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Identification and Characterization of a Novel Recombinant Porcine Astrovirus from Pigs in Anhui, China

XU CHEN
XU CHEN
, 
YUMIN HE
YUMIN HE
, 
WEINA LI
WEINA LI
, 
ULLAH KALIM
ULLAH KALIM
, 
YUQING XIAO
YUQING XIAO
, 
JIE YANG
JIE YANG
, 
XIAOCHUN WANG
XIAOCHUN WANG
, 
SHIXING YANG
SHIXING YANG
 et 
WEN ZHANG
WEN ZHANG
   | 27 déc. 2020
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Article Category: original-paper
Publié en ligne: 27 déc. 2020
Pages: 471 - 478
Reçu: 13 sept. 2020
Accepté: 09 nov. 2020
DOI: https://doi.org/10.33073/pjm-2020-051
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© 2020 Xu Chen et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Fig. 1.

Genomic structure and conserve amino acid motif of Ahast. (a) Genomic organization of Ahast. The three ORFs (ORF1a, ORF1b, and ORF2) are shown. The conserve ribosomal frameshift site is marked. (b) The conserve amino acid motif of Ahast. The viral encode polyproteins are marked with different colours, the conserve motif of protease (PRO), RNA-dependent RNA polymerse (RdRp), and genome-linked viral protein (VPg) are shown.
Genomic structure and conserve amino acid motif of Ahast. (a) Genomic organization of Ahast. The three ORFs (ORF1a, ORF1b, and ORF2) are shown. The conserve ribosomal frameshift site is marked. (b) The conserve amino acid motif of Ahast. The viral encode polyproteins are marked with different colours, the conserve motif of protease (PRO), RNA-dependent RNA polymerse (RdRp), and genome-linked viral protein (VPg) are shown.

Fig. 2.

Phylogenetic analysis of Ahast. Phylogenetic tree based on amino acid sequences of ORF1b of PAstVs. The tree was constructed using MrBayes 3.2.7 software and the average standard deviation of split frequencies were 0.005. The Markov chain was run for a maximum of 1 million generations, in which every 50 generations were sampled and the first 25% of Markov chain Monte Carlo (mcmc) samples were discarded as burn-in.The Ahast strain identified in this study is marked with red dot.
Phylogenetic analysis of Ahast. Phylogenetic tree based on amino acid sequences of ORF1b of PAstVs. The tree was constructed using MrBayes 3.2.7 software and the average standard deviation of split frequencies were 0.005. The Markov chain was run for a maximum of 1 million generations, in which every 50 generations were sampled and the first 25% of Markov chain Monte Carlo (mcmc) samples were discarded as burn-in.The Ahast strain identified in this study is marked with red dot.

Fig. 3.

Phylogenetic analysis of Ahast. Phylogenetic tree based on amino acid sequences of ORF2 of PAstVs. The tree was constructed using MrBayes 3.2.7 software and the average standard deviation of split frequencies were 0.001 respectively. The Markov chain was run for a maximum of 1 million generations, in which every 50 generations were sampled and the first 25% of Markov chain Monte Carlo (mcmc) samples were discarded as burn-in. The Ahast strain identified in this study is marked with red dot.
Phylogenetic analysis of Ahast. Phylogenetic tree based on amino acid sequences of ORF2 of PAstVs. The tree was constructed using MrBayes 3.2.7 software and the average standard deviation of split frequencies were 0.001 respectively. The Markov chain was run for a maximum of 1 million generations, in which every 50 generations were sampled and the first 25% of Markov chain Monte Carlo (mcmc) samples were discarded as burn-in. The Ahast strain identified in this study is marked with red dot.

Fig. 4.

Recombination analysis of Ahast. (a) Detected the potential recombination events based on complete genome of Ahast. GenBank No. of each putative recombinant is shown on upper right side of the recombinant. (b), (c) BOOTSCAN evidence for the two different recombination origins on the basis of pairwise distance, modeled with a window size 200, step size 20, and 100 Bootstrap replicates. (d), (e), and (f) Phylogenetic trees were constructed using the Maximun Likelihood in MEGA 5.0 based on the region of 3076–4540 nt, 4600–6023 nt, and 1822–2810 nt respectively. Bootstrap values (based on 500 replicates) for each node were given. The Ahast strain identified in this study is marked with red dot.
Recombination analysis of Ahast. (a) Detected the potential recombination events based on complete genome of Ahast. GenBank No. of each putative recombinant is shown on upper right side of the recombinant. (b), (c) BOOTSCAN evidence for the two different recombination origins on the basis of pairwise distance, modeled with a window size 200, step size 20, and 100 Bootstrap replicates. (d), (e), and (f) Phylogenetic trees were constructed using the Maximun Likelihood in MEGA 5.0 based on the region of 3076–4540 nt, 4600–6023 nt, and 1822–2810 nt respectively. Bootstrap values (based on 500 replicates) for each node were given. The Ahast strain identified in this study is marked with red dot.

Primers sequences used for screening and amplification for the complete genome of porcine astrovirus.

Primer IDApplicationPrimer sequences (5′-3′)
astWFastWRFirstroundATCACAGCAACCCTAGGCACAGGTGCAGGTCATTTCAGCA
astNFastNRSecondroundTGCCTATGGTCCTCTCCAGAATCCTGCAGTGCACATCTGT
5AstWF5AstWRFirstroundTGGTGGCTATGGCCCGTAGGTGCTGCCTCAAGTATGCACA
5AstNF5AstNRSecondroundTGGTGGCTATGGCCCGTAGGTGGGCACAAATGGTTTGCTG
3AstWF3AstWRFirstroundGCCCCGATAATGCAGGATGAOligo(dT)18
3AstNF3AstNRSecondroundTATTGAAGCCTGGGATGCGGTTTTGCTCAAATTTTTAAATGC
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