Alvin Crespo-Bellido

American mink (Neogale vison) are susceptible to SARS-CoV-2, but little is known about virus circulation in mink since 2021. Here, in the first active surveillance study of SARS-CoV-2 in apparently healthy farmed mink in the United States, we find a ~0.9% (760/85,656) RT-PCR positivity rate among nasal swabs collected in 18 farms across six states during 2022–2023. Phylogenetic analysis of 293 viral genome sequences shows that human-adapted SARS-CoV-2 variants (e.g., Omicron) repeatedly spill over into mink. Surprisingly, the detection of a Delta lineage virus (AY.39) on a mink farm four months after its last detection in humans within the same state suggests prolonged unsampled transmission. The spread of mink-adapted AY.39 viruses from a mink farm to neighboring free-ranging white-tailed deer represents a rare instance of SARS-CoV-2 transmission between livestock and wildlife. These findings demonstrate the value of active surveillance for identifying subclinical infections and interspecies transmission between humans, mink, and wildlife.

Highly pathogenic avian influenza (HPAI) virus H5N1 clade 2.3.4.4b was introduced into North America in 2021. In 2022, clade 2.3.4.4b spilled into domestic poultry in the United States (U.S.), resulting in the largest HPAI outbreak in U.S. history. In December 2023, H5N1 2.3.4.4b was detected on an upland game bird farm in Pennsylvania. History, clinical signs, and gross lesions were suggestive of marble spleen disease. However, HPAI was identified by real-time reverse-transcriptase polymerase chain reaction; gene sequencing confirmed genotype C2.1 with phylodynamic analyses providing evidence of a wild bird introduction. Predictive mathematical modeling estimated the time of virus introduction onto the farm (15 days (95% C.I., 11–23) before the date of confirmed detection) being similar or longer than previously described for domestic poultry. Although bioexclusion measures were unable to prevent the initial exposure due to industry rearing practices, biocontainment procedures appeared to prevent spread. The lessons learned from this case may be important for other animal agriculture commodities, especially those species that are infrequently handled or observed and may have inaccurately calculated mortality levels. This well-characterized outbreak and other experiences with natural infection should be taken as opportunities to better understand the field dynamics of this virus.

Summary: Since 2021, highly pathogenic avian influenza viruses (HPAIVs) belonging to H5N1 clade 2.3.4.4b have circulated widely in North American wild birds and repeatedly spilled over into mammals. In 2025, the first H5N1-associated deaths in humans were recorded in the Western hemisphere, raising questions about how the ongoing evolution of the virus in wild birds impacts spillover risk. Here, our analysis of 21,471 H5N1 genomes identified an evolutionary shift in mid-2024, driven by interhemispheric migration from Asia and reassortment with new antigens. The genotypes that dominated the early years of North America’s H5N1 epizootic traced their ancestry back to Europe, but Asia was the source of new “D1.1” genotype viruses that (a) spread faster, (b) have higher reassortment potential, (c) a broader host range, (d) repeatedly spill over to bovines, and (e) cause severe disease in humans, including non-farm workers.

Sweepoviruses are single stranded DNA viruses in the genus Begomovirus which infect sweet potato ( Ipomoea batatas ). The Geminiviridae and Tolecusatellitidae study group of the International Committee for the Taxonomy of Viruses (ICTV) specifies a percent nucleotide identity threshold for species demarcation, but these criteria have not been systematically applied across sweepoviruses. Simultaneously, ICTV aims for species to be monophyletic. A maximum likelihood phylogeny of 398 full genome sequences of sweepoviruses only supported the monophyly of four of 14 ICTV-recognized species. Another species has a well-supported paraphyly, which is a legitimate biological possibility for these viruses. These analyses revealed a distinct difference in isolates of the sweet potato leaf curl Hubei virus ( Begomovirus ipomoeahubeiense ) versus isolates of all other species, a result substantiated by previous findings that this species is the product of recombination with a non-sweepovirus begomovirus. We found extensive recombination among the sweepoviruses, including across species boundaries, which is at odds with the goal of monophyletic species. Reclassifying the current sequences of sweepoviruses under the ICTV-specified species delineation would cut the number of sweepovirus species in half, and only five of these seven species could be considered monophyletic. Our analyses highlight the failure of a percent nucleotide identity threshold to create monophyletic species. The particularly low threshold for novel species in Begomovirus also conflates lineages that are mostly separately evolving into a single species, leading to average percent nucleotide identities within species that are less than the threshold for being members of the same species (<91%).

Genomic sequencing of re-emerging highly pathogenic avian influenza A(H5N1) virus detected in Argentina in February 2025 revealed novel triple-reassortant viruses containing gene segments from Eurasian H5N1 and low pathogenic viruses from South and North American lineages. These findings underscore continued evolution and diversification of clade 2.3.4.4b H5N1 in the Americas.

Begomoviruses are globally distributed plant pathogens that significantly limit crop production. These viruses are traditionally described according to phylogeographic distribution and categorized into two groups: begomoviruses from the Africa, Asia, Europe and Oceania (AAEO) region and begomoviruses from the Americas. Monopartite begomoviruses are more common in the AAEO region, while bipartite viruses predominate in the Americas, where the begomoviruses lack the V2/AV2 gene involved in inter-cellular movement and RNA silencing suppression found in AAEO begomoviruses. While these features are generally accepted as lineage-defining, the number of known species has doubled due to sequence-based discovery since 2010. To re-evaluate the geographic groupings after the rapid expansion of the genus, we conducted phylogenetic analyses for begomovirus species representatives of the two longest and most conserved begomovirus proteins: the coat and replication-associated proteins. Both proteins still largely support the broad AAEO and Americas begomovirus groupings, except for sweet potato-infecting begomoviruses that form an independent, well-supported clade for their coat protein regardless of the region they were isolated from. Our analyses do not support more fine-scaled phylogeographic groupings. Monopartite and bipartite genome organizations are broadly interchanged throughout the phylogenies, and the absence of the V2/AV2 gene is highly reflective of the split between Americas and AAEO begomoviruses. We observe significant evidence of recombination within the Americas and within the AAEO region but rarely between the regions. We speculate that increased globalization of agricultural trade, the invasion of polyphagous whitefly vector biotypes and recombination will blur begomovirus phylogeographic delineations in the future.

Begomoviruses are globally distributed plant pathogens that significantly limit crop production. These viruses are traditionally described according to phylogeographic distribution and categorized into two groups: begomoviruses from the Africa, Asia, Europe, and Oceania (AAEO) region and begomoviruses from the Americas. Monopartite begomoviruses are more common in the AAEO region while bipartite viruses predominate in the Americas, where the begomoviruses lack the V2/AV2 gene involved in inter-cellular movement and RNA silencing suppression found in AAEO begomoviruses. While these features are generally accepted as lineage-defining, the number of known species has doubled due to sequence-based discovery since 2010. To reevaluate the geographic groupings after the rapid expansion of the genus, we conducted phylogenetic analyses for begomovirus species representatives of the two longest and most conserved begomovirus proteins: the coat and replication-associated proteins. Both proteins still largely support the broad AAEO and Americas begomovirus groupings, except for sweetpotato-infecting begomoviruses that form an independent, well-supported clade for their coat protein regardless of the region they were isolated from. Our analyses do not support more fine-scaled phylogeographic groupings. Monopartite and bipartite genome organizations are broadly interchanged throughout the phylogenies and the absence of the V2/AV2 gene is highly reflective of the split between Americas and AAEO begomoviruses. We observe significant evidence of recombination within the Americas and within the AAEO region, but rarely between the regions. We speculate that increased globalization of agricultural trade, the invasion of polyphagous whitefly vector biotypes and recombination will blur begomovirus phylogeographic delineations in the future.

Cassava mosaic disease (CMD) is a significant threat to cassava production throughout Africa and Asia. CMD is caused by a complex comprised of 11 recognized virus species exhibiting accelerated rates of evolution, driven by high frequencies of mutation and genetic exchange.

Begomoviruses (family Geminiviridae , genus Begomovirus ) significantly hamper crop production and threaten food security around the world. The frequent emergence of new begomovirus genotypes is facilitated by high mutation frequencies and the propensity to recombine and reassort. Homologous recombination has been especially implicated in the emergence of novel cassava mosaic begomovirus (CMB) genotypes, which cause cassava mosaic disease (CMD). Cassava ( Manihot esculenta ) is a staple food crop throughout Africa, and an important industrial crop in Asia, two continents where production is severely constrained by CMD. The CMD species complex is comprised of 11 bipartite begomovirus species with ample distribution throughout Africa and the Indian subcontinent. While recombination is regarded as a frequent occurrence for CMBs, a revised, systematic assessment of recombination and its impact on CMB phylogeny is currently lacking. We assembled datasets of all publicly available, full-length DNA-A (n=880) and DNA-B (n=369) nucleotide sequences from the 11 recognized CMB species. Phylogenetic networks and complementary recombination detection methods revealed extensive recombination among the CMB sequences. Six out of the eleven species have descended from unique interspecies recombination events. Estimates of recombination and mutation rates revealed that all species experience mutation more frequently than recombination, but measures of population divergence indicate that recombination is largely responsible for the genetic differences between species. Our results support that recombination has significantly impacted the CMB phylogeny and is driving speciation in the CMD species complex. IMPORTANCE: Cassava mosaic disease (CMD) is a significant threat to cassava production throughout Africa and Asia. CMD is caused by a complex comprised of 11 recognized virus species exhibiting accelerated rates of evolution, driven by high frequencies of mutation and genetic exchange. Here, we present a systematic analysis of the contribution of genetic exchange to cassava mosaic virus diversity. Most of these species emerged as a result of genetic exchange. This is the first study to report the significant impact of genetic exchange on speciation in a group of viruses.