Genome constellations of 24 porcine rotavirus group A strains circulating on commercial Thai swine farms between 2011 and 2016 (original) (raw)
Related papers
Infection, Genetics and Evolution, 2013
Group A rotavirus (RVA) is the most common cause of severe acute viral gastroenteritis in humans and animals worldwide. This study characterized the whole genome sequences of porcine RVAs, 2 G3P[23] strains (CMP40/08 and CMP48/08), 1 G9P[23] strain (CMP45/08), and 1 G3P[13] strain (CMP29/08). These strains were collected from diarrheic piglets less than 7 weeks of age in 4 pig farms in Chiang Mai, Thailand, in 2008. The VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5 genes of CMP40/08 and CMP48/08 strains were assigned as G3-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1 genotypes based on their nucleotide sequences and phylogenetic analyses. The CMP29/08 strain was different from the CMP40/ 08 and CMP48/08 strains only in the VP4 gene, since it was assigned as P[13] genotype. Furthermore, the VP7 gene of the CMP45/08 strain was classified as genotype G9, and the NSP3 gene as T7 genotype. The finding of this study supports the porcine-origin of T7 genotype, although the NSP3 gene of this strain was similar to the bovine UK strain at the highest nucleotide sequence identity of 92.6%. Whole genome sequence analysis of the porcine RVAs indicated that multiple inter-genotypic and intra-genotypic reassortment events had occurred among the porcine RVAs circulating in this studied area. Interestingly, the VP7 gene of the CMP45/08 strain, and the VP1, NSP2, and NSP4 genes of all four porcine RVAs strains described in this study revealed much similarity to those of two porcine-like human RVA strains (RVA/ Human-tc/THA/Mc323/1989/G9P[19] and RVA/Human-tc/THA/Mc345/1989/G9P[19]) detected in Thailand in 1989. The present study provided important information on the evolution of porcine RVA.
2018
Swine are economically important food animals, but highly contagious enteric viruses can affect entire swine herds and contribute significantly to piglet morbidity and mortality. The most frequent viruses associated with pig gastroenteritis have been reported as porcine epidemic diarrhea virus (PEDV) and rotavirus. Rotavirus is an important cause of diarrhea in piglets and pigs worldwide, and group A and C types are those that pig herds are mostly affected by. In Thailand, studies on rotavirus group A (RVA) have been reported continuously, whereas information on group C is still limited. In this study, we aimed to identify rotavirus group C (RVC) from the feces and intestinal contents of pigs affected with diarrhea. Seven hundred and sixty-nine samples were collected from swine herds located in difference provinces throughout Thailand. The specimens were tested using virus-specific RT-PCR to detect the gene encoding RVC capsid protein VP7 and VP4. Sequencing analyses showed that 6.6% (51/769) of samples were positive for RVC, one third of which tested as single positive for RVC (34/51). Co-infections with the most frequent enteric viruses, RVA and PEDV were also analyzed. Co-infections of RVA/RVC accounted for 21.6% (11/51) of samples and of PEDV/RVC for 7.8% (4/51) of samples, while three samples (5.9%) tested positive for all three viruses. Infections were not associated with seasonality, since the virus was detected throughout the year. RVC was detected in pigs up to 8 weeks old. Analysis of the partial VP7 gene sequences was suggestive that the predominant genotype was G1, which was closely related to the prototype Cowden strain. Due to P[5] was the most prevalent of VP4 genotype. This study demonstrated the low prevalence of RVC in Thailand, a virus not previously documented in this country.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2015
Group A rotaviruses (RVAs) are leading causes of viral diarrhea in children and in the young of many animal species, particularly swine. In the current study, porcine RVAs were found in fecal specimens from symptomatic piglets on 4 farms in Brazil during the years of 2012-2013. Using RT-PCR, Sanger nucleotide sequencing, and phylogenetic analyses, the whole genomes of 12 Brazilian porcine RVA strains were analyzed. Specifically, the full-length open reading frame (ORF) sequences were determined for the NSP2-, NSP3-, and VP6-coding genes, and partial ORF sequences were determined for the VP1-, VP2-, VP3-, VP4-, VP7-, NSP1-, NSP4-, and NSP5/6-coding genes. The results indicate that all 12 strains had an overall porcine-RVA-like backbone with most segments being designated as genotype 1, with the exception of the VP6- and NSP1-coding genes, which were genotypes I5 and A8, respectively. These results add to our growing understanding of porcine RVA genetic diversity and will provide a pl...
2000
Swine are economically important food animals, but highly contagious enteric viruses can affect entire swine herds and contribute significantly to piglet morbidity and mortality. The most frequent viruses associated with pig gastroenteritis have been reported as porcine epidemic diarrhea virus (PEDV) and rotavirus. Rotavirus is an important cause of diarrhea in piglets and pigs worldwide, and group A and C types are those that pig herds are mostly affected by. In Thailand, studies on rotavirus group A (RVA) have been reported continuously, whereas information on group C is still limited. In this study, we aimed to identify rotavirus group C (RVC) from the feces and intestinal contents of pigs affected with diarrhea. Seven hundred and sixty-nine samples were collected from swine herds located in difference provinces throughout Thailand. The specimens were tested using virus-specific RT-PCR to detect the gene encoding RVC capsid protein VP7 and VP4. Sequencing analyses showed that 6.6% (51/769) of samples were positive for RVC, one third of which tested as single positive for RVC (34/51). Co-infections with the most frequent enteric viruses, RVA and PEDV were also analyzed. Co-infections of RVA/RVC accounted for 21.6% (11/51) of samples and of PEDV/RVC for 7.8% (4/51) of samples, while three samples (5.9%) tested positive for all three viruses. Infections were not associated with seasonality, since the virus was detected throughout the year. RVC was detected in pigs up to 8 weeks old. Analysis of the partial VP7 gene sequences was suggestive that the predominant genotype was G1, which was closely related to the prototype Cowden strain. Due to P[5] was the most prevalent of VP4 genotype. This study demonstrated the low prevalence of RVC in Thailand, a virus not previously documented in this country.
Infection, Genetics and Evolution, 2017
Whole genomes of G9P[19] human (RVA/Human-wt/THA/CMH-S070-13/2013/G9P[19]) and porcine (RVA/Pigwt/THA/CMP-015-12/2012/G9P[19]) rotaviruses concurrently detected in the same geographical area in northern Thailand were sequenced and analyzed for their genetic relationships using bioinformatic tools. The complete genome sequence of human rotavirus RVA/Human-wt/THA/CMH-S070-13/2013/G9P[19] was most closely related to those of porcine rotavirus RVA/Pig-wt/THA/CMP-015-12/2012/G9P[19] and to those of porcine-like human and porcine rotaviruses reference strains than to those of human rotavirus reference strains. The genotype constellation of G9P[19] detected in human and piglet were identical and displayed as the G9-P[19]-I5-R1-C1-M1-A8-N1-T1-E1-H1 genotypes with the nucleotide sequence identities of VP7,
Virusdisease, 2018
Rotavirus (RV), is an etiological agent of acute infantile diarrhea in both humans and animals including poultry. Among the eight accepted species/types of RVs, RV-A is genetically and antigenically the most diverse. RV-A associated enteritis is a major problem in the weaning and post-weaning piglets. Due to high genetic variability in the antigenic regions, RV-A is thought to have high interspecies jumping probability. In this study, comparatively a large sized sample (n = 757) was screened, where the samples were collected from diarrheic porcine population of north (Uttar Pradesh), North eastern (Assam, Nagaland, Meghalaya, Tripura, Manipur, Mizoram and Arunachal Pradesh) and Southern states of India (Kerala, Karnataka and Tamil Nadu). The VP6 gene based reverse-transcription (RT)-PCR based screening of the samples for RV-A identified 42.4% (321/757) positivity, where highest identification was from Uttar Pradesh 119 (37.07%), followed by 74 (23.05%), 34 (10.6%), 31 (9.65%), 21 (6...
Infection, Genetics and Evolution, 2012
Group A rotaviruses (RVAs) are agents causing severe gastroenteritis in infants and young animals. G9 RVA strains are believed to have originated from pigs. However, this genotype has emerged as the fifth major human RVA genotype worldwide. To better understand the relationship between human and porcine RVA strains, complete RVA genome data are needed. For human RVA strains, the number of complete genome data have grown exponentially. However, there is still a lack of complete genome data on porcine RVA strains. Recently, G9 RVA strains have been identified as the third most important genotype in diarrheic pigs in South Korea in combinations with P[7] and P [23]. This study is the first report on complete genome analyses of 1 G9P[7] and 3 G9P[23] porcine RVA strains, resulting in the following genotype constellation: G9-P[7]/P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1. By comparisons of these genotype constellations, it was revealed that the Korean G9P[7] and G9P[23] RVA strains possessed a typical porcine RVA backbone, similar to other known porcine RVA strains. However, detailed phylogenetic analyses revealed the presence of intra-genotype reassortments among porcine RVA strains in South Korea. Thus, our data provide genetic information of G9 RVA strains increasingly detected in both humans and pigs, and will help to establish the role of pigs as a source or reservoir for novel human RVA strains.
Rotavirus is a major cause of diarrhea globally in animals and young children under 5 years. Here, molecular detection and genetic characterization of porcine rotavirus in smallholder and commercial pig farms in the Lusaka Province of Zambia were con-ducted. Screening of 148 stool samples by RT-PCR targeting the VP6 gene revealed a prevalence of 22.9 % (34/148). Further testing of VP6-positive samples with VP7-specific primers produced 12 positives, which were then Sanger-sequenced. BLASTn of the VP7 positives showed sequence similarity to porcine and human rota-virus strains with identities ranging from 87.5% to 97.1%. By next-generation se-quencing, the full-length genetic constellation of the representative strains RVA/pig-wt/ZMB/LSK0137 and RVA/pig-wt/ZMB/LSK0147 were determined. Geno-typing of these strains revealed a known Wa-like genetic backbone and their genetic constellations were G4-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1 and G9-P[13]-I5-R1-C1-M1-A8-N1-T1-E1-H1, respectively. Phy...
Porcine-like G3P[6] and G4P[6] rotavirus A strains detected from children with diarrhoea in Vietnam
Archives of virology, 2018
Animal rotavirus A (RVA) strains can infect children and cause diarrhoea. We determined the full genome sequences of one G3P[6] strain (NT0001) and five G4P[6] strains (NT0042, NT0077, NT0205, NT0599, and NT0621) detected from children with diarrhoea in Vietnam in 2007-2008. Strain NT0001 had a genotype constellation of: G3-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1, strain NT0042: G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1, strain NT0077: G4-P[6]-I5-R1-C1-M1-A8-N1-T7-E1-H1, and strains NT0205, NT0599, and NT0621: G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Sequence divergence data and phylogenetic analysis showed that they were different porcine RVA strains that independently and directly crossed the host species barrier to infect children.