Predicted RNA Folding Suggests PRRSV Major and Heteroclite Subgenomic Transcripts Result from Polymerase Switching at Unpaired Nucleotides
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Porcine reproductive and respiratory syndrome virus (PRRSV) has emerged as a major disease of swine worldwide, causing stillbirths and abortions in pregnant sows and reproductive failure in young swine. Even though modified-live vaccines have been used for many years, PRRSV continues to thrive and spread. Previous work has shown that one of the mechanisms which PRRSV uses to evade host defenses is to undergo viral recombination at a high frequency (Yuan et al 1999). The high frequency nidovirus recombination mechanism occurs by discontinuous transcription (Baric et al 1987) that appears to be guided by basepairing between sense and antisense strands at sites of secondary structure. Support for this model has been recently been obtained for equine arteritis virus subgenomic (sg) mRNAs, which utilize a common leader body junction site sequence which undergoes sequential basepairing at two distinct sites on the genome of the opposite strand (Marle et al 1999). In this report, we document that besides standard PRRSV sg mRNAs, other subgenomic RNAs, which utilize alternative junction sites, are transcribed during PRRSV infection. We also provide evidence that these novel subgenomic RNAs are produced by a similar basepairing mechanism, yet the newly identified RNAs appear to be generated in a less-stringent manner. Thus, the PRRSV polymerase complex appears to be more promiscuous than other nidoviruses complexes in deciding where and when to switch templates during transcription. The identification of these novel subgenomic RNAs during normal PRRSV infection will allow further characterization of the specific mechanism for nidovirus discontinuous transcription.
KeywordsRespiratory Syndrome Virus Junction Site Mouse Hepatitis Virus Negative Strand Subgenomic RNAs
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