Genome Sequences and Characterization of Chicken Astrovirus and Avian Nephritis Virus from Tanzanian Live Bird Markets

Henry M Kariithi; Jeremy D Volkening; Gaspar H Chiwanga; Mary J Pantin-Jackwood; Peter L M Msoffe; David L Suarez

doi:10.3390/v15061247

Genome Sequences and Characterization of Chicken Astrovirus and Avian Nephritis Virus from Tanzanian Live Bird Markets

Viruses. 2023 May 25;15(6):1247. doi: 10.3390/v15061247.

Authors

Henry M Kariithi^{1

2}, Jeremy D Volkening³, Gaspar H Chiwanga⁴, Mary J Pantin-Jackwood¹, Peter L M Msoffe⁵, David L Suarez¹

Affiliations

¹ Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA 30605, USA.
² Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kaptagat Rd, Nairobi P.O. Box 57811-00200, Kenya.
³ BASE2BIO, Oshkosh, WI 54904, USA.
⁴ Tanzania Veterinary Laboratory Agency, South Zone, Mtwara P.O. Box 186, Tanzania.
⁵ Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Chuo Kikuu, Morogoro P.O. Box 3000, Tanzania.

Abstract

The enteric chicken astrovirus (CAstV) and avian nephritis virus (ANV) are the type species of the genus Avastrovirus (AAstV; Astroviridae family), capable of causing considerable production losses in poultry. Using next-generation sequencing of a cloacal swab from a backyard chicken in Tanzania, we assembled genome sequences of ANV and CAstV (6918 nt and 7318 nt in length, respectively, excluding poly(A) tails, which have a typical AAstV genome architecture (5'-UTR-ORF1a-ORF1b-ORF2-'3-UTR). They are most similar to strains ck/ANV/BR/RS/6R/15 (82.72%) and ck/CAstV/PL/G059/14 (82.23%), respectively. Phylogenetic and sequence analyses of the genomes and the three open reading frames (ORFs) grouped the Tanzanian ANV and CAstV strains with Eurasian ANV-5 and CAstV-Aii viruses, respectively. Compared to other AAstVs, the Tanzanian strains have numerous amino acid variations (substitutions, insertions and deletions) in the spike region of the capsid protein. Furthermore, CAstV-A has a 4018 nt recombinant fragment in the ORF1a/1b genomic region, predicted to be from Eurasian CAstV-Bi and Bvi parental strains. These data should inform future epidemiological studies and options for AAstV diagnostics and vaccines.

Keywords: AAstV; ANV; Astroviridae; CAstV; NGS; de novo assembly; genogroup; recombination.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Astroviridae Infections* / epidemiology
Astroviridae Infections* / veterinary
Astroviridae* / genetics
Avastrovirus* / genetics
Chickens
Phylogeny
Poultry Diseases* / epidemiology
Tanzania / epidemiology

Grants and funding

This research was funded by the Agricultural Research Service (ARS), USDA CRIS Project 6040-32000-082-00-D, ARS project 6040-32000-082-001T, and by a postdoctoral appointment to the Oak Ridge Institute for Science and Education (ORISE). The mention of trade names or commercial products in this publication is solely for providing specific information and does not imply recommendation or endorsement by the USDA-ARS, BASE₂BIO LLC or ORISE.