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

Polish Journal of Microbiology
Volume 69 (2020): Issue 4 (December 2020)
By:
Open Access
|Dec 2020

Figures & Tables

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
DOI: https://doi.org/10.33073/pjm-2020-051 | Journal eISSN: 2544-4646 | Journal ISSN: 1733-1331
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Language: English
Page range: 471 - 478
Submitted on: Sep 13, 2020
Accepted on: Nov 9, 2020
Published on: Dec 27, 2020
Published by: Polish Society of Microbiologists
In partnership with: Paradigm Publishing Services
Publication frequency: 4 times per year
Keywords:
porcine astroviruses,
viral metagenomics,
genome recombination
Related subjects:
Life sciences,
Microbiology and virology

© 2020 XU CHEN, YUMIN HE, WEINA LI, ULLAH KALIM, YUQING XIAO, JIE YANG, XIAOCHUN WANG, SHIXING YANG, WEN ZHANG, published by Polish Society of Microbiologists
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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