Title

Yellow Head Virus: Transmission and Genome Analyses

Author

Hongwei Ma

Date of Award

2008

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Coastal Sciences, Gulf Coast Research Laboratory

First Advisor

Robin M. Overstreet

Advisor Department

Coastal Sciences, Gulf Coast Research Laboratory

Abstract

Yellow head virus (YHV) is an important pathogen to shrimp aquaculture. Among 13 species of naturally YHV-negative crustaceans in the Mississippi coastal area, the daggerblade grass shrimp, Palaemonetes pugio , and the blue crab, Callinectes sapidus , were tested for potential reservoir and carrier hosts of YHV using PCR and real time PCR. The YHV replicated in the daggerblade grass shrimp, and was still detectable on 36 d post-inoculation, causing 8% mortality after injection. However, YHV did not replicate in the blue crab. These data suggest that the daggerblade grass shrimp could act as a reservoir host for YHV. Storage conditions of hemolymph samples containing YHV may result in a decline of virus or exhibit false-negative results in viral detection. The YHV-positive hemolymph was stored at either 4 or 25°C for a 6-d period, the viral load number at 4°C was not significantly different from that stored at 25°C. The only difference was between the samples stored for 6-d at either 4 or 25°C and those stored at -80°C, suggesting that shrimp hemolymph can be stored at either 4 or 25°C for 3-5 d without a significant reduction in measured YHV RNA levels. The whole genome of 3 isolates in Penaeus monodon obtained from Thailand in 1992, 1995, and 1999 was sequenced. The only indel event in the coding region was located in the 5' end of ORF1a, containing a segment of 12 nt. Other indels occurred in the non-coding region. The 3' untranslated region (UTR) forms a putative pseudoknot, with an octonucleotide motif being the counterpart in the 3' UTR of Coronavirus . The phylogeny of Nidovirales was reconstructed based on 48 nidovirus proteome sequences, demonstrating a consistency with the contemporary phylogeny. Recombination in RNA viruses plays a major role in virus diversity and evolution. Seven recombination events were detected among the 4 YHV genomes with high statistical support. The divergence times for the most recent common ancestor of the YHV lineage were dated back to 1970-1980s based on 3 recombination-free data sets. These values were consistent with shrimp culture practice in Asia.