Genetic Analysis of Infectious Bronchitis Virus S1 Gene Reveals Novel Amino Acid Changes in the GI-16 Lineage in Peru

Abstract

Infectious bronchitis is a highly contagious viral disease that represents an economic threat for poultry despite the wide use of vaccination. To characterize the virus circulating in Peru, we analyzed 200 samples, including nasopharyngeal swabs and multiple tissues collected from animals suspected of being infected with infectious bronchitis virus (IBV) between January and August in 2015. All animals had at least one positive sample for IBV by RT-PCR. Out of these positive samples, eighteen (18) were selected for viral isolation and a partial S1 sequencing. Phylogenetic analysis showed that sixteen isolates clustered with members of GI-16 lineage, also known as Q1, with nucleotide homology ranging from 93% to 98%. The two remaining isolates grouped with members of the GI-1 lineage. Our study reveals circulation of GI-16 lineage during this period in poultry systems in Peru, along with GI-1 lineage (vaccine-derived). Moreover, those IBV GI-16 isolates showed unique nucleotide and amino acid changes compared to their closest relatives. Altogether, these findings reveal the circulation of GI-16 lineage while describing changes at key regions of the S protein that might be of relevance for vaccine evasion. These results highlight the importance of genetic surveillance for improving vaccination strategies against infectious bronchitis.

Highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b from Peru forms a monophyletic group with Chilean isolates in South America

“…Our results allowed the identification of avian influenza viruses with a highly variable viral load based on the Ct values observed. Although Ct values can be used as approximation method to assess the viral load for other viral infections 27 , we did not find evidence of correlation in terms of severity and viral levels based on Ct values (data not shown). Thus, clinical presentation and the PCR results indicate that influenza virus was likely responsible for the severe cases.…”

Evolution and Epidemic Spread of the Avian Infectious Bronchitis Virus (IBV) GI-23 in Brazil

“…GI-1 is a lineage deriving from the live vaccine strain Massachusetts largely used in immunization programs in all of South America, GI-16 is more widespread in Western countries bordering the Pacific Ocean (Chile, Colombia, Peru, etc.) [ 24 , 33 ], and GI-11 is more frequent in Brazil, which borders the Atlantic Ocean [ 3 , 34 ]. Noteworthily, IBV lineages’ diversity in South America follows a similar pattern to that of IBDV variants.…”

Avian infectious bronchitis virus (AIBV) review by continent

“…According to a recent Peruvian study, the circulation of GI-16 has been determined along with the GI-1 (vaccine derived) lineage in the poultry industry of Peru. GI-I is prevalent in tropical areas, and GI-16 is prevalent in coastal areas ( Icochea et al., 2023 ).…”

“…The IBV genotype GII lineage was identified in Georgia, USA, in 2000, and its whole genome was submitted to GenBank under accession number AF274435.1 ( Icochea et al., 2023 ).…”