|KARIITHI, HENRY - Orise Fellow|
|VOLKENING, JEREMY - Base2bio|
|CHIWANGA, GASPAR - Tanzania Veterinary Laboratory Agency|
|MSOFFE, PETER - Sokoine University Of Agriculture|
Submitted to: Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/24/2023
Publication Date: 5/25/2023
Citation: Kariithi, H.M., Volkening, J.D., Chiwanga, G.H., Pantin Jackwood, M.J., Msoffe, P., Suarez, D.L. 2023. Genome sequences and characterization of chicken astrovirus and avian nephritis virus from Tanzanian live bird markets. Viruses. 15(6):1247. https://doi.org/10.3390/v15061247.
Interpretive Summary: Sequencing technology continues to improve with the availability of next generation sequencing platforms that allows for huge amounts of sequence data to be generated. Efforts are ongoing to be able to identify any pathogen in a sample using a non-targeted amplification approach. Using this new sequence methodology, two unique viruses were identified in the astrovirus family. Astroviruses can cause clinical disease in poultry and are often associated with digestive issues, including diarrhea, and kidney problems. The two astroviruses identified were related to known viruses in other parts of the country. Unfortunately, it is difficult to grow astroviruses in the laboratory, so the sequence information is all that can be identified in this sample from a chicken. However, the sequence information can be used in future studies to see if these viruses are linked to clinical disease in chickens.
Technical 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 (50-UTRORF1a-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.