Phylodynamic analysis and molecular diversity of the avian infectious bronchitis virus of chickens in Brazil

Abstract

Avian infectious bronchitis virus (IBV) is the etiological agent of a highly contagious disease, which results in severe economic losses to the poultry industry. The spike protein (S1 subunit) is responsible for the molecular diversity of the virus and many sero/genotypes are described around the world. Recently a new standardized classification of the IBV molecular diversity was conducted, based on phylogenetic analysis of the S1 gene sequences sampled worldwide. Brazil is one of the biggest poultry producers in the world and the present study aimed to review the molecular diversity and reconstruct the evolutionary history of IBV in the country. All IBV S1 gene sequences, with local and year of collection information available on GenBank, were retrieved. Phylogenetic analyses were carried out based on a maximum likelihood method for the classification of genotypes occurring in Brazil, according to the new classification. Bayesian phylogenetic analyses were performed with the Brazilian clade and related international sequences to determine the evolutionary history of IBV in Brazil. A total of 143 Brazilian sequences were classified as GI-11 and 46 as GI-1 (Mass). Within the GI-11 clade, we have identified a potential recombinant strain circulating in Brazil. Phylodynamic analysis demonstrated that IBV GI-11 lineage was introduced in Brazil in the 1950s (1951, 1917-1975 95% HPD) and population dynamics was mostly constant throughout the time. Despite the national vaccination protocols, our results show the widespread dissemination and maintenance of the IBV GI-11 lineage in Brazil and highlight the importance of continuous surveillance to evaluate the impact of currently used vaccine strains on the observed viral diversity of the country.

Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure

“…In order to understand the variation degree of the S1, E, M, and N genes and the correlation between gene variation and selection pressure, the analyses of entropy of amino acid sequences, molecular evolutionary rate, and positive selection were carried out in our study. The results showed that mean substitution rates were between 3.7 × 10 −3 and 4.6 × 10 −3 substitutions per site per year in different genes, which is comparable with previous description [58]. Both the average entropy and mean substitution rates sorted from large to small as follows: S1, E, M, and N genes, and the dN/dS ratios of S1, E, M, and N genes were 0.283, 0.266, 0.146, and 0.147, respectively.…”

“…Therefore, we have identified 11 recombinants so far and 7 recombinants were derived from the 4/91-type strain during 1985–2017. High frequencies of recombination between vaccine and field strains have been reported frequently worldwide [4,5,15,22,57,58]. The 4/91 vaccine strain has been commonly used in China for a long time, so it is not surprising that 4/91-type recombinants were found in the field.…”

“…Molecular evolutionary rate analysis can accurately estimate the molecular dating and it was used to determine successfully the timing of ancestors of classical swine fever virus (CSFV) [64], SARS virus [65], and IBV [30,58]. According our previous investigation [1], the first IBV strain was isolated in 1985, demonstrating that the IBV was already present at that time.…”

Molecular characterization of an avian GA13-like infectious bronchitis virus full-length genome from Costa Rica

“…The IBV sequence with the lowest identity (86.03%) was ck/CH/LHLJ/08-6. The S1 gene region is highly variable, with nucleotide sequence identities varying between 58.3–88.48% among the different IBV serotypes, due to a high mutation frequency as well as recombination events [ 2 , 3 , 11 , 29 ]. For this reason, it is important to point out that the isolate in this study exhibits a very high sequence identity in the S1 gene (96.89%) with the Georgia 13 genotype (Ga-13/14255/14).…”

Emergence of Avian coronavirus genotype GI-11 in Colombia

“…GI-11 probably emerged in the 1960s and was believed to be restricted to Argentina, Brazil, and Uruguay [ 21 ]. GI-11 represents 74% of AvCoV types in Brazil [ 11 , 15 ] and was implicated in nephrosis, orchitis, respiratory, and enteric diseases [ 12 , 24 ].…”