Abstract
Porcine reproductive and respiratory syndrome virus genotype 2 (PRRSV-2) genetic diversity in the U.S. was assessed using a database comprising 10 years’ worth of sequence data obtained from swine production systems routine monitoring and outbreak investigations. A total of 26,831 ORF5 PRRSV-2 sequences from 34 production systems were included in this analysis. Within group mean genetic distance (i.e. mean proportion of nucleotide differences within ORF5) per year according to herd type was calculated for all PRRSV-2 sequences. The percent nucleotide difference between each sequence and the ORF5 sequences from four commercially available PRRSV-2 vaccines (Ingelvac PRRS MLV, Ingelvac PRRS ATP, Fostera PRRS, and Prevacent PRRS) within the same lineage over time was used to classify sequences in wild-type or vaccine-like. The mean ORF5 genetic distance fluctuated from 0.09 to 0.13, being generally smaller in years in which there was a relative higher frequency of dominant lineage. Vaccine-like sequences comprised about one fourth of sequences obtained through routine monitoring of PRRS. We found that lineage 5 sequences were mostly Ingelvac PRRS MLV-like. Lineage 8 sequences up to 2011 were 62.9% Ingelvac PRRS ATP-like while the remaining were wild-type viruses. From 2012 onwards, 51.9% of lineage 8 sequences were Ingelvac PRRS ATP-like, 45.0% were Fostera PRRS-like, and only 3.2% were wild-type. For lineage 1 sequences, 0.1% and 1.7% of the sequences were Prevacent PRRS-like in 2009–2018 and 2019, respectively. These results suggest that repeated introductions of vaccine-like viruses through use of modified live vaccines might decrease within-lineage viral diversity as vaccine-like strains become more prevalent. Overall, this compilation of private data from routine monitoring provides valuable information on PRRSV viral diversity.
Highlights
Viral evolution plays an important role in the ecology of infectious diseases, for RNA viruses such as Porcine reproductive and respiratory syndrome virus (PRRSV), which is in the Arteriviridae family in the order Nidovirales with a genome 14.9 to 15.5kb in length [1,2]
Data for this project ranged between January, 2009 to December, 2019 was obtained through the Morrison Swine Health Monitoring Project (MSHMP), which is a voluntary initiative in the U.S that monitors PRRS occurrence in the country, while working towards foreign disease preparedness
We observed a mean open reading frame 5 (ORF5) genetic distance fluctuating within the expected range throughout the study period according to the frequency of the predominant lineage, regardless of herd type
Summary
Viral evolution plays an important role in the ecology of infectious diseases, for RNA viruses such as Porcine reproductive and respiratory syndrome virus (PRRSV), which is in the Arteriviridae family in the order Nidovirales with a genome 14.9 to 15.5kb in length [1,2]. During the early 1990’s, two types of PRRSV were isolated for the first time both in Europe and North America. The European strain was named the Lelystad virus and the North American strain as VR2332 [9]. Genotypical differences between the European and North American first isolates led to the classification of PRRSV into two distinct species, Betaarterivirus suid 1 (PRRSV-1) and Betaarterivirus suid 2 (PRRSV-2) [10]. Technological development of PRRSV diagnosis has shifted towards rapid viral identification and characterization through widespread sequencing
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