Detection and Phylogenetic Analyses of Taura Syndrome Virus from Archived Davidson’s-Fixed Paraffin-Embedded Shrimp Tissue

Taura syndrome is a World Organization for Animal Health (OIE)-listed disease of marine shrimp that is caused by Taura syndrome virus (TSV), a single-stranded RNA virus. Here we demonstrate the utility of using 15-year-old archived Davidson’s-fixed paraffin-embedded (DFPE) shrimp tissues for TSV detection and phylogenetic analyses. Total RNA was isolated from known TSV-infected DFPE tissues using three commercially available kits and the purity and ability to detect TSV in the isolated RNA were compared. TSV was successfully detected through RT-qPCR in all the tested samples. Among the TSV-specific primers screened through RT-PCR, primer pair TSV-20 for the RNA-dependent RNA polymerase (RdRp), primers TSV-15 and TSV-16 for the capsid protein gene VP2 and primers TSV-5 for the capsid protein gene VP1 amplified the highest number of samples. To assess the phylogenetic relation among different TSV isolates, the VP1 gene was amplified and sequenced in overlapping segments. Concatenated sequences from smaller fragments were taken for phylogenetic analyses. The results showed that the TSV isolates from this study generally clustered with homologous isolates from the corresponding geographical regions indicating RNA derived from DFPE tissues can be used for pathogen detection and retrospective analyses. The ability to perform genomic characterization from archived tissue will expedite pathogen discovery, development of diagnostic tools and prevent disease spread in shrimp and potentially other aquaculture species worldwide.

Pemantauan Virus Dengan Metode PCR (Polymerase Chain Reaction) Di Pantai Utara Jawa Timur [Monitoring Virus By PCR Method (Polymerase Chain Reaction) In North Coast, East Java]

The disease most dangerous for the cultivation activity is virus. Viruses are organisms subseluler that contain only nucleic acid (RNA or DNA) as genetic material. Koi Herpes Virus is one type of virus that causes mortality in cultured Cyprinids. KHV disease in Indonesia started in Blitar, East Java on March 2002 because the entry of imported koi fish that carry the virus KHV, while mortality prosentase could reach 80% - 85%, which causes loss of about 5 billion rupiah. In addition of KHV, there are several types of viral diseases in shrimp is White Spot Syndrome Virus (WSSV), Taura Syndrome Virus (TSV), dan Yellow Head Virus (YHV). Disease can cause losses in farming activities, such as WSSV. WSSV is an endemic disease since 1995. disease WSSV is exotic viral disease that attacks the shrimp monodon in 1998/1999 has resulted in decreased production of very large, so the Indonesian shrimp exports down 33,000 tons. Treatment of viral diseases is difficult because the virus resistant to certain antibiotics and chemical compounds. Therefore, prevention needs to be done, one through the monitoring activities conducted on the northern coast of East Java. The method implemented is monitoring in location and identification of viruses by PCR (Polymerase Chain Reaction). Monitoring in location includes water quality measurements and sampling. Identification of virus carried by IQ 2000TM. The identification procedure includes extraction, amplification and electrophoresis. Regional monitoring conducted on the northern coast of East Java includes Gresik, Lamongan, Tuban, Bangkalan, Sampang, Pamekasan, and Sumenep. Water quality at locations quite well. Results activities of monitoring on the northern coast of East Java is disease White Spot Syndrome Virus (WSSV) was found positive in several locations: Gresik, Lamongan and Tuban, while the virus Taura Syndrome Virus (TSV) and Yellow Head Virus (YHV) was not found at all locations . In tilapia, disease Koi Herpes Virus (KHV) was found positive in Tuban.

Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome

Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin. The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics. The IRES rearranges from extended to bent to extended conformations. This inchworm-like movement is coupled with ribosomal inter-subunit rotation and 40S head swivel. eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site. Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center. This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites. The structures suggest missing links in our understanding of tRNA translocation.