Research article - Peer-reviewed, 2020
Extinction and emergence of genomic haplotypes during the evolution of Avian coronavirus in chicken embryos
Brandao, Paulo E.; Hora, Aline S.; Silva, Sheila O. S.; Taniwaki, Sueli A.; Berg, MikaelAbstract
Avian coronavirus (AvCoV) is ubiquitously present on poultry as a multitude of virus lineages. Studies on AvCoV phenotypic traits are dependent on the isolation of field strains in chicken embryonated eggs, but the mutant spectrum on each isolate is not considered. This manuscript reports the previously unknown HTS (high throughput sequencing)-based complete genome haplotyping of AvCoV isolates after passages of two field strains in chicken embryonated eggs. For the first and third passages of strain 23/2013, virus loads were 6.699 log copies/mu L and 6 log copies/mu L and, for 38/2013, 5.699 log copies/mu L and 2.699 log copies/mu L of reaction, respectively. The first passage of strain 23/2013 contained no variant haplotype, while, for the third passage, five putative variant haplotypes were found, with > 99.9% full genome identity with each other and with the dominant genome. Regarding strain 38/2013, five variant haplotypes were found for the first passage, with > 99.9% full genome identity with each other and with the dominant genome, and a single variant haplotype was found. Extinction and emergence of haplotypes with polymorphisms in genes involved in receptor binding and regulation of RNA synthesis were observed, suggesting that phenotypic traits of AvCoV isolates are a result of their mutant spectrum.Keywords
Avian coronavirus; haplotype; mutant spectrum; NGS; evolutionPublished in
Genetics and Molecular Biology2020, volume: 43, number: 2, article number: e20190064
Publisher: SOC BRASIL GENETICA
Authors' information
Brandao, Paulo E.
Univ Sao Paulo
Hora, Aline S.
Univ Fed Uberlandia
Silva, Sheila O. S.
Univ Sao Paulo
Taniwaki, Sueli A.
Univ Sao Paulo
Swedish University of Agricultural Sciences, Department of Biomedical Science and Veterinary Public Health
UKÄ Subject classification
Pathobiology
Publication Identifiers
DOI: https://doi.org/10.1590/1678-4685-GMB-2019-0064
URI (permanent link to this page)
https://res.slu.se/id/publ/105969