Novel Picobirnaviruses in Respiratory and Alimentary Tracts of Cattle and Monkeys with Large Intra- and Inter-Host Diversity
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Mammal and Poultry Surveillance and Sample Collection
2.3. RNA Extraction
2.4. RT-PCR for PBVs and DNA Sequencing
2.5. Complete/Near-Complete Segment 2 Sequencing of Genogroups I and II PBVs
2.6. Genome Segment 2 Analysis
2.7. Estimation of Synonymous and Non-Synonymous Substitution Rates
2.8. Nucleotide Sequence Accession Numbers
3. Results
3.1. Detection of PBVs in Respiratory Specimens of Animals
3.2. Complete/Near-Complete Segment 2 Sequence Analysis of Cattle and Monkey PBVs
3.3. Phylogenetic Analysis of Cattle and Monkey PBVs’ Complete/Near-Complete Segment 2 Sequences
3.4. Estimation of Substitution Rates
4. Discussion
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Animal Type | Sample Types | No. of Specimens Obtained | No. (%) of Specimens Positive for Genogroup I PBVs | No. (%) of Specimens Positive for Genogroup II PBVs |
---|---|---|---|---|
Mammals | ||||
Cattle | Nasopharyngeal swab | 51 | 3 (5.9%) | 1 (1.9%) |
Monkey 1 | Throat swab | 52 | 3 (5.8%) | 0 (0%) |
Dog | Nasopharyngeal swab | 50 | 0 (0%) | 0 (0%) |
Cat | Nasopharyngeal swab | 50 | 0 (0%) | 0 (0%) |
Bat 2 | Mouth swab | 157 | 0 (0%) | 0 (0%) |
Horse 3 | Nasopharyngeal swab | 116 | 0 (0%) | 0 (0%) |
Poultry | ||||
Chicken | Tracheal swab | 100 | 0 (0%) | 0 (0%) |
PBV | Genome Features | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Size (bp) | G+C Content (%) | ORF Features | 5′ UTR Features | 3′ UTR Features | ||||||||||
ORF | Location (nt) | Length (nt) | Length (aa) | Frame | Length (nt) | G+C Content (%) | Beginning Bases | Length (nt) | G+C Content (%) | Ending Bases | ||||
Reference genogroup I PBVs segment 2 sequences | ||||||||||||||
Human 1 | 1745 | 46.36 | RdRp | 94-1698 | 1605 | 534 | +1 | 93 | 21.51 | GTAAA | 47 | 53.19 | CTGC | |
Human 2 | 1696 | 43.63 | RdRp | 58-1650 | 1593 | 530 | +1 | 57 | 24.56 | GTAAA | 46 | 50.00 | CTGC | |
Reference genogroup II PBV segment 2 sequence | ||||||||||||||
Human 3 | 1674 | 43.91 | RdRp | 88-1641 | 1554 | 517 | +1 | 87 | 16.09 | GTAAA | 33 | 57.58 | CTC | |
Genogroup I PBVs detected in this study | ||||||||||||||
PBVs (Clade) | GenBank accession no. | |||||||||||||
Monkey/11T-1 (M-R1;) | KY120190 | 1678 | 42.55 | RdRp | 28-1632 | 1605 | 534 | +1 | 27 | 14.81 | GTAAA | 46 | 52.17 | CTGC |
Monkey/11T-2 (M-R2) | KY120191 | 1681 | 41.05 | RdRp | 47-1636 | 1590 | 529 | +2 | 46 | 26.09 | GTAAA | 45 | 51.11 | CTGC |
Monkey/35T (M-R1) | KY120193 | 1678 | 42.61 | RdRp | 28-1632 | 1605 | 534 | +1 | 27 | 14.81 | GTAAA | 46 | 52.17 | CTGC |
Monkey/21T (M-R1) | KY120192 | 1678 | 42.49 | RdRp | 28-1632 | 1605 | 534 | +1 | 27 | 14.81 | GTAAA | 46 | 52.17 | CTGC |
Monkey/1R-1 4 (M-R3) | KY120194 | 1613 | 42.72 | RdRp | 2-1564 | 1563 | 520 | NA | NA | NA | NA | 49 | 53.06 | CTGC |
Monkey/1R-2 (M-R2) | KY120182 | 1681 | 41.52 | RdRp | 47-1636 | 1590 | 529 | +2 | 46 | 26.09 | GTAAA | 45 | 51.11 | CTGC |
Monkey/2R (M-R1) | KY120183 | 1678 | 42.37 | RdRp | 28-1632 | 1605 | 534 | +1 | 27 | 14.81 | GTAAA | 46 | 50.00 | CTGC |
Monkey/12R (M-R1) | KY120184 | 1678 | 42.61 | RdRp | 28-1632 | 1605 | 534 | +1 | 27 | 14.81 | GTAAA | 46 | 52.17 | CTGC |
Monkey/13R-1 (M-R3) | KY120185 | 1734 | 41.64 | RdRp | 75-1685 | 1611 | 536 | +3 | 74 | 25.68 | GTAAA | 49 | 53.06 | CTGC |
Monkey/13R-2 (M-R1) | KY120186 | 1678 | 42.55 | RdRp | 28-1632 | 1605 | 534 | +1 | 27 | 14.81 | GTAAA | 46 | 52.17 | CTGC |
Monkey/14R (M-R1) | KY120187 | 1678 | 42.55 | RdRp | 28-1632 | 1605 | 534 | +1 | 27 | 14.81 | GTAAA | 46 | 52.17 | CTGC |
Monkey/15R-1 (M-R1) | KY120188 | 1678 | 42.31 | RdRp | 28-1632 | 1605 | 534 | +1 | 27 | 14.81 | GTAAA | 46 | 50.00 | CTGC |
Monkey/15R-2 (M-R3) | KY120189 | 1734 | 41.64 | RdRp | 75-1685 | 1611 | 536 | +3 | 74 | 25.68 | GTAAA | 49 | 53.06 | CTGC |
Cattle/C345N-2 | KY120170 | 1671 | 43.93 | RdRp | 49-1629 | 1581 | 526 | +1 | 48 | 25.00 | GTAAA | 42 | 52.38 | CATC |
Cattle/C345N-3 | KY120171 | 1694 | 42.15 | RdRp | 44-1657 | 1614 | 537 | +2 | 43 | 23.26 | GTAAA | 37 | 59.46 | CTGC |
Cattle/C346N-1 | KY120172 | 1701 | 47.68 | RdRp | 49-1656 | 1608 | 535 | +1 | 48 | 29.17 | GTAAA | 45 | 44.44 | CTGC |
Cattle/C346N-2 | KY120173 | 1696 | 44.99 | RdRp | 52-1647 | 1596 | 531 | +1 | 51 | 27.45 | GTAAA | 49 | 46.94 | CTGC |
Cattle/C361N | KY120174 | 1696 | 44.58 | RdRp | 49-1653 | 1605 | 534 | +1 | 48 | 35.42 | GTAAA | 43 | 44.19 | CTGC |
Cattle/C343R-1 | KY120175 | 1692 | 44.03 | RdRp | 50-1642 | 1593 | 530 | +2 | 49 | 20.41 | GTAAA | 50 | 58.00 | CTGC |
Cattle/C343R-2 | KY120176 | 1695 | 45.25 | RdRp | 48-1652 | 1605 | 534 | +3 | 47 | 25.53 | GTAAA | 43 | 44.19 | CTGC |
Cattle/C369R-1 | KY120177 | 1736 | 42.45 | RdRp | 36-1721 | 1686 | 561 | +3 | 35 | 22.86 | GTAAA | 15 | 40.00 | CTTC |
Cattle/C369R-2 5 | KY120179 | 1659 | 44.91 | RdRp | 24-1616 | 1593 | 530 | NA | 23 | 30.43 | NA | 43 | 55.81 | CTGC |
Cattle/C374R-1 5 | KY120180 | 1651 | 44.16 | RdRp | 8-1606 | 1599 | 532 | NA | 7 | 28.57 | NA | 45 | 55.56 | CTGC |
Cattle/C374R-2 5 | KY120181 | 1669 | 47.15 | RdRp | 24-1625 | 1602 | 533 | NA | 23 | 34.78 | NA | 44 | 47.73 | CTGC |
Genogroup II PBVs detected in this study | ||||||||||||||
Cattle/C372N | KY120178 | 1622 | 40.44 | RdRp | 55-1599 | 1545 | 514 | +1 | 54 | 16.67% | GTAAA | 23 | 52.17 | CTCC |
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Share and Cite
Woo, P.C.Y.; Teng, J.L.L.; Bai, R.; Tang, Y.; Wong, A.Y.P.; Li, K.S.M.; Lam, C.S.F.; Fan, R.Y.Y.; Lau, S.K.P.; Yuen, K.-Y. Novel Picobirnaviruses in Respiratory and Alimentary Tracts of Cattle and Monkeys with Large Intra- and Inter-Host Diversity. Viruses 2019, 11, 574. https://doi.org/10.3390/v11060574
Woo PCY, Teng JLL, Bai R, Tang Y, Wong AYP, Li KSM, Lam CSF, Fan RYY, Lau SKP, Yuen K-Y. Novel Picobirnaviruses in Respiratory and Alimentary Tracts of Cattle and Monkeys with Large Intra- and Inter-Host Diversity. Viruses. 2019; 11(6):574. https://doi.org/10.3390/v11060574
Chicago/Turabian StyleWoo, Patrick C. Y., Jade L. L. Teng, Ru Bai, Ying Tang, Annette Y. P. Wong, Kenneth S. M. Li, Carol S. F. Lam, Rachel Y. Y. Fan, Susanna K. P. Lau, and Kwok-Yung Yuen. 2019. "Novel Picobirnaviruses in Respiratory and Alimentary Tracts of Cattle and Monkeys with Large Intra- and Inter-Host Diversity" Viruses 11, no. 6: 574. https://doi.org/10.3390/v11060574