Genome Variability of Infectious Bronchitis Virus in Mexico: High Lineage Diversity and Recurrent Recombination

Abstract

The avian infectious bronchitis virus (IBV) is a coronavirus that mutates frequently, leading to a contagious and acute disease that results in economic losses to the global poultry industry. Due to its genetic and serological diversity, IBV poses a challenge in preventing and controlling the pathogen. The full-length S1 sequence analysis identifies seven main genotypes (GI-GVII) comprising 35 viral lineages. In addition to the previously described lineage, a new GI lineage (GI-30) and two lineages from novel genotypes (GVIII-1 and GIX-1) have been described in Mexico. To prevent the spread of IBV outbreaks in a specific geographic location and select the suitable vaccine, it is helpful to genetically identify the circulating IBV types. Moreover, sequencing genomes can provide essential insights into virus evolution and significantly enhance our understanding of IBV variability. However, only genomes of previously described lineages (GI-1, GI-9, GI-13, and GI-17) have been reported for Mexican strains. Here, we sequenced new genomes from Mexican lineages, including the indigenous GI-30, GVIII-1, and GIX-1 lineages. Comparative genomics reveals that Mexico has relatively homogenous lineages (i.e., GI-13), some with greater variability (i.e., GI-1 and GI-9), and others extremely divergent (GI-30, GVIII-1, and GIX-1). The circulating lineages and intra-lineage variability support the unique diversity and dynamic of Mexican IBV.

Keywords: IBV; Mexico; genomes; lineages.

Figure 1

The phylogenetic tree was obtained with the maximum-likelihood method and GTR model with gamma distribution and invariant sites. Phylogenetic reconstruction was carried out using complete S1 sequences of the genomes here obtained (n = 14), other Mexican genomes available (n = 33), prototype IBV strains (n = 32) [17], and additional viruses from recently identified lineages and genotypes (n = 3). The Mexican strains are indicated with a green background, and the strains sequenced in this study are shown in bold. The gray circles represent node support values; the cutoff value is 50%.

Figure 2

Reticulate network using Mexican complete genome sequences constructed with SplitsTree program. The Mexican strains sequenced in this study are highlighted. A color was assigned to each lineage.

Figure 3

Temporal circulation in Mexico of eight lineages of the GI, GVIII, and GIX genotypes (GI-1, GI-3, GI-9, GI-13, GI-17, GI-30, GVIII-1, and GIX-1). The lineages are detailed with different colors, and the years in which sequence reports are available are indicated.