Cross-species Transmission Research Articles

Emergence of a novel porcine pestivirus with potential for cross-species transmission in China, 2023

Pestiviruses, RNA viruses belonging to the Flaviviridae family, have a broad host range. Their pathogenicity varies greatly and they have caused significant economic losses in animal husbandry. In this study, a novel pestivirus, porcine abortion-associated pestivirus (PAAPeV), was isolated from pigs in China in 2023. Clinically, PAAPeV causes abortions in sows and leads to congenital tremors and death in piglets. PAAPeV replicates efficiently in ST cells. Morphologically, PAAPeV virions are spherical particles with a diameter of approximately 80 nm. Phylogenetic analysis reveals that PAAPeV is closely related to Wenzhou Pipistrellus abramus pestivirus and clusters into a distinct branch, suggesting that it represents a new species: Pestivirus chinensis. Animal experiments demonstrated that PAAPeV-infected piglets and mice exhibit significant histopathological changes. In piglets, histopathological examination revealed myocarditis, hepatitis, glial vacuolation and cerebrovascular inflammation. In mice, findings included hepatic monocyte aggregation, glomerular atrophy, pulmonary edema, inflammatory cell infiltration, and capillary dilation. Viremia has been detected in both piglets and mice, with high viral genome loads found in various organs. In vitro results revealed that PAAPeV replicates in ST cells and, to a lesser extent, in human (A549 and HepG2) and monkey (Vero) cells. Overall, PAAPeV infects both pigs and mice and has the potential to infect other mammals, indicating its ability for cross-species transmission. This poses significant risks to the pig industry and public health. Strengthening monitoring and prevention efforts for PAAPeV is crucial. Our findings greatly increase the understanding of pestivirus diversity and its broader pathogen spectrum.

Limited similarity in microbial composition among coral reef fishes from the Great Barrier Reef, Australia.

Reef fishes exhibit enormous biodiversity within a highly interactive ecosystem. Relatively little is known about the diversity and evolution of microbial species associated with reef fish, even though this may provide valuable insights into the factors that shape microbial communities. Through metatranscriptomic sequencing we characterised the viruses, bacteria, and single-celled eukaryotes from 126 reef fish species inhabiting Lizard Island and Orpheus Island on the Great Barrier Reef, Australia. We assessed whether microbial communities differed between islands that are separated by 450 kilometres, and to what extent fish viruses emerge in new hosts. Despite strong ecological interactions within the species-rich reef environment, and the presence of the same families of viruses on both islands, there was minimal evidence for the presence of individual viruses shared among fish species, reflecting low levels of cross-species transmission. Among bacteria, we identified the opportunistic bacterial pathogen Photobacterium damselae in apparently healthy cardinalfish species from both islands, indicating that these fish species are natural reservoirs. These data suggest that reef fishes have microbial-host associations that arose prior to the formation of the Great Barrier Reef, likely leading to strong host barriers to cross-species transmission and hence infectious disease emergence.

SARS-CoV-2 outbreak in lions, tigers, and hyenas at Denver Zoo.

In late 2019, SARS-CoV-2 spilled over from an animal host into humans, where it efficiently spread, resulting in the COVID-19 pandemic. Through both natural and experimental infections, we learned that many animal species are susceptible to SARS-CoV-2. Importantly, animals in close proximity to humans, including companion, farmed, and those at zoos and aquariums, became infected, and many studies demonstrated transmission to/from humans in these settings. In this study, we first review the literature of SARS-CoV-2 infections in tigers and lions and compare species, sex, age, virus and antibody detection assay, and types, frequency, and length of clinical signs, demonstrating broad heterogeneity among infections. We then describe a SARS-CoV-2 outbreak in lions, tigers, and hyenas at Denver Zoo in late 2021. Animals were tested for viral RNA (vRNA) for 4 months. Lions had significantly more vRNA in nasal swabs than both tigers and hyenas, and many individual lions experienced viral recrudescence after weeks of undetectable vRNA. Infectious virus was correlated with high levels of vRNA and was more likely to be detected earlier during infection. Four months post-infection, all tested animals generated robust neutralizing antibody titers. Animals were infected with Delta lineage AY.20 identical to a variant circulating at less than 1% in Colorado humans at that time, suggesting a single spillover event from an infected human spread within and between species housed at the zoo. Better understanding of epidemiology and susceptibility of SARS-CoV-2 infections in animals is critical to limit the current and future spread and protect animal and human health.IMPORTANCESurveillance and experimental testing have shown many animal species, including companion, wildlife, and conservatory, are susceptible to SARS-CoV-2. Early in the COVID-19 pandemic, big cats at zoological institutions were among the first documented cases of naturally infected animals; however, challenges in the ability to collect longitudinal samples in zoo animals have limited our understanding of SARS-CoV-2 kinetics and clearance in these settings. We measured SARS-CoV-2 infections over 4 months in lions, tigers, and hyenas at Denver Zoo and detected viral RNA, infectious virus, neutralizing antibodies, and recrudescence after initial clearance. We found lions had longer and higher levels of virus compared to the other species. All animals were infected by a rare viral lineage circulating in the human population, suggesting a single spillover followed by interspecies transmission. These data are important in better understanding natural SARS-CoV-2 spillover, spread, and infection kinetics within multiple species of zoo animals.

Genetics and biological characteristics of duck reoviruses isolated from ducks and geese in China

The emergence and circulation of duck reovirus have caused severe threats to domestic waterfowl production because of the lethal infections they cause in ducks and geese. However, the evolution of circulating duck reoviruses and their replication and pathogenicity in domestic birds have not been fully investigated. In this study, we identified and isolated six duck reoviruses from clinical samples of sick or deceased farmed ducks and geese and sequenced their full genomes. Phylogenetic analysis revealed the evolutionary landscape of duck reoviruses and the complex reassortment of these circulating viruses with avian orthoreovirus and Muscovy duck reovirus. Animal infection studies revealed differences in the replication and pathogenicity of the reoviruses identified in this study in ducks, geese and chickens. Lethal infection with highly pathogenic viruses causes severe focal necrosis and hemorrhage in the liver, spleen, bursa of Fabricius and thymus, resulting in high mortality in inoculated birds. Importantly, chickens are susceptible to circulating duck reovirus, highlighting the potential risk of duck reovirus infection in chickens. Our study revealed the evolution, pathogenicity and potential cross-species transmission risk of duck reoviruses, further emphasizing the importance of continued and systemic surveillance at the interface of domestic waterfowl and chickens.

Detection and subtyping of Blastocystis sp. in human and animal stool samples using high-resolution melting analysis

ObjectiveThis study aimed to investigate the prevalence and subtype distribution of the genus Blastocystis using high-resolution melting curve analysis (HRM), a novel molecular technique. Blastocystis sp., a unicellular, anaerobic, and zoonotic parasite, is commonly found in the digestive tracts of humans and animals. Transmission occurs via the fecal-oral route, with prevalence rates ranging from 20% in developed countries to over 60% in developing regions. Although the pathogenicity of Blastocystis remains debated, it has been detected in both symptomatic and asymptomatic individuals. Traditionally, direct microscopy with wet mounts is used for the rapid identification of Blastocystis in stool samples. However, molecular diagnostics have become essential for the accurate detection and differentiation of Blastocystis subtypesMaterials and methodsWe collected 730 stool samples from humans and domestic animals. Initial screening for Blastocystis sp. was performed using direct microscopy. Negative samples were cultured in a two-phase culture medium and re-examined after 2–3 days. HRM analysis was then employed to identify and differentiate Blastocystis subtypes using specific primers via real-time PCR.ResultsSix subtypes were identified, with ST7 (30%) being the most prevalent, followed by ST3 (28%), ST2 (16%), ST1 (14%), ST5 (6%), and ST14 (6%). In humans, ST3 was the most common subtype, also found in poultry and sheep, whereas ST7 was mainly detected in domestic animals. Notably, ST1-ST3 were identified in domesticated animals, indicating a pattern of cross-species transmission.ConclusionST3 (28%) and ST7 (30%) were the most prevalent subtypes across all samples, with distinct distributions in human and animal hosts. The HRM technique demonstrated efficiency and cost-effectiveness, providing a rapid and accurate method for Blastocystis subtype identification in developing countries, which can expedite diagnostic responses and reduce the need for sequencing. This supports the potential for HRM to improve epidemiological surveillance and understanding of cross-species transmission.

Prophage dynamics in gastric and enterohepatic environments: unraveling ecological barriers and adaptive transitions

Abstract Phage predation plays a critical role in shaping bacterial genetic diversity, with prophages playing a comparable role. However, the prevalence and genetic variability of prophages within the Helicobacter genus remain inadequately studied. Helicobacter species are clinically significant and occupy distinct digestive system regions, with gastric species (e.g., Helicobacter pylori) residing in the gastric mucosa and enterohepatic species colonizing the liver and intestines of various vertebrates. Here, we address this knowledge gap by analyzing prophage presence and diversity across 343 non-pylori Helicobacter genomes, mapping their distribution, comparing genomic features between gastric and enterohepatic prophages, and exploring their evolutionary relationships with hosts. We identified and analyzed a catalogue of 119 new complete and 78 incomplete prophages. Our analysis reveals significant differences between gastric and enterohepatic species. Gastric prophages exhibit high synteny, and cluster in a few groups, indicating a more conserved genetic structure. In contrast, enterohepatic prophages show greater diversity in gene order and content, reflecting their adaptation to varied host environments. Helicobacter cinaedi stands out, harboring a large number of prophages among the enterohepatic species, forming a distinct cohesive group. Phylogenetic analyses reveal a co-evolutionary relationship between several prophages and their bacterial hosts, though exceptions, such as the enterohepatic prophages from H. canis, Helicobacter equorum, H. jaachi, and the gastric prophage from H. himalayensis, suggesting more complex co-evolutionary dynamics like host jumps, recombination and horizontal gene transfer. The insights gained from this study enhance our understanding of prophage dynamics in Helicobacter, emphasizing their role in bacterial adaptation, virulence, and host specificity.

Host Jumps and Pathogenicity of Botryosphaeriaceae Species on Grapevines (Vitis vinifera) in Chile

Botryosphaeria dieback disease is a significant grapevine trunk disease (GTD) caused by species of Botryosphaeriaceae in Chile and worldwide. Moreover, Botryosphaeriaceae have been described attacking fruit and nut crops in Chile. However, it remains unknown whether fungal isolates from tree hosts have the potential to infect grapevines in Chile. The aggressiveness and potential cross infection of species of Botryosphaeriaceae collected from crops (grapevines, apples, blueberries, and walnuts), was assessed on grapevines. Plant materials, including nursery cuttings, lignified canes, and green shoots of grapevine cultivars (Cabernet Sauvignon, Syrah, Sauvignon Blanc, Malbec, Aspirant Bouschet, and Merlot), were inoculated with Diplodia mutila, D. seriata, Dothiorella sarmentorum, Lasiodiplodia theobromae, Neofusicoccum arbuti, and N. parvum, under greenhouse and vineyard conditions. Regardless of the origin of the isolates, most species of Botryosphaeriaceae were pathogenic on plant materials, causing necrotic lesions of mean lengths from 11.9 to 86.2 mm using mycelial suspension and from 24.8 to 253.7 mm with mycelial plugs. Notably, Neofusicoccum species were the most aggressive, regardless of host origin. Other less aggressive species included L. theobromae, D. mutila, and D. seriata isolated from apple and walnut. This study highlights the potential of species of Botryosphaeriaceae from alternative fruit hosts as inoculum sources for grapevines in Chile.

Persistent cross-species transmission systems dominate Shiga toxin-producing Escherichia coli O157:H7 epidemiology in a high incidence region: A genomic epidemiology study

Several areas of the world suffer a notably high incidence of Shiga toxin-producing Escherichia coli. To assess the impact of persistent cross-species transmission systems on the epidemiology of E. coli O157:H7 in Alberta, Canada, we sequenced and assembled E. coli O157:H7 isolates originating from collocated cattle and human populations, 2007–2015. We constructed a timed phylogeny using BEAST2 using a structured coalescent model. We then extended the tree with human isolates through 2019 to assess the long-term disease impact of locally persistent lineages. During 2007–2015, we estimated that 88.5% of human lineages arose from cattle lineages. We identified 11 persistent lineages local to Alberta, which were associated with 38.0% (95% CI 29.3%, 47.3%) of human isolates. During the later period, six locally persistent lineages continued to be associated with human illness, including 74.7% (95% CI 68.3%, 80.3%) of reported cases in 2018 and 2019. Our study identified multiple locally evolving lineages transmitted between cattle and humans persistently associated with E. coli O157:H7 illnesses for up to 13 y. Locally persistent lineages may be a principal cause of the high incidence of E. coli O157:H7 in locations such as Alberta and provide opportunities for focused control efforts.

Persistent cross-species transmission systems dominate Shiga toxin-producing Escherichia coli O157:H7 epidemiology in a high incidence region: A genomic epidemiology study.

Several areas of the world suffer a notably high incidence of Shiga toxin-producing Escherichia coli. To assess the impact of persistent cross-species transmission systems on the epidemiology of E. coli O157:H7 in Alberta, Canada, we sequenced and assembled E. coli O157:H7 isolates originating from collocated cattle and human populations, 2007-2015. We constructed a timed phylogeny using BEAST2 using a structured coalescent model. We then extended the tree with human isolates through 2019 to assess the long-term disease impact of locally persistent lineages. During 2007-2015, we estimated that 88.5% of human lineages arose from cattle lineages. We identified 11 persistent lineages local to Alberta, which were associated with 38.0% (95% CI 29.3%, 47.3%) of human isolates. During the later period, six locally persistent lineages continued to be associated with human illness, including 74.7% (95% CI 68.3%, 80.3%) of reported cases in 2018 and 2019. Our study identified multiple locally evolving lineages transmitted between cattle and humans persistently associated with E. coli O157:H7 illnesses for up to 13 y. Locally persistent lineages may be a principal cause of the high incidence of E. coli O157:H7 in locations such as Alberta and provide opportunities for focused control efforts.

Detection and characterization of bovine hepacivirus in cattle and sheep from Hulunbuir, northeastern China

BackgroundBovine hepacivirus (BovHepV) is a recently identified member of the expanding genus Hepacivirus within the family Flaviviridae. However, the genetic diversity, geographical distribution, and host range of the virus remains poorly understood.MethodsIn this study, serum samples from cattle and sheep were obtained in Hulunbuir and pooled to establish RNA libraries, which were then analyzed using transcriptome sequencing. BovHepV-positive samples were confirmed using semi-nested PCR with primers designed based on the obtained viral sequences. Comprehensive bioinformatics analyses were employed to assess sequence similarity, phylogenetic evolution, and recombination of the obtained viral strains.ResultsA total of 988 serum samples from sheep (520) and cattle (468) were collected from 12 administrative districts in Hulunbuir from June to August, 2022. Semi-nested PCR revealed 6 BovHepV-positive districts with prevalence ranging from 2.0% to 35.0% in cattle, and one BovHepV-positive district with prevalence of 2.5% in sheep. The nucleotide sequence identities between viral strains from sheep and cattle ranged from 91.3% to 93.8%, while the amino acid sequence identities were between 95.4% and 96.7%. Phylogenetic analyses classified the obtained BovHepV strains within subtype G, genotype 1. Recombination analysis revealed the intergenerational relationships among the viral strains obtained from cattle and sheep.ConclusionWe identified genetic diversity in subtype G strains in cattle and detected a BovHepV strain in a sheep for the first time in northeastern China, confirming cross-species transmission and co-circulation between cattle and sheep, thus expanding the virus’s host range.

Association of poultry vaccination with interspecies transmission and molecular evolution of H5 subtype avian influenza virus.

The effectiveness of poultry vaccination in preventing the transmission of highly pathogenic avian influenza viruses (AIVs) has been debated, and its impact on wild birds remains uncertain. Here, we reconstruct the movements of H5 subtype AIV lineages among vaccinated poultry, unvaccinated poultry, and wild birds, worldwide, from 1996 to 2023. We find that there is a time lag in viral transmission among different host populations and that movements from wild birds to unvaccinated poultry were more frequent than those from wild birds to vaccinated poultry. Furthermore, our findings suggest that the HA (hemagglutinin) gene of the AIV lineage that circulated predominately in Chinese poultry experienced greater nonsynonymous divergence and adaptive fixation than other lineages. Our results indicate that the epidemiological, ecological, and evolutionary consequences of widespread AIV vaccination in poultry may be linked in complex ways and that much work is needed to better understand how such interventions may affect AIV transmission to, within, and from wild birds.

Prevalence of Methicillin-Resistant Staphylococcus aureus in Livestock in Japan: A Systematic Review and Meta-Analysis

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is an important health issue that is estimated to have caused 130,000 deaths worldwide in 2021. As more instances of cross-species transmission of MRSA have been reported, concerns have been raised regarding the spread of livestock-associated MRSA to humans. The prevalence of MRSA in livestock varies globally. This study systematically reviews the prevalence of MRSA at the farm and animal levels in Japan. Methods: Relevant studies published in English or Japanese between 2000 and 2023 were retrieved from four databases. Pooled prevalences at the farm and animal levels in Japanese farms were calculated using a random-effects model. Subgroup and meta-regression analyses were also performed to explore sources of heterogeneity. Results: The 13 studies included in this meta-analysis yielded an MRSA prevalence of 3.54% (95% confidence interval [CI] 0.65–8.30%) at the individual pig level, 13.07% (95% CI 5.42–23.04%) at the pig farm level, 0.0% (95% CI 0.00–0.04%) at the individual cattle level, and 0% (95% CI 0.00–0.44%) at the individual chicken level. A significant increase in MRSA prevalence over time was evident at the individual pig level by both subgroup analysis (p = 0.020) and meta-regression (p = 0.019). Conclusions: Our results indicated that the proportion of pigs that can be a source of MRSA infection in humans has been steadily increasing in Japan. Despite some limitations, our findings strongly imply a need for more attention to pig-to-human MRSA transmission in Japan.

Potential Zoonotic Infections Transmitted by Free-Ranging Macaques in Human-Monkey Conflict Areas in Thailand.

Nonhuman primates (NHPs) can transmit zoonotic diseases to humans because of their close genetic relationship, facilitating the cross-species transmission of certain pathogens. In Thailand, Macaca is the most common NHP genus and their inhabits area are in close proximity of human, particularly in urban and suburban areas, where frequent interactions with humans increase the risk of pathogen transmission. The risk is influenced by factors such as the type of pathogen, the mode of transmission (e.g. direct contact or vector-borne), and the density of human and macaque populations in the regions. This study aims to investigate potential zoonotic infections in free-ranging macaques residing in human-monkey conflict areas. From 2014 to 2023, 2703 macaques across 29 provinces in Thailand were tested for 18 pathogens using PCR, RT-PCR, or real-time PCR. The associations between disease occurrence, demographic variables, and sample types of macaques were analysed using univariable and multivariable regression. The overall pathogen infection percentage was 35.7% (965/2703). Simian foamy virus (SFV) had the highest infection percentage at 52.5% (759/1446), followed by Herpesviridae at 41.4% (353/852), Plasmodium spp. at 1.8% (14/758), and hepatitis B virus at 0.1% (2/1403). Significant differences were observed among different sampling sites, macaque age groups, and species in infection proportion of SFV, and Herpesviridae. Identifying the pathogens carried by macaques is crucial for preparing for potential disease epidemics and outbreaks.

Receptor binding, structure, and tissue tropism of cattle-infecting H5N1 avian influenza virus hemagglutinin.

The ongoing circulation of highly pathogenic avian influenza (HPAI) A (H5N1) viruses, particularly clade 2.3.4.4b strains, poses a significant threat to animal and public health. Recent outbreaks in cattle highlight concerns about cross-species transmission and zoonotic spillover. Here, we found that the hemagglutinin (HA) protein from a cattle-infecting H5N1 virus has acquired slight binding to human-like α2-6-linked receptors while still exhibiting a strong preference for avian-like α2-3-linked sialic acid receptors. Immunohistochemical staining revealed HA binding to bovine pulmonary and mammary tissues, aligning with clinical observations. HA also binds effectively to human conjunctival, tracheal, and mammary tissues, indicating a risk for human transmission, notably in cases of conjunctivitis. High-resolution cryo-electron microscopy (cryo-EM) structures of this H5 HA in complex with either α2-3 or α2-6 receptors elucidate the molecular mechanisms underlying its receptor-binding properties. These findings provide critical insights into the tropism and transmission potential of this emerging pathogen.

High astrovirus diversity in an endemic bat species suggests multiple spillovers from synanthropic rodents and birds.

Beyond the role of bats as natural host reservoirs of infectious agents, the impact of viral spillover from other animal species to bats has been neglected. Given the limited virus-host specificity of astroviruses (AstVs) and their propensity for cross-species transmission, we hypothesized that AstVs could be transmitted within animal communities (rodents, birds, and bats) and that native endemic bats may be exposed to viruses hosted by other species. We investigated the presence of AstV RNA in 3,796 biological samples collected in Reunion Island from Mormopterus francoismoutoui (N = 3421), an endemic free-tailed bat species, and also from small terrestrial mammals and birds: Rattus rattus (N = 146), Rattus norvegicus (N = 74), Mus musculus domesticus (N = 36), Suncus murinus (N = 99), and Columba livia (N = 20). We found significant differences in AstV prevalence between species (ranging from 1% ± 1.97% in S. murinus to 75% ± 18.9% in C. livia) as well as variation of pairwise identity of AstV sequences among host species, with a high diversity in M. francoismoutoui (mean pairwise identity: 53.2% ± 11.2%). Phylogenetic analyses further revealed that AstVs detected in bats did not cluster in a single clade and were genetically related to AstVs found in birds, rodents, pigs, dogs, cats, and reptiles. Our study suggests that bats may be exposed to viruses associated to synanthropic and alien species. Cascade effects of virus spillover toward endemic and endangered bat species need to be fully assessed.IMPORTANCEEpidemiological consequences of cross-species transmission of zoonotic viruses are mostly considered from a health and economic perspective. Virus spillovers resulting from human-introduced species are much less considered, although they may have major consequences on the conservation of endemic and endangered bat species, in particular in an island context. Based on astrovirus detection and sequencing in an endemic bat species and five non-native species on a tropical island, we identified multiple and repeated viral introductions from synanthropic rodents and birds to bats, rather than the opposite. Such findings call for more investigations in these isolated and vulnerable ecosystems to better understand and mitigate the risks associated with pathogen spillovers.

Novel cycloviruses identified by mining human blood metagenomic data show close relationship to those from animals.

The family Circoviridae includes the genera Circovirus and Cyclovirus. Cycloviruses have been found in serum samples from chronic HBV, HCV, or HIV-infected individuals as well as asymptomatic blood donors. However, research on cycloviruses is relatively limited. We used viral metagenomics to mine, analyze, and visualize the human blood virome, successfully identifying three new genomes, each encoding Rep and Capsid proteins. These proteins are crucial for viral replication and host-cell interaction: the Rep protein is involved in initiating viral genome replication, while the Capsid protein plays a key role in the assembly of new virions and the virus's ability to interact with host immune systems. Distance matrix and phylogenetic analyses show that these cycloviruses share high sequence similarity with viruses found in both humans and animals across different regions of Africa. This finding not only confirms the presence of previously uncharacterized cycloviruses in human blood, but also provides insight into their potential role in host transmission and their ecological significance. Further research is needed to explore the functional roles of these cycloviruses in viral pathogenesis, particularly how they may influence host immunity and contribute to chronic infections. Additionally, studies investigating the host range and mechanisms of cross-species transmission will be essential to understanding the broader implications of cycloviruses in human and animal health.

Major change in swine influenza virus diversity in France owing to emergence and widespread dissemination of a newly introduced H1N2 1C genotype in 2020.

Swine influenza A viruses (swIAVs) are a major cause of respiratory disease in pigs worldwide, presenting significant economic and health risks. These viruses can reassort, creating new strains with varying pathogenicity and cross-species transmissibility. This study aimed to monitor the genetic and antigenic evolution of swIAV in France from 2019 to 2022. Molecular subtyping revealed a marked increase in H1avN2 cases from 2020 onwards, altering the previously stable subtypes' distribution. Whole-genome sequencing and phylogenetic analyses of H1av (1C) strains identified 10 circulating genotypes, including 5 new genotypes. The most predominant genotype from 2020 onwards, denominated H1avN2#E, was characterized by an HA-1C.2.4, an N2-Gent/84, and internal protein-encoding genes belonging to a newly defined subclade within the Eurasian avian-like (EA) lineage termed EA-DK. H1avN2#E emerged in Brittany, the country's most pig-dense region, and rapidly became the most frequently detected swIAV genotype across France. This drastic change in the swIAV lineage proportions at a national scale was unprecedented, making H1avN2#E a unique case for understanding swIAV evolution and spreading patterns. Phylogenetic analyses suggested an introduction of the H1avN2#E genotype from a restricted source, likely originating from Denmark. It spread rapidly with low genetic diversity at the start of the epizootic in 2020, showing increasing diversification in 2021 and 2022 as the inferred population size grew and stabilized, and exhibited reassortments with other enzootic genotypes. Amino acid sequence alignments of H1avN2#E antigenic sites revealed major mutations and deletions compared to commercial vaccine 1C strain (HA-1C.2.2) and previously predominant H1avN1 strains (HA-1C.2.1). Antigenic cartography confirmed significant antigenic distances between H1avN2#E and other 1C strains, suggesting that the new genotype has escaped the pre-existing immunity of the swine population. Epidemiologically, the H1avN2#E virus exhibited epizootic hallmarks with more severe clinical outcomes compared to H1avN1 viruses. These factors likely contributed to the spread of H1avN2#E within the pig population. The rapid rise of H1avN2#E highlighted the dynamic nature of swIAV genetic and antigenic diversity, underscoring the importance of tailored surveillance programs to support risk assessment during potential new outbreaks. It also demonstrates the need to strengthen biosecurity measures when introducing pigs into a herd, including swIAV positivity assessment followed by quarantine, and restrict the trade of swIAV-excreting live swine between European countries.

Evolution of ceftazidime/avibactam resistance and plasmid dynamics in OXA-48-producing Klebsiella spp. during long-term patient colonization.

To prospectively monitor the evolution of the resistome of OXA-48-producing Klebsiella species in a patient with long-term colonization, with a particular focus into the plasmid dynamics and the evolution of ceftazidime/avibactam resistance. All OXA-48-producing Klebsiella spp. isolates from a single patient admitted to a hospital during seven months were prospectively collected. MICs were determined through reference broth microdilution. Multilocus sequence types, SNPs analysis, resistance mechanisms, genetic context of β-lactamases and plasmid dynamics were determined by WGS and bioinformatic analysis. The impact of β-lactamase variant obtained after ceftazidime/avibactam exposure was determined via cloning experiments. Four isolates, two before (one OXA-48-producing K. pneumoniae and one CTX-M-15-like-producing K. pneumoniae) and two after treatment with ceftazidime/avibactam (one OXA-48- and CTX-M-15-like-producing K. pneumoniae and one OXA-48- and CTX-M-15-like-producing K. aerogenes) were collected. The plasmid dynamics analysis demonstrated that the IncL and IncFIIK plasmids, in which blaOXA-48 and blaCTX-M-15-like genes were located, respectively, exhibited a high degree of conservation indicating a potential for both intra- and interspecies transmission. The K. pneumoniae isolate obtained after treatment, which differed from the previous isolate by just six SNPs, exhibited resistance to ceftazidime/avibactam through P167S substitution in CTX-M-15, which is now designated CTX-M-273. Cloning experiments demonstrated enhanced resistance to ceftazidime/avibactam. The transfer of plasmid-borne β-lactamase resistance genes between intra- and interspecies bacterial populations enables the rapid diversification of the bacterial genome. The emergence of ceftazidime/avibactam resistance through the modification of CTX-M-enzymes represents a mechanism by which OXA-48-producing Enterobacterales may evolve toward ceftazidime/avibactam resistance in vivo.

Interactions Between Humans and White-Tailed Deer in Illinois: A Cross-Sectional Survey.

SARS-CoV-2 has been found in multiple species, including cervids such as wild white-tailed deer (WTD), in multiple regions in the United States, including Illinois. The virus has been shown to transmit among WTD, and across species in both directions (deer-to-humans and humans-to-deer). Cross-species transmission requires infectious contact between WTD and humans, the form and frequency of which is poorly understood. The aim of this cross-sectional survey was to understand the frequency and type of contact between the general public in the state of Illinois and WTD, and to identify human populations at highest risk for such contact. An online survey was distributed using convenience sampling from list serves, social media, and community partners or extension liaisons. Questions addressed frequency and distance of contact with WTD, encompassing live animals and bodily fluids. Standard and ordinal logistic regression were used to identify factors associated with contact. An overall risk score was calculated, and linear regression was used to identify factors associated with risk. We found that hunters and those who have deer feeding on their property are more likely to report contact with deer, and that people reporting a larger lot size and living in counties with higher proportions of potential deer habitat are more likely to report deer feeding on their property. These results will better identify people with a high likelihood of WTD contact for messaging and further research. Our survey did not distinguish between contact with live and dead WTD, thus the findings are most relevant to deer-to-human cross-species transmission than the human-to-deer direction.

Host Specificity and Geographic Dispersion Shape Virome Diversity in Rhinolophus Bats.

Rhinolophus bats have been identified as natural reservoirs for viruses with global health implications, including severe acute respiratory syndrome-related coronaviruses (SARSr-CoV) and swine acute diarrhoea syndrome-related coronavirus (SADSr-CoV). In this study, we characterised the individual viromes of 603 bats to systematically investigate the diversity, abundance and geographic distribution of viral communities within R. affinis, R. sinicus and 11 other bat species. The massive metatranscriptomic data revealed substantial viral genome resources of 133 vertebrate-infecting viral clusters, which contain occasional cross-species transmission across mammalian orders and especially across bat families. Notably, those viruses included nine clusters closely related to human and/or livestock pathogens, such as SARS-CoVs and SADS-CoVs. The investigation also highlighted distinct features of viral diversity between and within bat colonies, which appear to be influenced by the distinct host population genetics of R. affinis and R. sinicus species. The comparison of SARSr-CoVs further showed varied impact of host specificity along genome-wide diversification and modular viral evolution among Rhinolophus species. Overall, the findings point to a complex interaction between host genetic diversity, and the way viruses spread and structure within natural populations, calling for continued surveillance efforts to understand factors driving viral transmission and emergence in human populations. These results present the underestimated spillover risk of bat viruses, highlighting the importance of enhancing preparedness and surveillance for emerging zoonotic viruses.