Prevalence and genome characteristics of canine astrovirus in southwest China

Li, Mingxiang; Yan, Nan; Ji, Conghui; Wang, Min; Zhang, Bin; Yue, Hua; Tang, Cheng

doi:10.1099/jgv.0.001077

Cited by 23 publications

(30 citation statements)

References 30 publications

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“…These recombination patterns were supported by RDP, GENECONV, MaxChi, Chimaera, SiScan, 3Seq, LARD, Phylpro and Bootscan programs as shown in Table 2. The potential recombination event 2 reported in this study supports the previous suggestion that the ORF1b/ORF2 junction region is prone to the recombination region in AstVs [49,50]. The co-existence of different PoAstVs within swine farms is absolutely possible due to the high prevalence of PoAstV in swine farms [3,12], and this may promote co-infections of one animal with more than one AstV strain at the same time as observed in this study.…”

Section: Recombination Analysissupporting

confidence: 88%

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Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Genotypes Circulating in East African Smallholder Pig Farms

Amimo¹,

Machuka²,

Abworo³

et al. 2020

Preprint

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Astroviruses (AstVs) are occurs globally and are common causes of gastroenteritis in human and animals. The genetic diversity and epidemiology of AstVs in Africa is not well known, hence, we aimed to genetically characterize astroviruses in asymptomatic smallholder piglets in East Africa. Twenty-four samples randomly selected from 446 piglets (<6 months old), initially collected for rotavirus study, was sequenced for metagenomic analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of 7 strains with complete (or near complete) genome revealed variable nucleotide and amino acid sequence identities with known PoAstV strains. The U083 and K321 strains had nucleotide sequence similarities ranging from 66.4 to 75.4 % to the known PoAstV2 strains, nucleotide sequence similarity of U460 strain with known PoAstV3 ranged 57.0 to 65.1 % to the, while K062, K366, K451, and K456 strains showed nucleotide sequence similarities of 63.5 to 80 % to the known PoAstV4 strains. The low sequence identities (<90 %) indicate that novel genotypes of PoAstVs are circulating in the study area. Multiple recombination events were detected in our PoAstV4 strains, indicating that the genetic diversity observed in these strains may be due to recombination. Importantly, we identified potential candidate epitopes with conserved peptides in our PoAstV strains that could aid in the design of immune diagnosis tools and subunit vaccines. Our data provide new intuitions into the genetic structure of porcine astroviruses in East African.

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Section: Recombination Analysissupporting

confidence: 88%

“…These novel viruses may potentially cross species barriers at some point. Many prior studies have reported evidence for recombination amongst astrovirus types in human, pigs, marine mammals, turkey, small ruminants and dogs [49,[51][52][53][54]. (Table S5).…”

Section: Recombination Analysismentioning

confidence: 99%

Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Genotypes Circulating in East African Smallholder Pig Farms

Amimo¹,

Machuka²,

Abworo³

et al. 2020

Preprint

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show abstract

“…These recombination patterns were supported by RDP, GENECONV, MaxChi, Chimaera, SiScan, 3Seq, LARD, Phylpro, and Bootscan programs, as shown in Table 2. Potential recombination event 2 reported in this study supports the previous suggestion that the ORF1b/ORF2 junction region is prone to the recombination region in AstVs [51,52]. The co-occurrence of different strains within swine farms is certainly feasible due to the high incidence of PoAstV in swine farms [2,43], and this may promote co-infections of individual pigs with multiple strains at the same time, as observed in this study.…”

Section: Recombination Analysissupporting

confidence: 88%

“…These novel viruses may potentially cross species barriers at some point. Previous studies have found evidence for recombination amongst astrovirus serotypes in humans, pigs, marine mammals, turkeys, small ruminants, and dogs [51,[53][54][55][56].…”

Section: Recombination Analysismentioning

confidence: 98%

Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms

Amimo

Machuka

Abworo

et al. 2020

Viruses

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Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains; U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3; and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (<90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa.

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“…Each ORF encodes a different protein, with different degrees of sequence conservation. Compared with other genes, the Cap gene is most highly conserved [ 8 ], indicating that the design of specific primers in this gene is appropriate. CaAstV was first reported in 1980 in the USA [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

Establishment of a duplex SYBR green I-based real-time polymerase chain reaction assay for the rapid detection of canine circovirus and canine astrovirus

Wang

Cui

et al. 2020

Molecular and Cellular Probes

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The similar clinical characteristics of canine circovirus (CaCV) and canine astrovirus (CaAstV) infections and high frequency of co-infection make diagnosis difficult. In this study, a duplex SYBR Green I-based real-time polymerase chain reaction (PCR) assay was established for the rapid, simultaneous detection of CaCV and CaAstV. Two pairs of specific primers were designed based on the Rep gene of CaCV and the Cap gene of CaAstV. By using the real-time PCR assay method, the two viruses can be distinguished by the difference in melting temperatures, 79 °C and 86 °C for CaCV and CaAstV, respectively. This assay had high specificity, showing no cross-reaction with other common canine viruses, as well as high sensitivity, with minimum detection limits of 9.25 × 10 1 copies/μL and 6.15 × 10 1 copies/μL for CaCV and CaAstV, respectively. Based on the mean coefficient of variation, the method had good reproducibility and reliability. In a clinical test of 57 fecal samples, the rates of positive detection by real-time PCR were 14.04% (8/57) and 12.28% (7/57) for CaCV and CaAstV, respectively, and the rate of co-infection was 8.77% (5/57). In conclusion, the newly established duplex SYBR Green I-based real-time PCR assay is sensitive, specific, reliable, and rapid and is an effective tool for the detection of co-infections with CaCV and CaAstV.

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Prevalence and genome characteristics of canine astrovirus in southwest China

Cited by 23 publications

References 30 publications

Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Genotypes Circulating in East African Smallholder Pig Farms

Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Genotypes Circulating in East African Smallholder Pig Farms

Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms

Establishment of a duplex SYBR green I-based real-time polymerase chain reaction assay for the rapid detection of canine circovirus and canine astrovirus

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