Temporal dynamics of co-circulating lineages of porcine reproductive and respiratory syndrome virus

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the most important endemic pathogen in the U.S. swine industry. Despite control efforts involving improved biosecurity and different vaccination protocols, the virus continues to circulate and evolve. One of the foremost challenges in its control is high levels of genetic and antigenic diversity. Here, we quantify the co-circulation, emergence and sequential turnover of multiple PRRSV lineages in a single swine-producing region in the United States over a span of 9 years (2009–2017). By classifying over 4,000 PRRSV sequences (open-reading frame 5) into phylogenetic lineages and sub-lineages, we document the ongoing diversification and temporal dynamics of the PRRSV population, including the rapid emergence of a novel sub-lineage that appeared to be absent globally pre-2008. In addition, lineage 9 was the most prevalent lineage from 2009 to 2010, but its occurrence fell to 0.5% of all sequences identified per year after 2014, coinciding with the emergence or re-emergence of lineage 1 as the dominant lineage. The sequential dominance of different lineages, as well as three different sub-lineages within lineage 1, is consistent with the immune-mediated selection hypothesis for the sequential turnover in the dominant lineage. As host populations build immunity through natural infection or vaccination toward the most common variant, this dominant (sub-) lineage may be replaced by an emerging variant to which the population is more susceptible. An analysis of patterns of non- synonymous and synonymous mutations revealed evidence of positive selection on immunologically important regions of the genome, further supporting the potential that immune-mediated selection shapes the evolutionary and epidemiological dynamics for this virus. This has important implications for patterns of emergence and re-emergence of genetic variants of PRRSV that have negative impacts on the swine industry. Constant surveillance on PRRSV occurrence is crucial to a better understanding of the epidemiological and evolutionary dynamics of co-circulating viral lineages. Further studies utilizing whole genome sequencing and exploring the extent of cross-immunity between heterologous PRRS viruses could shed further light on PRRSV immunological response and aid in developing strategies that might be able to diminish disease impact

Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study

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

Phylogenetic Structure and Sequential Dominance of Sub-Lineages of PRRSV Type-2 Lineage 1 in the United States

The genetic diversity and frequent emergence of novel genetic variants of porcine reproductive and respiratory syndrome virus type-2 (PRRSV) hinders control efforts, yet drivers of macro-evolutionary patterns of PRRSV remain poorly documented. Utilizing a comprehensive database of >20,000 orf5 sequences, our objective was to classify variants according to the phylogenetic structure of PRRSV co-circulating in the U.S., quantify evolutionary dynamics of sub-lineage emergence, and describe potential antigenic differences among sub-lineages. We subdivided the most prevalent lineage (Lineage 1, accounting for approximately 60% of available sequences) into eight sub-lineages. Bayesian coalescent SkyGrid models were used to estimate each sub-lineage’s effective population size over time. We show that a new sub-lineage emerged every 1 to 4 years and that the time between emergence and peak population size was 4.5 years on average (range: 2–8 years). A pattern of sequential dominance of different sub-lineages was identified, with a new dominant sub-lineage replacing its predecessor approximately every 3 years. Consensus amino acid sequences for each sub-lineage differed in key GP5 sites related to host immunity, suggesting that sub-lineage turnover may be linked to immune-mediated competition. This has important implications for understanding drivers of genetic diversity and emergence of new PRRSV variants in the U.S

Potential novel N-glycosylation patterns associated with the emergence of new genetic variants of PRRSV-2 in the U.S.

Glycosylation of proteins is a post-translational process where oligosaccharides are attached to proteins, potentially altering their folding, epitope availability, and immune recognition. In Porcine reproductive and respiratory syndrome virus-type 2 (PRRSV-2), positive selection pressure acts on amino acid sites potentially associated with immune escape through glycan shielding. Here, we describe the patterns of potential N-glycosylation sites over time and across different phylogenetic lineages of PRRSV-2 to better understand how these may contribute to patterns of coexistence and emergence of different lineages. We screened 19,179 PRRSV GP5 sequences (2004-2021) in silico for potential N-glycosylated sites. The emergence of novel combinations of N-glycosylated sites coincided with past PRRSV epidemics in the U.S. For lineage L1A, glycosylation at residues 32, 33, 44, 51, and 57 first appeared in 2012, but represented &gt;62% of all L1A sequences by 2015, coinciding with the emergence of the L1A 1-7-4 strain that increased in prevalence from 8 to 86% of all L1A sequences from 2012 to 2015. The L1C 1-4-4 strain that emerged in 2020 also had a distinct N-glycosylation pattern (residues 32, 33, 44, and 51). From 2020 to 2021, this pattern was responsible for 44-47% of the L1C sequences, contrasting to &lt;5% in years prior. Our findings support the hypothesis that antigenic evolution contributes to the sequential dominance of different PRRSV strains and that N-glycosylation patterns may partially account for antigenic differences amongst strains. Further studies on glycosylation and its effect on PRRSV GP5 folding are needed to further understand how glycosylation patterns shape PRRSV occurrence

Infecção pelo complexo Mycobacterium tuberculosis em carneiro da Barbária (Ammotragus lervia) no Zoológico de Curitiba, sul do Brasil: relato de caso

A tuberculose é uma das doenças mundiais de notificação obrigatória mais importantes causada pelo complexo Mycobacterium tuberculosis que pode infectar pessoas e animais. A morte repentina de um carneiro da Barbária no Zoológico de Curitiba, que apresentou nódulos multifocais no pulmão à necropsia, levantou a suspeita de tuberculose. Foi realizada a Reação em Cadeia da Polimerase Quantitativa (qPCR) de fragmentos de órgãos e fluido. A qPCR detectou a presença do complexo M. tuberculosis nas amostras de pulmão. Este estudo relata a infecção pelo complexo M. tuberculosis no carneiro da Barbária, uma zoonose de grande relevância para a saúde pública, ressaltando-se a necessidade da implementação de medidas de prevenção. Além disso, pode prover um melhor entendimento sobre conservação de espécies, ocorrência e transmissão de doenças em cativeiro, potencial reservatório e impacto na saúde pública para visitantes e funcionários dos zoológicos.Tuberculosis is one of the most important mandatory notification diseases in the world caused by bacteria of the Mycobacterium tuberculosis complex, infecting both humans and animals. A sudden death of a Barbary sheep in Curitiba Zoo, and presence of multifocal nodules in lungs at necropsy raised suspicion of tuberculosis. Quantitative polymerase chain reaction (qPCR) from organs and fluid was performed and detected M. tuberculosis complex in a lung sample. This research reports the M. tuberculosis complex infection in Barbary sheep, a zoonosis of great relevance to public health and emphasizes the need to implement prevention measures. Furthermore, the research may provide a better understanding for species conservation, occurrence and transmission of diseases in captivity, reservoir potential and public health impact to zoo personnel and visitors.

A stage structured mosquito model incorporating effects of precipitation and daily temperature fluctuations

An outbreak of dengue fever in Guangdong province in 2014 was the most serious outbreak ever recorded in China. Given the known positive correlation between the abundance of mosquitoes and the number of dengue fever cases, a stagestructured mosquito model was developed to investigate the cause of the large abundance of mosquitoes in 2014 and its implications for outbreaks of the disease. Data on the Breteau index (number of containers positive for larvae per 100 premises investigated), temperature and precipitation were used for model fitting. The egg laying rate, the development rate and the mortality rates of immatures and adults were obtained from the estimated parameters. Moreover, effects of daily fluctuations of temperature on these parameters were obtained and the effects of temperature and precipitation were analyzed by simulations. Our results indicated that the abundance of mosquitoes depended not only on the total annual precipitation but also on the distribution of the precipitation. The daily mean temperature had a nonlinear relationship with the abundance of mosquitoes, and large diurnal temperature differences can reduce the abundance of mosquitoes. In addition, effects of increasing precipitation and temperature were interdependent. Our findings suggest that the large abundance of mosquitoes in 2014 was mainly caused by the distribution of the precipitation. In the perspective of mosquito control, our results reveal that it is better to clear water early and spray insecticide between April and August in case of limited resources