-1jgqofbr	2001	
cord-346643-os2kyvvf	2016	
cord-348896-a2mjj5dt	2010