Phylodynamic analysis of avian infectious bronchitis virus in South America

Abstract

Infectious bronchitis virus (IBV) is a coronavirus of chickens that causes great economic losses to the global poultry industry. The present study focuses on South American IBVs and their genetic relationships with global strains. We obtained full-length sequences of the S1 coding region and N gene of IBV field isolates from Uruguay and Argentina, and performed Phylodynamic analysis to characterize the strains and estimate the time of the most recent common ancestor. We identified two major South American genotypes, which were here denoted South America I (SAI) and Asia/South America II (A/SAII). The SAI genotype is an exclusive South American lineage that emerged in the 1960s. The A/SAII genotype may have emerged in Asia in approximately 1995 before being introduced into South America. Both SAI and A/SAII genotype strains clearly differ from the Massachusetts strains that are included in the vaccine formulations being used in most South American countries.

Fig. 1.

Phylogenetic tree inferred by using the maximum-likelihood method with GTR+I+G substitution model. Phylogenetic reconstruction was carried out using the full-length S1 coding region of South American IBV strains and reference strains. Mapping uncertainties for internal nodes are shown as approximate likelihood ratio test values.

Fig. 2.

Posterior probability densities for the tMRCA inferences for SAI and A/SAII genotypes. The SAI genotype dataset (n = 81) comprised strains collected from 1975 to 2012, and the A/SAII genotype dataset (n = 25) comprised strains collected from 1996 to 2011. Vertical dashed lines represent the mean estimated time for each ancestor and coloured boxes reflect the 95 % high probability density values.

Fig. 3.

Phylogenetic tree inferred by using the maximum-likelihood method with GTR+I+G substitution model. Phylogenetic reconstruction was carried out using the full-length N gene sequence of South American IBV strains and reference strains. Mapping uncertainties for internal nodes are shown as approximate likelihood ratio test values.