0772f6da39332ee33018bfa1592cf747 pmc_10535563.pdf 4a362d2048e918d8c0ad045ee2b234d0b90ccb2a pmc_10535563.pdf 6ddc0750d35d07d4fdb7635858befb3abce273029ec095a86d99c195a932a4f1 pmc_10535563.pdf Title: Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study Subject: Describing PRRSV whole-genome viral diversity data over time within the host and within-farm is crucial for a better understanding of viral evolution and its implications. A cohort study was conducted at one naïve farrow-to-wean farm reporting a PRRSV outbreak. All piglets 3–5 days of age (DOA) born to mass-exposed sows through live virus inoculation with the recently introduced wild-type virus two weeks prior were sampled and followed up at 17–19 DOA. Samples from 127 piglets were individually tested for PRRSV by RT-PCR and 100 sequences were generated using Oxford Nanopore Technologies chemistry. Female piglets had significantly higher median Ct values than males (15.5 vs. 13.7, Kruskal–Wallis p < 0.001) at 3–5 DOA. A 52.8% mortality between sampling points was found, and the odds of dying by 17–19 DOA decreased with every one unit increase in Ct values at 3–5 DOA (OR = 0.76, 95% CI 0.61–0.94, p = 0.01). Although the within-pig percent nucleotide identity was overall high (99.7%) between 3–5 DOA and 17–19 DOA samples, ORFs 4 and 5a showed much lower identities (97.26% and 98.53%, respectively). When looking solely at ORF5, 62% of the sequences were identical to the 3–5 DOA consensus. Ten and eight regions showed increased nucleotide and amino acid genetic diversity, respectively, all found throughout ORFs 2a/2b, 4, 5a/5, 6, and 7. Keywords: porcine reproductive and respiratory syndrome; genetic variation; whole-genome sequencing; molecular epidemiology Author: Mariana Kikuti, Carles Vilalta, Juan Sanhueza, Nakarin Pamornchainavakul, Jessica Kevill, My Yang, Igor A. D. Paploski, Tatiana Lenskaia, Nkechi M. Odogwu, Ross Kiehne, Kimberly VanderWaal, Declan Schroeder and Cesar A. 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D. Paploski, Tatiana Lenskaia, Nkechi M. Odogwu, Ross Kiehne, Kimberly VanderWaal, Declan Schroeder and Cesar A. Corzo Subject: Describing PRRSV whole-genome viral diversity data over time within the host and within-farm is crucial for a better understanding of viral evolution and its implications. A cohort study was conducted at one naïve farrow-to-wean farm reporting a PRRSV outbreak. All piglets 3 5 days of age (DOA) born to mass-exposed sows through live virus inoculation with the recently introduced wild-type virus two weeks prior were sampled and followed up at 17 19 DOA. Samples from 127 piglets were individually tested for PRRSV by RT-PCR and 100 sequences were generated using Oxford Nanopore Technologies chemistry. Female piglets had significantly higher median Ct values than males (15.5 vs. 13.7, Kruskal Wallis p < 0.001) at 3 5 DOA. A 52.8% mortality between sampling points was found, and the odds of dying by 17 19 DOA decreased with every one unit increase in Ct values at 3 5 DOA (OR = 0.76, 95% CI 0.61 0.94, p = 0.01). Although the within-pig percent nucleotide identity was overall high (99.7%) between 3 5 DOA and 17 19 DOA samples, ORFs 4 and 5a showed much lower identities (97.26% and 98.53%, respectively). When looking solely at ORF5, 62% of the sequences were identical to the 3 5 DOA consensus. Ten and eight regions showed increased nucleotide and amino acid genetic diversity, respectively, all found throughout ORFs 2a/2b, 4, 5a/5, 6, and 7. 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