Genomic haplotypes of Avian coronavirus

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/ μL and 6 log copies/ μL and, for 38/2013, 5.699 log copies/μL and 2.699 log copies/μL 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.

Link to the publication

https://doi.org/10.1590/1678-4685-gmb-2019-0064

Reference

Brandão, PE, Hora, AS., Silva, SOS., Taniwaki, SA., Berg M. (2020) Extinction and emergence of genomic haplotypes during the evolution of Avian coronavirus in chicken embryos. Genetics and Molecular Biology 43, 2.