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Extinction and emergence of genomic haplotypes during the evolution of Avian coronavirus in chicken embryos

Brandao, Paulo E. and Hora, Aline S. and Silva, Sheila O. S. and Taniwaki, Sueli A. and Berg, Mikael (2020). Extinction and emergence of genomic haplotypes during the evolution of Avian coronavirus in chicken embryos. Genetics and Molecular Biology. 43 , e20190064 , 1-8
[Journal article]

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Abstract

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.

Authors/Creators:Brandao, Paulo E. and Hora, Aline S. and Silva, Sheila O. S. and Taniwaki, Sueli A. and Berg, Mikael
Title:Extinction and emergence of genomic haplotypes during the evolution of Avian coronavirus in chicken embryos
Year of publishing :2020
Volume:43
Article number:e20190064
Number of Pages:8
Publisher:Sociedade Brasileira de Genética
ISSN:1415-4757
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 403 Veterinary Science > Pathobiology
Keywords:Avian coronavirus, haplotype, mutant spectrum, NGS, evolution
URN:NBN:urn:nbn:se:slu:epsilon-p-105969
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-105969
Additional ID:
Type of IDID
DOI10.1590/1678-4685-GMB-2019-0064
Web of Science (WoS)000529398300001
ID Code:17157
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Department of Biomedical Science and Veterinary Public Health
Deposited By: SLUpub Connector
Deposited On:30 Jun 2020 10:39
Metadata Last Modified:30 Jun 2020 10:39

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