key: cord-0780129-etx6b55q
authors: Tataje-Lavanda, Luis; Izquierdo-Lara, Ray; Ormeño-Vásquez, Phillip; Huamán-Gutiérrez, Katherine; Zimic-Peralta, Mirko; Fernández-Díaz, Manolo
title: Near-Complete Genome Sequence of Infectious Bronchitis Virus Strain VFAR-047 (GI-16 Lineage), Isolated in Peru
date: 2019-01-31
journal: Microbiol Resour Announc
DOI: 10.1128/mra.01555-18
sha: 26a222223bf9fe6164feaa2f4231923c9abcc77e
doc_id: 780129
cord_uid: etx6b55q

Here, we report the near-complete genome sequence of the infectious bronchitis virus (IBV) strain VFAR-047, isolated in Peru in 2014. This strain was classified into GI lineage 16 (GI-16) based on both the genome and Spike 1 (S1) sequence analysis. Furthermore, four potential recombination events with other GI-16 and GI-11 strains were identified.

sharing 98% to 93% identity with GI-16 representative strains gammaCoV/Ck/Italy/I2022/13 (GenBank accession number KP780179), ck/CH/LDL/97I (JX195177 and JX195178), UY/ 09/CA/01 (MF421319), and IZO 28/86 (KJ941019). Phylogenetic analysis of the nearcomplete genome showed that VFAR-047 is grouped in the same branch with UY/09/CA/ 01, UY/11/CA/18 (MF421320), gammaCoV/Ck/Italy/I2022/13, and CK/CH/LDL/97I, with average nucleotide identities ranging from 93% to 92%. The phylogenetic network ( Fig. 1 ) and the phi test showed statistically significant evidence of recombination (P ϭ 0.0). Furthermore, five recombined sequences were identified with high reliability by six methods embedded in RDP4, which include four potential recombination events with GI-16 and GI-11 strains.

The VFAR-047 genome will facilitate future development of new vaccines and other infection control strategies in the poultry industry.

Data availability. The near-complete genome sequence of infectious bronchitis virus isolate VFAR-047 has been deposited in GenBank under the accession number MH878976. Raw data were deposited in the SRA under BioSample number SAMN10521748 and SRA run number SRR8281084, which are part of SRA study number SRP172861.

We thank Ricardo Montesinos, Ángela Montalván, and Edison Huaccachi for their outstanding technical support.

We declare no competing interests. 

Chapter 2.3.2. Avian infectious bronchitis

Coronavirus avian infectious bronchitis virus

Infectious bronchitis virus variants: molecular analysis and pathogenicity investigation

Molecular characterization of major structural protein genes of avian coronavirus infectious bronchitis virus isolates in southern China

Recombination in avian gamma-coronavirus infectious bronchitis virus

S1 gene-based phylogeny of infectious bronchitis virus: an attempt to harmonize virus classification

A 15-year analysis of molecular epidemiology of avian infectious bronchitis coronavirus in China

Review of infectious bronchitis virus around the world

Phylodynamic analysis of avian infectious bronchitis virus in South America

Whole-genome characterization of Uruguayan strains of avian infectious bronchitis virus reveals extensive recombination between the two major South American lineages

First evidence of detection of Asia/South America II (A/SAII) infectious bronchitis virus in a commercial broiler flock in Peru

VirusTAP: viral genometargeted assembly pipeline

NextGEne 2.4.2-Next Generation Sequencing Software for Biologists-User Manual

Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees

MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms

Application of phylogenetic networks in evolutionary studies

RDP4: detection and analysis of recombination patterns in virus genomes