Biology subjects

Herrera da Silva, J. P.

Publications and source records attributed to Herrera da Silva, J. P..

4 recordsLinked to original sources

bioRxiv2026

Porcine epidemic diarrhea virus Whole-Genome Diversity Reveals Divergence of Contemporary Populations in the United States

Porcine epidemic diarrhea virus (PEDV) was introduced into the United States (USA) in 2013 and has circulated ever since. PEDV causes significant losses in the swine industry, with the greatest impact observed during the first years following its introduction into the country. However, the evolutionary dynamics of the virus remain underexplored. Recently, analyses of the Spike protein subunit S1 suggested that the PEDV population currently circulating in the USA represents a fraction of its historical diversity and comprises only two clades restricted to specific geographic regions. These observations were based on a limited set of S1 sequences. Furthermore, our understanding of evolutionary dynamics at the genomic level is even more limited, as complete PEDV genomes have not been generated since 2017. Here, we characterized the evolutionary dynamics of PEDV populations in the USA using complete genomes and assessed the contribution of different evolutionary mechanisms to shaping population structure. We analyzed 338 complete genomes, of which 25 were obtained in this study, together with 623 Spike S1 sequences, of which 41 were obtained in this study. All sequences obtained in this study were assigned to the non-S-INDEL strain. No S-INDEL sequences were recovered in this study, although these viruses continue to circulate in the country. Our analyses revealed that most sequences sampled after 2023 formed a monophyletic clade divergent from sequences collected in previous years, suggesting an ongoing temporal population structuring. Population structure analyses further supported evidence of population differentiation over time. Recombination analyses indicated that sequences belonging to the contemporary clade shared a single recombination event, suggesting that this clade may have emerged through recombination. Time-scaled S1 phylogenies were consistent with previous findings, supporting the circulation of only two contemporary clades; however, one of these clades was detected for the first time outside its previously reported geographic range. Our findings document temporal genetic differentiation in US PEDV populations, consistent with continued viral evolution, and broaden the known geographic distribution of contemporary S1 clades. These results highlight the value of continued genomic surveillance to monitor changes in PEDV diversity and distribution and provide sequence data to inform vaccine research.

microbiology↗

bioRxiv2026

Shifts in Genetic Diversity of Porcine Reproductive and Respiratory Syndrome Virus 2 in Vietnam Before and After African Swine Fever: Increased Diversity and Novel Sub-lineages

Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) remains one of the most important transboundary pathogens affecting swine production in Vietnam; however, it remains poorly understood how long-term evolutionary dynamics were impacted by the African swine fever (ASF) epidemic, a period of time where swine population demographics and movement were heavily perturbed. We investigated the molecular epidemiology, evolutionary history, and phylogeographic dynamics of PRRSV-2 circulating in Vietnam between 2007 and 2024 by integrating 366 Vietnamese ORF5 sequences with a globally curated lineage reference. Maximum-likelihood phylogenetic, Bayesian phylodynamic, and discrete phylogeographic analyses revealed that the Vietnamese PRRSV-2 population underwent substantial reshaping after the ASF epidemic, shifting from a predominantly endemic sub-lineage L8E population to a genetically diverse viral community comprising multiple established and newly emerging sub-lineages. Despite these epidemiological changes, the endemic sub-lineage L8E population maintained a relatively stable evolutionary rate across the pre- and post-ASF periods, suggesting that ASF reshaped viral population structure rather than intrinsic evolutionary dynamics. Two previously unclassified viral clusters circulating in Vietnam and Thailand fulfilled all criteria for formal designation and were recognized as the novel sub-lineages L1M and L10B by the International PRRSV-2 Nomenclature Consortium. Phylogeographic reconstruction further demonstrated contrasting transmission patterns among major sub-lineages, including long-term endemic persistence of L8E, repeated unidirectional introductions of sub-lineages L1M and L10B from Thailand, and bidirectional transpacific dissemination of sub-lineage L1A linking Southeast Asia and North America. Collectively, these findings demonstrate that the ASF epidemic coincided with a fundamental reshaping of the PRRSV-2 epidemiological landscape in Vietnam while revealing Southeast Asia as an active center of ongoing viral diversification. This study provides an updated evolutionary framework for PRRSV-2 surveillance and highlights the importance of continuous genomic monitoring and regional collaboration for the early detection and control of emerging transboundary variants.

genetics↗

bioRxiv2026

Timing the regional spread of PRRSV-2 variants across the United States

Porcine Reproductive and Respiratory Syndrome Virus 2 (PRRSV-2) represents a major threat to the global swine industry. The epidemiological dynamics of PRRSV-2 are characterized by the recurrent annual emergence of dozens of variants. Long-distance spread of PRRSV-2 is largely driven by animal shipments. Spatiotemporal dynamics of PRRSV-2 in the USA have been explored; however, how fast variants spread to new regions after their emergence remains unclear, and this information could improve preparedness. To address this, we analyzed 14,835 sequences, retrieved from the Morrison Swine Health Monitoring Project (MSHMP), representing 156 variants sampled from 2015 to 2024, covering the five major swine-producing regions in the USA: the Upper Midwest (UM), Lower Midwest (LM), Atlantic Seaboard (AS), Northeast (NE), and Great Plains (GP). Time to spread was assessed using the time-to-dispersal event analysis and waiting time analyses. Genetic diversity was measured using Hill numbers. The UM had the highest variant richness (n=123), followed by the LM (n=47), AS (n=35), NE (n=45), and GP (n=38). Of the 62 variants that initially emerged in the UM, 17 later spread to other regions. The UM also received the highest number of variant introductions (n=24), followed by LM (n=14), NE (n=14), AS (n=4), and GP (n=7), highlighting regional differences in connectivity and risk. Our results suggest faster dispersal corridors among interior regions (e.g., GP to UM and LM to UM, [~]1.2-2.0 years) and slower for coast to interior pathways (AS to interior, [~]2-3 years). These findings may help anticipate the risk of PRRSV-2 variant introduction and provide more accurate dispersal time estimates, which are useful for improving epidemiological models and disease preparedness.

ecology↗

bioRxiv2025

Evolution of ssDNA plant viruses in the natural environment - a journey through time

Begomoviruses pose a major threat to food security, particularly in developing countries. These small ssDNA viruses exhibit substitution rates comparable to those of RNA viruses. The temporal dynamics of begomoviruses in non-agricultural environments have been largely overlooked, and little is known about how these viruses evolve in the absence of anthropogenic influence. In this study, we investigated the temporal dynamics of begomoviruses in a small fragment of regenerating Atlantic Forest area in the state of Minas Gerais, Brazil. Samples of Sida acuta, a wild plant native from South America, were collected at the same location over a 12-year period (2011-2022). Five distinct begomoviruses were detected infecting this host: OxYVV, SiYLCV, SimMV, MaYVV, and SiMV. OxYVV and SimMV were subdivided into multiple variants, revealing their potential as reservoirs of viral biodiversity. Several shifts in species and variant composition were observed in the viral community over time, with the most drastic change occurring in 2016, when SiYLCV outnumbered OxYVV. The reasons behind this turnover remain uncertain, but the most compelling clues point to a population expansion of SiYLCV. We detected a strong temporal signal in two of the most abundant viruses (OxYVV and SiYLCV), which allowed us to calibrate molecular clocks and estimate substitution rates for both of them. Our results indicate that, even in the natural environment, begomoviruses can evolve at rates similar to those reported in agricultural systems.

microbiology↗