Abstract To understand the population genetics events during coronavirus host switches, the Beaudette strain of Avian coronavirus (AvCoV) adapted to BHK-21 cells was passaged 15 times in VERO cells, the virus load and the variants at each passage being determined by RT-qPCR and genome-length deep sequencing. From BHK-21 P2 to VERO P3, a trend for the extinction of variants was followed by stability up to VERO P11 and both the emergence and the rise in frequency in some variants, while the virus loads were stable up to VERO P12. At the spillover from BHK-21 to VERO cells, variants that both emerged, showed a rise in frequency or were extinguished were detected on the spike, while variants at the M gene showed the same pattern only at VERO passage 13. Furthermore, nsps 3-5, 9 and 15 variants were detected at lower passages compared to the consensus sequences, with those at nsp3 being detected in the spectra also at higher passages. This suggests that quasispecies coronavirus evolution in spillovers follows the virus life cycle, starting with the evolution of the receptor binding proteins, followed by the replicase and then proteins involved in virion assembly, keeping the general fitness of the mutant spectrum stable.

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/ 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.

O vírus da imunodeficiência felina (FIV) é um lentivírus que causa distúrbios imunológicos em gatos domésticos. Devido à alta variabilidade genética do FIV, já foram identificados cinco subtipos (A a E) e a diversidade dentro de cada subtipo é freqüente e o seu estudo pode auxiliar no conhecimento da patogenia e epidemiologia da doença. Assim, o presente trabalho objetivou analisar filogeneticamente cepas do FIV de gatos domésticos oriundos do estado de São Paulo. Para tanto, foi realizado o seqüenciamento de 658 pares de bases do gene gag de amostras coletadas de 23 animais, cujos resultados foram analisados pelo método de substituição nucleotídica Tamura-Nei. A análise filogenética demonstrou que todas as amostras pertenciam ao subtipo B e, claramente, três subgrupos foram formados dentro deste subtipo. Adicionalmente, o resultado obtido sugeriu um ancestral comum entre as cepas do FIV oriundas do Japão e uma amostra brasileira obtida neste estudo. Em conclusão, este trabalho traz as primeiras informações sobre a diversidade genética do FIV no Estado de São Paulo. Estudos adicionais são necessários para melhor entender o cenário real e a distribuição dos tipos e subtipos do FIV na população de gatos domésticos do país.

Feline immunodeficiency virus (FIV) is a lentivirus associated with immunologic disorders in domestic cats. Due to the high genetic variability of FIV, five subtypes (A to E) have been identified and diversity within each subtype is also frequent. The study of the genetic diversity can aid the understanding the pathogenesis and epidemiology of the disease. Therefore, the present work aimed to analyze phylogenetically FIV isolates of domestic cats from the state of São Paulo, Brazil. The sequencing of 658 bp of the gag gene from 23 samples was performed and the results were analyzed using the Tamura-Nei nucleotidic substitution method. The phylogenetic analysis showed that all viruses belong to subtype B, and clearly three subgroups were present within this subtype. Additionally, these results suggest a common ancestor between the FIV strains derived from Japan and one Brazilian virus. In conclusion, this work presents the first information about the genetic diversity of FIV in the state of São Paulo. Additional studies are necessary to characterize the real scenario of the distribution of FIV subtypes in the population of Brazilian cats.