New Insights into Avian Infectious Bronchitis Virus in Colombia from Whole-Genome Analysis

Abstract

Infectious Bronchitis (IB) is a respiratory disease caused by a highly variable Gammacoronavirus, which generates a negative impact on poultry health worldwide. GI-11 and GI-16 lineages have been identified in South America based on Infectious Bronchitis virus (IBV) partial S1 sequences. However, full genome sequence information is limited. In this study we report, for the first time, the whole-genome sequence of IBV from Colombia. Seven IBV isolates obtained during 2012 and 2013 from farms with respiratory disease compatible with IB were selected and the complete genome sequence was obtained by NGS. According to S1 sequence phylogenetic analysis, six isolates belong to lineage GI-1 and one to lineage GVI-1. When whole genome was analyzed, five isolates were related to the vaccine strain Ma5 2016 and two showed mosaic genomes. Results from complete S1 sequence analysis provides further support for the hypothesis that GVI-1, considered a geographically confined lineage in Asia, could have originated in Colombia. Complete genome information reported in this research allow a deeper understanding of the phylogenetic evolution of variants and the recombination events between strains that are circulating worldwide, contributing to the knowledge of coronavirus in Latin America and the world.

Keywords: Gammacoronavirus; genome sequencing; poultry; respiratory tract diseases.

Figure 1

Geographical location of the farms from which the Infectious Bronchitis Virus (IBV) isolates included in the study were obtained. The lower right image shows the exact location of the farms and the seven IBV isolates (V2, V3, V5, V6, V8, V9, and V10).

Figure 2

Maximum-likelihood (ML) phylogenetic tree of IBV S1 Colombian sequences (n = 7), plus S1 IBV worldwide gene sequences (n = 1972). The circular band of colors around the tree indicates the genotype and lineage of each clade. Black bands indicate unique variants as designated by Valastro et al. 2016. Red lines in the second layer (outer to inner) indicate the placement of the Colombian samples. The SH-aLRT support values were >99% for all the genotypes and defined lineages. The tree was midpoint rooted and the length of the branches are drawn to scale with the bar at the middle indicating nucleotide substitution per site.

Figure 3

Maximum-likelihood phylogenetic tree of Infectious Bronchitis Virus (IBV) S1 gene sequences from the GI-1 clade (n = 203). Red labels correspond to IBV Colombian sequences and green labels to vaccine strains. Circles at the nodes denote SH-aLRT branch support values larger than 80%. The tree was midpoint rooted and the length of the branches are drawn to scale with the bar at the middle indicating nucleotide substitution per site.

Figure 4

Maximum-likelihood phylogenetic tree of IBV complete genomes (n = 438). Red labels correspond to IBV Colombian sequences and green labels to vaccine strains. Circles at the nodes denote SH-aLRT branch support values larger than 80%. The tree was midpoint rooted and the lengths of the branches are drawn to scale with the bar at the middle indicating nucleotide substitution per site. Clusters that contain a) V8 b) V6 and c) V2, V3, V5, V9 and V10 Colombian strains are highlighted and magnified. SH-aLRT branch support values are indicated at key nodes and the branch lengths are drawn to scale with the bar at the top indicating nucleotide substitution per site.

Figure 5

ORF prediction and recombination analyses. (a) Genomic organization of V3, V10, V6, and V8. Red labels and yellow boxes highlight variation regions in detected ORFs. (b) and (c) Bootscan analysis (Simplot 3.5.1) of V6 and V8 whole genome sequences, respectively (windows size: 500 bp, step size: 100 bp). The dotted lines indicate a bootstrap value of 70%, and gray boxes indicate regions with recombination events.