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Arch Virol ; 165(1): 145-156, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31745717


Bovine viral diarrhea virus (BVDV) is a major pathogen worldwide, causing significant economic losses to the livestock sector. In Uruguay, BVDV seroprevalence at the farm level is >80%. In this work, 2546 serum, blood or tissue samples collected from animals suspected of being affected by BVD between 2015 and 2017 were analyzed by reverse transcription PCR and sequencing. Analysis of the BVDV genomic regions 5'UTR/Npro, Npro and E2 revealed that BVDV-1a, 1i and 2b circulate in the country, with BVDV-1a being the most prevalent subtype. Population dynamics studies revealed that BVDV-1a has been circulating in our herds since ~1990. This subtype began to spread and evolve, accumulating point mutations at a rate of 3.48 × 10-3 substitutions/site/year, acquiring specific genetic characteristics that gave rise to two local genetic lineages of BVDV-1a. These lineages are divergent from those circulating worldwide, as well as the vaccine strain currently used in Uruguay. The most notable differences between field and vaccine strains were found in the E2 glycoprotein, suggesting that the amino acid substitutions could result in failure of cross-protection/neutralization after vaccination. This is the first study that compares Uruguayan BVDV field and vaccine strains with other BVDV strains from throughout the world. The results obtained in this study will be very useful for developing a suitable immunization program for BVDV in Uruguay by identifying local field strains as candidates for vaccine development.

Virus de la Diarrea Viral Bovina/clasificación , Mutación Puntual , Análisis de Secuencia de ARN/métodos , Sustitución de Aminoácidos , Animales , Bovinos , Virus de la Diarrea Viral Bovina/genética , Virus de la Diarrea Viral Bovina/inmunología , Evolución Molecular , Filogenia , Estudios Seroepidemiológicos , Uruguay , Proteínas del Envoltorio Viral/genética , Proteínas del Envoltorio Viral/inmunología , Vacunas Virales/inmunología
Arch Virol ; 164(11): 2715-2724, 2019 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-31456086


Bovine coronavirus (BCoV) is a recognized cause of severe neonatal calf diarrhea, with a negative impact on animal welfare, leading to economic losses to the livestock industry. Cattle production is one of the most important economic sectors in Uruguay. The aim of this study was to determine the frequency of BCoV infections and their genetic diversity in Uruguayan calves and to describe the evolutionary history of the virus in South America. The overall detection rate of BCoV in Uruguay was 7.8% (64/824): 7.7% (60/782) in dairy cattle and 9.5% (4/42) in beef cattle. The detection rate of BCoV in samples from deceased and live calves was 10.0% (6/60) and 7.6% (58/763), respectively. Interestingly, there was a lower frequency of BCoV detection in calves born to vaccinated dams (3.3%, 8/240) than in calves born to unvaccinated dams (12.2%, 32/263) (OR: 4.02, 95%CI: 1.81-8.90; p = 0.00026). The frequency of BCoV detection was higher in colder months (11.8%, 44/373) than in warmer months (1.5%, 3/206) (OR: 9.05, 95%CI: 2.77-29.53, p = 0.000013). Uruguayan strains grouped together in two different lineages: one with Argentinean strains and the other with Brazilian strains. Both BCoV lineages were estimated to have entered Uruguay in 2013: one of them from Brazil (95%HPD interval: 2011-2014) and the other from Argentina (95%HPD interval: 2010-2014). The lineages differed by four amino acid changes, and both were divergent from the Mebus reference strain. Surveillance should be maintained to detect possible emerging strains that can clearly diverge at the antigenic level from vaccine strains.

Antígenos Virales/genética , Enfermedades de los Bovinos/epidemiología , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/veterinaria , Coronavirus Bovino/aislamiento & purificación , Animales , Antígenos Virales/inmunología , Argentina/epidemiología , Brasil/epidemiología , Bovinos , Enfermedades de los Bovinos/prevención & control , Enfermedades de los Bovinos/virología , Infecciones por Coronavirus/prevención & control , Coronavirus Bovino/genética , ADN Viral/genética , Disentería/epidemiología , Disentería/veterinaria , Disentería/virología , Variación Genética/genética , Uruguay/epidemiología , Vacunación
Infect Genet Evol ; 54: 245-250, 2017 10.
Artículo en Inglés | MEDLINE | ID: mdl-28705717


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.

Infecciones por Coronavirus/veterinaria , Genoma Viral , Genómica , Virus de la Bronquitis Infecciosa/clasificación , Virus de la Bronquitis Infecciosa/genética , Enfermedades de las Aves de Corral/virología , Recombinación Genética , Animales , Biología Computacional/métodos , Bases de Datos Genéticas , Evolución Molecular , Orden Génico , Genómica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento , Anotación de Secuencia Molecular , Filogenia , ARN Viral , América del Sur
J Gen Virol ; 96(Pt 6): 1340-6, 2015 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-25667323


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.

Infecciones por Coronavirus/veterinaria , Variación Genética , Virus de la Bronquitis Infecciosa/clasificación , Proteínas de la Nucleocápside/genética , Enfermedades de las Aves de Corral/epidemiología , Enfermedades de las Aves de Corral/virología , Glicoproteína de la Espiga del Coronavirus/genética , Animales , Argentina/epidemiología , Pollos , Análisis por Conglomerados , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/virología , Genotipo , Virus de la Bronquitis Infecciosa/genética , Virus de la Bronquitis Infecciosa/aislamiento & purificación , Epidemiología Molecular , Datos de Secuencia Molecular , Filogenia , Análisis de Secuencia de ADN , Uruguay/epidemiología