Phylogenetic and molecular diversity of avian infectious bronchitis virus GI-1 in Brazil

Abstract The avian infectious bronchitis virus (IBV) affects chickens ( Gallus gallus ), causing respiratory disease, nephritis, and lesions in the oviduct, which can lead to weight loss and decreased egg production. IBV is classified into nine genotypes (GI–GIX), covering 41 genetic lineages (1–41), based on differences in the spike ( S ) gene. IBV GI-1 was the first lineage to be identified and includes the classical Massachusetts (Mass) and Connecticut (Conn) serotypes. Mass strains have been used as live attenuated vaccines for over 50 years worldwide. This study aimed to investigate the genetic diversity of avian IBV GI-1 in Brazil. Three hundred field samples were collected from chicken flocks exhibiting clinical signs of IBV infection between 2018 and 2023. IBV detection and identification of three lineages (GI-1, −11, and −23) present in Brazil was performed using four RT-PCR assays. A partial region of the S1 gene, including hypervariable regions 1 and 2 (HVR1 and HVR2), was further sequenced from the IBV GI-1 positive samples as well as four vaccines from this lineage (all Mass strains) commercialized in Brazil. Phylogenetic and nucleotide/amino acid similarities analyses were additionally performed to compare field and vaccine samples. The results demonstrated that 17 field samples and four vaccines were identified as IBV GI-1. Phylogenetic analysis, including 222 field and vaccine sequences of IBV GI-1, revealed two distinct clades: Conn ( n = 16) and Mass ( n = 206), the latter being subdivided into H120 ( n = 148) and M41 ( n = 58). The Brazilian sequences clustered within the H120 ( n = 19, including three vaccines) and M41 ( n = 2, including one vaccine) clades. Similarity analyses showed that 18 here sequenced samples (85.7%, including the four vaccines) shared 99–100% identity with reference Mass vaccine sequences, suggesting that all these IBVs are vaccine strains or closely related variants. In contrast, three field sample sequences exhibited ~94.1% similarity, evidencing Mass-like field variants. Molecular signatures with specific amino acids were found in the Mass subclades, highlighting the Y101H substitution that allows the differentiation of the H120 subclade from M41. This study demonstrates that HVR1/2 sequences from IBV GI-1 field samples are mostly similar to vaccines, highlighting H120, but there are also Mass-like field variants in Brazilian commercial poultry flocks. These findings contribute to clarifying epidemiological aspects and enriching the understanding of IBV GI-1 in Brazil.