Can Sanger sequencing mask a wild-type PRRSV strain after vaccination?
In mixtures containing modified-live vaccine and wild-type PRRSV, ORF5 Sanger sequencing primarily represented the dominant viral population and could mask a minority strain.
In mixtures containing modified-live vaccine and wild-type PRRSV, ORF5 Sanger sequencing primarily represented the dominant viral population and could mask a minority strain.
Problem: When modified-live vaccine and wild-type PRRSV occur in the same sample, an ORF5 consensus sequence may fail to reveal both viral populations.
Methods: The authors prepared nine concentration combinations of a lineage-5 modified-live vaccine virus and a lineage-1A wild-type virus, with three replicates per combination, and performed ORF5 Sanger sequencing.
1. When vaccine-virus concentration was equal to or greater than wild-type concentration, a vaccine-like sequence was obtained in 14 of 15 corresponding samples.
2. A 100% match to the vaccine virus occurred in 12 of those 15 samples, while mixtures containing similar concentrations of both viruses showed greater sequence ambiguity and variability.
3. These in-vitro results indicate that Sanger primarily represents the dominant population and may therefore mask a minority strain; the authors suggest complementary methods such as NGS or vaccine-blocking approaches when coinfection is suspected.
Original publication
Alvarez-Norambuena J, Rovira A, Corzo CA, Kikuti M. In vitro evaluation of PRRSV ORF5 sequences in samples containing PRRSV modified-live vaccine and wild-type strains. Journal of Veterinary Diagnostic Investigation. 2025;37:716–721.