Homologous genetic recombination in the yellow head complex of nidoviruses infecting Penaeus monodon shrimp

Abstract

Yellow head virus (YHV) is a highly virulent pathogen of Penaeus monodon shrimp. It is one of six known genotypes in the yellow head complex of nidoviruses which also includes mildly pathogenic gill-associated virus (GAV, genotype 2) and four other genotypes (genotypes 3-6) that have been detected only in healthy shrimp. In this study, comparative phylogenetic analyses conducted on replicase- (ORF1b) and glycoprotein- (ORF3) gene amplicons identified 10 putative natural recombinants amongst 28 viruses representing all six genotypes from across the Indo-Pacific region. The approximately 4.6 kb genomic region spanning the two amplicons was sequenced for three putative recombinant viruses from Vietnam (genotype 3/5), the Philippines (genotype 5/2) and Indonesia (genotype 3/2). SimPlot analysis using these and representative parental virus sequences confirmed that each was a recombinant genotype and identified a recombination hotspot in a region just upstream of the ORF1b C-terminus. Maximum-likelihood breakpoint analysis predicted identical crossover positions in the Vietnamese and Indonesian recombinants, and a crossover position 12 nt upstream in the Philippine recombinant. Homologous genetic recombination in the same genome region was also demonstrated in recombinants generated experimentally in shrimp co-infected with YHV and GAV. The high frequency with which natural recombinants were identified indicates that genetic exchange amongst genotypes is occurring commonly in Asia and playing a significant role in expanding the genetic diversity in the yellow head complex. This is the first evidence of genetic recombination in viruses infecting crustaceans and has significant implications for the pathogenesis of infection and diagnosis of these newly emerging invertebrate pathogens.

Identification and Characterization of a Ribose 2′- O -Methyltransferase Encoded by the Ronivirus Branch of Nidovirales

“…GAV and YHV are morphologically indistinguishable, and they are both highly pathogenic for P. monodon (26,27). GAV, as well as the other five genotypes, is an enveloped, rod-shaped, positivesense ssRNA virus with a genome of about 26 kb (23,25,28). In common with other nidoviruses, the 5=-terminal 20 kb of the GAV genome includes two long, overlapping open reading frames (ORFs) and is translated into two large polyproteins, pp1a and pp1ab, via a Ϫ1 ribosomal frameshift (29).…”

Pathogenicity of gill-associated virus and Mourilyan virus during mixed infections of black tiger shrimp (Penaeus monodon)

“…2). However, as reported previously, GAV is far less virulent than YHV for which the LD 50 is typically 10 8 -to 10 9 -fold lower in inocula containing equivalent viral genetic loads (Sittidilokratna et al, 2009a;Wijegoonawardane et al, 2009). Consequently, YHV lethal challenge experiments in which very effective RNAiinduced inhibition of infection was observed employed a virus dose~10 5 -fold lower than was possible for GAV (Yodmuang et al, 2006).…”

“…1) contains a large replicase gene comprising two long reading frames (ORF1a/ORF1b) encoding protease, RNA-dependent RNA polymerase (RdRp), helicase and other conserved enzymic domains, a nucleoprotein gene (ORF2), a polyglycoprotein gene (ORF3) encoding the two envelope glycoproteins (gp64 and gp116) and a small pseudogene (ORF4) Cowley & Walker, 2002;Jitrapakdee et al, 2003). Natural genetic recombination between GAV and other genotypes in the yellow head complex has been reported (Wijegoonawardane et al, 2009).…”

Diseases in marine invertebrates associated with mariculture and commercial fisheries

“…Furthermore, despite this variance in pathogenicity, all the genotypes in the yellow head complex are currently classified by the ICTV as a single species (gill-associated virus), from the genus Okavirus, family Roniviridae, order Nidovirales (OIE, 2013). This is mainly because there is strong evidence of genetic recombination between the different genotypes (Wijegoonawardane et al, 2009). Again similar to WSSV and TSV, YHD is listed as an OIE notifiable disease and as an exotic disease within Europe, EC Council Directive 2006/88/ EC.…”