Abstract
This paper describes the results of two experiments regarding porcine reproductive and respiratory syndrome virus (PRRSV1): the first one studied the existence of bottlenecks in an experimental one-to-one model of transmission in pigs; while the second analysed the differences between viral quasi-species in vaccinated pigs that developed shorter or longer viraemias after natural challenge. Serum samples, as well as the initial inoculum, were deep-sequenced and a viral quasi-species was constructed per sample. For the first experiment, the results consistently reported a reduction in the quasi-species diversity after a transmission event, pointing to the existence of bottlenecks during PRRSV1 transmission. However, despite the identified preferred and un-preferred transmitted variants not being randomly distributed along the virus genome, it was not possible to identify any variant producing a structural change in any viral protein. In contrast, the mutations identified in GP2, nsp9 and M of the second experiment pointed to changes in the amino acid charges and the viral RNA-dependent RNA polymerase structure. The fact that the affected proteins are known targets of the immunity against PRRSV, plus the differential level of neutralizing antibodies present in pigs developing short or long viraemias, suggests that the immune response selected those changes.
Highlights
The comprehension of how the transmission of pathogens occurs is key to the understanding of infectious diseases
The RNA Next Generation Sequencing (NGS) method was suitable for assessing viral quasi‐species Deep sequencing results for PRRSV1, obtained from four un-passaged sera with high viral loads and from four cell culture supernatants of single-passaged samples from the same sera, produced similar viral quasi-species
The results obtained from un-passaged sera or single-passaged isolates only differed at this error rate, which was considered an acceptable bias
Summary
The comprehension of how the transmission of pathogens occurs is key to the understanding of infectious diseases. Successful transmission founders can be thought of as either the result of a non-selective bottleneck—the particles that crossed by chance the portal of entry—, Cortey et al Vet Res (2018) 49:107 or viewed as a selective bottleneck, where only the variants fit enough to cross the portal of entry are transmitted. In the case of RNA viruses, which exist as quasi-species, these different scenarios could imply very different outcomes. A nondirectional unspecific bottleneck would produce a new quasi-species cloud from randomly selected variants. On the other hand, a directional bottleneck would promote the expansion in the recipient host of variants derived from founders fit for transmission that are subsequently selected, since they are not necessarily the fittest, neither the most efficient for replication in the host
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