Genotyping of white spot syndrome virus on wild and farm crustaceans from Sonora, Mexico

Gonzalez-Galaviz, Jose Reyes; Rodriguez-Anaya, Libia Zulema; Molina-Garza, Zinnia Judith; Ibarra‐Gámez, Jose Cuauhtémoc; Galaviz‐Silva, Lucio

doi:10.2298/abs1303945g

Cited by 5 publications

(7 citation statements)

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“…This could indicate that this haplotype was generated in -or entered -the northwestern region of Mexico from the north and spread southward (Table S1). The presence of the 3-RU haplotypes has been reported in India and Sonora, Mexico, previously, but this is the first report of the distribution of SNPs at Position 48 of RUs in America; therefore, it is possible that they have the same haplotype described here, though this was not reported (Pradeep et al 2008, Gonzalez-Galaviz et al 2013. Simrouni et al (2014) reported 2 variants of ORF 94 with 3 RUs isolated in Iran in 2012 that have different patterns from those reported in this work, as they found SNP patterns G,G,G and T,T,T.…”

Section: Orf 94mentioning

confidence: 43%

“…Most of the epidemiological studies performed with WSSV and these 3 markers are based only on the size of the mini-satellite and are expressed as the number of RUs (Dieu et al 2004, Pradeep et al 2008, Dieu et al 2010, Tan & Shi 2011, Shekar et al 2012, and Mexico is no exception (Galaviz-Silva et al 2009, Gonzalez-Galaviz et al 2013. However, each RU may contain SNPs that are useful for differentiating haplotypes that have the same number of RUs.…”

Section: Introductionmentioning

confidence: 99%

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Genotyping WSSV isolates from northwestern Mexican shrimp farms affected by white spot disease outbreaks in 2010-2012

Durán‐Avelar¹,

Pérez‐Enríquez²,

Zambrano‐Zaragoza³

et al. 2015

Dis. Aquat. Org.

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White spot disease (WSD) causes high mortality in cultured shrimp throughout the world. Its etiologic agent is the white spot syndrome virus (WSSV). The genomic repeat regions ORF 75, ORF 94, and ORF 125 have been used to classify WSSV isolates in epidemiological studies using PCR with specific primers and sequencing. The present study investigated the variation in nucleotide sequences from 107, 150, and 143 isolates of WSSV collected from Litopenaeus vannamei shrimp ponds with WSD outbreaks in northwestern Mexico during the period 2010−2012, in the genomic repeat regions ORFs 75, 94, and 125, respectively. The haplotypic nomenclature for each isolate was based on the number of repeat units and the position of single nucleotide polymorphisms on each ORF. We report finding 17, 43, and 66 haplotypes of ORFs 75, 94, and 125, respectively. The study found high haplotypic diversity in WSSV using the complete sequences of ORFs 94 and 125 as independent variables, but low haplotypic diversity for ORF 75. Different haplotypes of WSSV were found from region-to-region and year-to-year, though some individual haplotypes were found in different places and in more than one growing cycle. While these results suggest a high rate of mutation of the viral genome at these loci, or perhaps the introduction of new viral strains into the area, they are useful as a tool for epidemiological surveys. Two haplotypes from some of the ORFs in the same shrimp were encountered, suggesting the possibility of multiple infections.

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Section: Orf 94mentioning

confidence: 43%

Section: Introductionmentioning

confidence: 99%

Genotyping WSSV isolates from northwestern Mexican shrimp farms affected by white spot disease outbreaks in 2010-2012

Durán‐Avelar¹,

Pérez‐Enríquez²,

Zambrano‐Zaragoza³

et al. 2015

Dis. Aquat. Org.

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“…The present report is based on three minisatellites ORF 75, 94 and 125. Application of these methods for typing WSSV isolates has been reported widely from the shrimp growing countries in the world (Dieu et al, 2004;Hoa et al, 2012;Gonzalez-Galaviz et al, 2013) while similar studies are limited from India (Musthaq et al, 2006;Pradeep et al, 2008;John et al, 2010) and the present study is the first report of WSSV genotyping from the state of Gujarat.…”

mentioning

confidence: 72%

Genetic variations among white spot syndrome virus (WSSV) isolates from shrimp farms in Gujarat, north-west coast of India

Patil¹,

Solanki²,

Otta³

et al. 2017

Indian J. Fish.

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The present paper documents the molecular diagnosis and genotyping of white spot syndrome virus (WSSV) isolates collected from different shrimp farms of Gujarat, north-west coast of India. Preliminary diagnosis was done using single tube PCR and genotyping of isolates by analysis of variable number tandem repeat sequence (VNTRS) in minisatellites viz., ORF 94, ORF 125, ORF 75 and ORF 75 flank. Out of the 79 samples analysed, 32 (33.80%) were positive with low (54.17%), medium (8.33%) and high (37.50%) severity of infection. Genotyping, using ORF 94 revealed that repeat units (RUs) 4 and 11 were the most frequent ones (32%) while ORF 125 showed 5 different repeat types of which RU 5 was the most common (45.83%). Two genotypes were observed for ORF 75, one showed multiple repeats of two 45 bp, followed by a 57 bp, whereas the other showed two repeats that included 5 and 4 repeats of 45 bp. Sequence analysis of the 54 bp variable sequence of ORF 94 RU type 4 revealed single-nucleotide polymorphism (SNP) at 47 th base. Based on the results from ORF 94, dominance of RU types 11or 4 were recorded for the first time in India and one sample showed 2 bands of different sizes indicating the prevalence of two different genotypes infecting the same pond at a given time. Further, no correlation could be observed between the virus genotype and the severity of the mortality in the outbreaks. The results suggest the widespread occurrence of WSSV in the region and circulation of distinct virus genotypes.

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“…These variables loci have been considered as important molecular markers for WSSV genotyping. The single nucleotide mutations, including deletions, insertions, and single nucleotide polymorphisms (SNP) have been suggested as markers for genetic diversity studies of WSSV (John et al, 2010;Hoa et al, 2011;González-Galaviz et al, 2013).…”

mentioning

confidence: 99%

“…This region shows more variation, with a wide range of compound repeat units (RUs) between the WSSV isolates originating from farming and wild hosts (Wongteerasupaya et al, 2003;Dieu et al, 2004;Musthaq et al, 2006;Pradeep et al, 2008;John et al, 2010;González-Galaviz et al, 2013). Several studies have suggested a correlation between the RUs of ORF94 and WSSV virulence as follows: the fewer RUs (<9) the higher mortality rate in shrimps (Waikhom et al, 2006;Pradeep et al, 2008;Hoa et al, 2012).…”

mentioning

confidence: 99%

Analysis of repeated compound units in ORF94 of white spot syndrome virus isolated from Litopenaeus vannamei from outbreak and non outbreak shrimp farms in Sonora, Mexico

Rodriguez-Anaya

Ibarra‐Gámez

Lares‐Villa

et al. 2016

lajar

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ABSTRACT. White spot syndrome virus (WSSV) is the viral pathogen with the most negative impact on shrimp farming. In Sonora, Litopenaeus vannamei culture has decreased 50% during 2010-2012 due to WSSV outbreaks. The ORF94 has proven to be most useful for the analysis of WSSV variability. Several studies have suggested a correlation between its Repeat Units (RUs) and WSSV virulence as follows: the fewer RUs (<9) the higher mortality rate. In order to support this, we analyzed shrimps from eight farm periods and identified the WSSV-variety present in each one. In outbreaks, the presence of <8 RUs with a dominance of 3 RUs was notable in the last four years. Although it is still not clear how host-virus interactions and pond´s environment affect the transition of the infection just from the presence of the virus in shrimps to an outbreak, these results are a step forward in understanding the pond status and ways of predicting the likelihood of a WSSV infection becoming an outbreak. Keywords: Litopenaeus vannamei, shrimp farming, WSSV, ORF94, repeat unit, outbreak, Mexico.Análisis de las unidades repetidas compuestas en el ORF94 del virus del síndrome de la mancha blanca, aislado de Litopenaeus vannamei en granjas camaroneras con brotes y sin brotes en Sonora, México RESUMEN. El virus del síndrome de la mancha blanca (VSMB) es un patógeno viral que impacta negativamente la producción de camarón de cultivo. En Sonora, el cultivo de camarón Litopenaeus vannamei disminuyó un 50% durante el período 2010-2012 debido a las mortalidades ocasionadas por la presencia del VSMB. El ORF94 es una región minisatélite muy usada para determinar la variabilidad genómica del virus. Varios estudios han sugerido una correlación entre sus unidades repetidas (UR) y la virulencia de VSMB: a menor UR (<9) mayor frecuencia de mortalidad. Para soportar esta hipótesis, se analizaron camarones de ocho ciclos de cultivo y se identificaron variantes del VSMB presente en cada uno de los ciclos. En ciclos con mortalidades masivas se notó la presencia de UR <8 con una dominancia de 3 UR en los últimos cuatro años. Aunque no está muy claro, la interacción VSMB-hospedero y como afectan los parámetros ambientales de las granjas en la transición de la sola presencia del VSMB a causar mortalidades masivas, estos resultados son solo un avance en el entendimiento de como una infección por el virus puede ocasionar un brote de la enfermedad con mortalidades masivas.

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Genotyping of white spot syndrome virus on wild and farm crustaceans from Sonora, Mexico

Cited by 5 publications

References 6 publications

Genotyping WSSV isolates from northwestern Mexican shrimp farms affected by white spot disease outbreaks in 2010-2012

Genotyping WSSV isolates from northwestern Mexican shrimp farms affected by white spot disease outbreaks in 2010-2012

Genetic variations among white spot syndrome virus (WSSV) isolates from shrimp farms in Gujarat, north-west coast of India

Analysis of repeated compound units in ORF94 of white spot syndrome virus isolated from Litopenaeus vannamei from outbreak and non outbreak shrimp farms in Sonora, Mexico

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