Phylodynamic analysis of avian infectious bronchitis virus in South America

Marandino, Ana; Pereda, Ariel; Tomás, Gonzalo; Hernández, Martı́n; Iraola, Gregorio; Craig, María Isabel; Hernández, Diego; Banda, Alejandro; Villegas, Pedro; Panzera, Yanina; Pérez, Ruben

doi:10.1099/vir.0.000077

Cited by 39 publications

(51 citation statements)

References 53 publications

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“…The complete genomes of 110 LX4 genotype IBV strains were analyzed and compared to each other and to that of three reference types including Beaudette, H120 and M41 as Massachusetts type, 4/91 as a 793/B type and ck/CH/LDL/97I as ck/CH/LDL/97I type. The latter is another very important genotype that first emerged in China and spread to other regions of the world (Ababneh et al, 2012;Marandino et al, 2015). This comparison revealed that most of the viruses (108 out of 110) had a previously known genomic organization (5 0 -UTR-Gene 1 (ORF1a, 1b)-S-Gene 3 (3a-3c)-M-Gene 5 (5a and 5b)-N-UTR-3 0 ), although various lengths of genomes have been found which may be the result of insertions/deletions.…”

Section: Discussionmentioning

confidence: 99%

Origin and evolution of LX4 genotype infectious bronchitis coronavirus in China

Zhao

Gao

et al. 2017

Veterinary Microbiology

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We investigated the genomic characteristics of 110 LX4 genotype strains of infectious bronchitis viruses (IBVs) isolated between 1995 and 2005 in China. The genome of these IBVs varies in size from 27596bp to 27790bp. Most IBV strains have the typical genomic organization of other gamacoronaviruses, however, two strains lacked 3a and 5b genes as a result of a nucleotide change within the start codon in the 3a or 5b genes. Analysis of our 110 viruses revealed that recombination events may be responsible for the emergence of the LX4 genotype with different topologies. Most of these viruses disappeared (before mid-2005) because they were not "fit" to adaptation in chickens. Finally, those of the "fit" viruses (after mid-2005) continued to evolve and have become widespread and predominant in commercial poultry. In addition, few of these viruses experienced recombination with those of the vaccine strains at the 3' end of the genome.

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Section: Discussionmentioning

confidence: 99%

Origin and evolution of LX4 genotype infectious bronchitis coronavirus in China

Zhao

Gao

et al. 2017

Veterinary Microbiology

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“…e l s e v i e r . c o m / l o c a t e / m e e g i d (Alvarado et al, 2005;Marandino et al, 2015;Rimondi et al, 2009). These lineages are responsible for most outbreaks in commercial flocks and cause major economic losses in countries with high production levels, such as Brazil and Argentina, which are among the world's top producers of broiler meat (USDA, 2014).…”

Section: Contents Lists Available At Sciencedirectmentioning

confidence: 99%

“…These lineages are responsible for most outbreaks in commercial flocks and cause major economic losses in countries with high production levels, such as Brazil and Argentina, which are among the world's top producers of broiler meat (USDA, 2014). GI-11 is an exclusive South American lineage that emerged in the 1960s and is now apparently restricted to Argentina, Brazil and Uruguay (Chacon et al, 2011;Felippe et al, 2010;Marandino et al, 2015;Villarreal et al, 2007). The GI-16 lineage contains viruses collected in South America (Argentina, Chile, Colombia, Peru and Uruguay), Asia (China and Taiwan) and Europe (Italy, Russia and Slovenia) (Alvarado et al, 2005;Han et al, 2011;Huang et al, 2004;Liu et al, 2009;Marandino et al, 2015;Sesti et al, 2014;Tataje-Lavanda et al, 2016;Toffan et al, 2013;Valastro et al, 2016).…”

Section: Contents Lists Available At Sciencedirectmentioning

confidence: 99%

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

Marandino

Tomás

Panzera

et al. 2017

Infection, Genetics and Evolution

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Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus that causes one of the most persistent respiratory diseases in poultry. The virus is classified in genotypes and lineages with different epidemiological relevance. Two lineages of the GI genotype (11 and 16) have been widely circulating for decades in South America. GI-11 is an exclusive South American lineage while the GI-16 lineage is distributed in Asia, Europe and South America. Here, we obtained the whole genome of two Uruguayan strains of the GI-11 and GI-16 lineages using Illumina high-throughput sequencing. The strains here sequenced are the first obtained in South America for the infectious bronchitis virus and provide new insights into the origin, spreading and evolution of viral variants. The complete genome of the GI-11 and GI-16 strains have 27,621 and 27,638 nucleotides, respectively, and possess the same genomic organization. Phylogenetic incongruence analysis reveals that both strains have a mosaic genome that arose by recombination between Euro Asiatic strains of the GI-16 lineage and ancestral South American GI-11 viruses. The recombination occurred in South America and produced two viral variants that have retained the full-length S1 sequences of the parental lineages but are extremely similar in the rest of their genomes. These recombinant virus have been extraordinary successful, persisting in the continent for several years with a notorious wide geographic distribution. Our findings reveal a singular viral dynamics and emphasize the importance of complete genomic characterization to understand the emergence and evolutionary history of viral variants.

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“…The high mutation and recombination rate of IBV, especially in the S1 subunit of the S protein gene, has led to the emergence of new variants, particularly in Europe and North America, and more recently in intensive poultry farms in China. Among the IBVs, two very important genotypes, LX4 (QXlike) and ck/CH/LDL/97I, are believed to have originated in China in mid-1995 and have since spread to other regions of the world (Ababneh et al, 2012;Marandino et al, 2015). More recently, another novel genotype, Guandong/Xindadi (XDN), which is also believed to have originated in China from independent recombination events between the LX4 and 793/B IBV genotypes, have emerged in Italy and Spain (Moreno et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Identification and molecular characterization of a novel serotype infectious bronchitis virus (GI-28) in China

Chen

Jiang

Zhao

et al. 2017

Veterinary Microbiology

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Avian infectious bronchitis coronavirus (IBV) is a major poultry pathogen. A characteristic feature of IBV is the occurrence of many different strains belonging to different serotypes, which renders complete control of the disease by vaccination a challenging task due to the poor cross-protection between different serotypes. In this study, based on the results of S1 sequence analysis and virus cross-neutralization tests, IBV strain ck/CH/LGX/111119 was found to be genetically and antigenically different from other known IBV types, representing not only a novel genotype, but also a novel serotype (designated as GI-28). Viruses belonging to this novel serotype have been isolated from several regions in China in recent years, suggesting endemic circulation of the serotype in various geographic locations in China. Further studies by complete genomic analysis showed that strain ck/CH/LGX/111119 may have originated from recombination events involving LX4 genotype IBVs and an as-yet-unidentified IBV donating a S1 gene, or from the result of accumulation of mutations and selections, especially in the S1 gene, from a LX4 genotype virus. ck/CH/LGX/111119 is a nephropathogenic strain, although it had broader tissue tropism (respiratory, digestive, urinary, and reproductive tracts) among chickens challenged at one day old. Infection of the oviducts with ck/CH/LGX/111119 found in this study may have severe implications because the virus will likely induce the occurrence of false layers.

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Phylodynamic analysis of avian infectious bronchitis virus in South America

Cited by 39 publications

References 53 publications

Origin and evolution of LX4 genotype infectious bronchitis coronavirus in China

Origin and evolution of LX4 genotype infectious bronchitis coronavirus in China

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

Identification and molecular characterization of a novel serotype infectious bronchitis virus (GI-28) in China

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