ABSTRACT
BACKGROUND: Recombination is an important contributor to the genetic diversity of most viruses. A reverse genetics system using green fluorescence protein (GFP)- and enhanced GFP (EGFP)-expressing infectious clones was developed to study the requirements for recombination. However, it is still unclear what types of cross-over events occurred to produce the viable offspring. OBJECTIVE: We utilized 454 sequencing to infer recombination events in this system. METHOD: Two porcine reproductive and respiratory syndrome virus (PRRSV) infectious clones, P129-EGFP-97C and P129-GFPm-d (2-6), were co-transfected into HEK-293T cells. P129-EGFP-97C is a fully functional virus that contains a non-fluorescent EGFP. P129-GFPm-d (2-6) is a defective virus but contains a fluorescent GFPm. Successful recombination was evident by the appearance of fully functional progeny virus that expresses fluorescence. Total RNA was extracted from infected cells expressing fluorescence, and the entire fluorescent gene was amplified to prepare an amplicon library for 454 sequencing. RESULTS: Deep sequencing showed that the nucleotide identities changed from ~37% (in the variable region from 21nt to 165nt) to 20% (T289C) to ~38% (456-651nt) then to 100% (672-696nt) when compared to EGFP. The results indicated that cross-over events occurred in three conserved regions (166-288nt, 290-455nt, 652-671nt), which were also supported by sequence alignments. Remarkably, the short conserved region (652-671nt) showed to be a cross-over hotspot. In addition, four cross-over patterns (two single and two double cross-over) might be used to produce viable recombinants. CONCLUSION: The reverse genetics system incorporating the use of high throughput sequencing creates a genetic platform to study the generation of viable recombinant viruses.
ABSTRACT
Porcine reproductive and respiratory syndrome virus (PRRSV) is the most costly viral pathogen facing a modern pig industry. A unique feature of the virus is the ability to cause severe clinical disease and maintain a life-long subclinical infection. Persistence at the population level poses the biggest challenge for the successful control and elimination of the disease. A mechanistic basis for persistence includes the evasion of innate and adaptive immune responses. Recent advances include the study of how the non-structural proteins (nsp's) inhibit the induction of type 1 interferon genes.
