Random nature of coronavirus RNA recombination in the absence of selection pressure

Abstract

RNA-RNA recombination is thought to occur preferentially at certain selected sites and in only a few RNA viruses; the mechanism for these restrictions is unknown. In this paper we report the development of a recombination assay for coronavirus, using polymerase chain reaction, in the absence of selection pressure. Our results showed that within a 1-kb region of the peplomer gene, RNA recombination occurred at almost every potential crossover site. Thus, coronavirus RNA recombination appears to be more random than previously realized. However, after serial passages of the recombinant viruses in tissue culture, the recombination sites among the progeny viruses became clustered in the region which contains the previously reported "hot spot" for coronavirus recombination. These results suggest that RNA recombination is common and random in nature, but only certain recombinants can be selected. Thus, the presence of recombinational "hot spots" for coronavirus or other RNA viruses most likely resulted from selection of certain recombinant viruses and not restriction on the occurrence of RNA recombination. The failure to detect recombinants in other RNA viruses may therefore be due to unfavorable properties of recombinant viruses. This approach can be used to detect recombinants in these viruses.

Recombination in RNA viruses and in virus-resistant transgenic plants.

“…For example, previous studies have identified a recombinational hot-spot region in mouse hepatitis coronavirus (Banner et al, 1990). However, in the absence of selection, initial recombination events were randomly distributed, but after several passages of the recombinant viruses in tissue culture, recombination sites became localized to a restricted region corresponding to the initially identified hot spot (Banner & Lai, 1991). This study suggests that RNA recombination is more frequent than previously thought, and also that the recombinant viruses obtained may reflect the results of selective pressure rather than the mechanism of recombination itself.…”

Comparison of M and N gene sequences distinguishes variation amongst equine arteritis virus isolates

“…Putative leader-body junction sites have also been identified on the genomes of LV (Meulenberg et al, 1993) and LDV (Kuo et al, 1992). Arterivirus replication is similar to that of coronaviruses (de Vries et al, 1990;den Boon et al, 1991) during which RNA recombination, unusual amongst RNA viruses, has been reported to occur (Banner et al, 1990;Banner & Lai, 1991;Keck et al, 1988;Lai et al, 1985;Makino et al, 1986;Wang et al, 1993).…”

Genetic variation in porcine reproductive and respiratory syndrome virus isolates in the midwestern United States

“…The data provide statistical evidence for intragenic recombination in ORFs 2, 3, 4, 5 and 7, but not ORF 6 ( Table 2). The apparent lack of recombination in ORF 6 may be due to selection against recombinant forms, as described in coronaviruses (Banner & Lai, 1991 …”