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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.

Bayesian space-time regression models are helpful tools to describe and predict the distribution of infectious disease outbreaks and to delineate high-risk areas for disease control. In these models, structured and unstructured spatial and temporal effects account for various forms of non-independence amongst case counts across spatial units. Structured spatial effects capture correlations in case counts amongst neighboring provinces arising from shared risk factors or population connectivity. For highly mobile populations, spatial adjacency is an imperfect measure of connectivity due to long-distance movement, but we often lack data on host movements. Phylogeographic models inferring routes of viral dissemination across a region could serve as a proxy for patterns of population connectivity. The objective of this study was to investigate whether the effects of population connectivity in space-time regressions of case counts were better captured by spatial adjacency or by inferences from phylogeographic analyses. To compare these two approaches, we used foot-and-mouth disease virus (FMDV) outbreak data from across Vietnam as an example. We identified that accounting for virus movement through phylogeographic analysis serves as a better proxy for population connectivity than spatial adjacency in spatial-temporal risk models. This approach may contribute to design surveillance activities in countries lacking movement data.

Modeling the windborne transmission of aerosolized pathogens is challenging. We adapted an atmospheric dispersion model (ADM) to simulate the windborne dispersion of porcine reproductive and respiratory syndrome virus (PRRSv) between swine farms. This work focuses on determining ADM applicable parameter values for PRRSv through a literature and expert opinion-based approach. The parameters included epidemiological features of PRRSv, characteristics of the aerosolized particles, and survival of aerosolized virus in relation to key meteorological features. A case study was undertaken to perform a sensitivity analysis on key parameters. Farms experiencing ongoing PRRSv outbreaks were assigned as particle emitting sources. The wind data from the North American Mesoscale Forecast System was used to simulate dispersion. The risk was estimated semi-quantitatively based on the median daily deposition of particles and the distance to the closest emitting farm. Among the parameters tested, the ADM was most sensitive to the number of particles emitted, followed by the model runtime, and the release height was the least sensitive. Farms within 25 km from an emitting farm were at the highest risk; with 53.66% being within 10 km. An ADM-based risk estimation of windborne transmission of PRRSv may inform optimum time intervals for air sampling, plan preventive measures, and aid in ruling out the windborne dispersion in outbreak investigations.

African buffalo are the natural reservoirs of the SAT serotypes of foot-and-mouth disease virus (FMDV) in sub-Saharan Africa. Most buffalo are exposed to multiple FMDV serotypes early in life, and a proportion of them become persistently infected carriers. Understanding the genetic diversity and evolution of FMDV in carrier animals is critical to elucidate how FMDV persists in buffalo populations. In this study, we obtained oropharyngeal (OPF) fluid from naturally infected African buffalo, and characterized the genetic diversity of FMDV. Out of 54 FMDV-positive OPF, 5 were co-infected with SAT1 and SAT2 serotypes. From the five co-infected buffalo, we obtained eighty-nine plaque-purified isolates. Isolates obtained directly from OPF and plaque purification were sequenced using next-generation sequencing (NGS). Phylogenetic analyses of the sequences obtained from recombination-free protein-coding regions revealed a discrepancy in the topology of capsid proteins and non-structural proteins. Despite the high divergence in the capsid phylogeny between SAT1 and SAT2 serotypes, viruses from different serotypes that were collected from the same host had a high genetic similarity in non-structural protein-coding regions P2 and P3, suggesting interserotypic recombination. In two of the SAT1 and SAT2 co-infected buffalo identified at the first passage of viral isolation, the plaque-derived SAT2 genomes were distinctly grouped in two different genotypes. These genotypes were not initially detected with the NGS from the first passage (non-purified) virus isolation sample. In one animal with two SAT2 haplotypes, one plaque-derived chimeric sequence was found. These findings demonstrate within-host evolution through recombination and point mutation contributing to broad viral diversity in the wildlife reservoir. These mechanisms may be critical to FMDV persistence at the individual animal and population levels, and may contribute to the emergence of new viruses that have the ability to spill-over to livestock and other wildlife species.

Porcine reproductive and respiratory syndrome (PRRS) is an economically devastating disease of swine in many parts of the world. Porcine reproductive and respiratory syndrome virus (PRRSV) type 1 is endemic in Europe, and prevalence of the subtypes differ spatially. In this study, we investigated a severe PRRS outbreak reported in 30 farms located in eastern Russia that belong to a large swine production company in the region that was also experiencing a pseudorabies outbreak in the system. Data included 28 ORF5 sequences from samples across 18 of the 25 infected sites, reverse transcriptase real-time polymerase chain reaction (RT-qPCR) results from diagnostic testing, reports of clinical signs, and animal movement records. We observed that the outbreak was due to two distinct variants of wildtype PRRSV type 1 subtype 1 with an average genetic distance of 15%. Results suggest that the wildtype PRRSV variants were introduced into the region around 2019, before affecting this production system (i.e., sow farms, nurseries, and finisher farms). Clinical signs did not differ between the variants, but they did differ by stage of pig production. Biosecurity lapses, including movement of animals from infected farms contributed to disease spread.

The genetic diversity of foot-and-mouth disease virus (FMDV) poses a challenge to the successful control of the disease, and it is important to identify the emergence of different strains in endemic settings. The objective of this study was to evaluate the sampling of clinically healthy livestock at slaughterhouses as a strategy for genomic FMDV surveillance. Serum samples ( n = 11,875) and oropharyngeal fluid (OPF) samples ( n = 5045) were collected from clinically healthy cattle and buffalo on farms in eight provinces in southern and northern Vietnam (2015-2019) to characterize viral diversity. Outbreak sequences were collected between 2009 and 2019. In two slaughterhouses in southern Vietnam, 1200 serum and OPF samples were collected from clinically healthy cattle and buffalo (2017 to 2019) as a pilot study on the use of slaughterhouses as sentinel points in surveillance. FMDV VP1 sequences were analyzed using discriminant principal component analysis and time-scaled phylodynamic trees. Six of seven serotype-O and -A clusters circulating in southern Vietnam between 2017-2019 were detected at least once in slaughterhouses, sometimes pre-dating outbreak sequences associated with the same cluster by 4-6 months. Routine sampling at slaughterhouses may provide a timely and efficient strategy for genomic surveillance to identify circulating and emerging FMDV strains.