Emerging Infectious Diseases

The panzootic caused by high pathogenicity avian influenza (HPAI) H5N1 clade 2.3.4.4b has been devastating for animals, globally. Despite global spread, the virus remains absent in Oceania. Herein we report the results of our fourth year of enhanced migratory bird surveillance, coinciding with the spring migration of wild birds in 2025; none of the 847 migratory wild birds or 38 marine mammals were positive for HPAI H5N1, although we did detect LPAI. Surveillance remains a critical tool for HPAI H5N1 response, with early detection and rapid response being critical to mitigate the impacts of this virus on animal, environment and human health.

Powassan virus (POWV) is a tick-borne flavivirus that can cause lethal or debilitating neurological illness. It is canonically transmitted by Ixodes genus ticks but may interact with sympatric Dermacentor species. Here, we report the first detection of POWV lineage I from a pool of field-collected D. variabilis in New York state.

In summer 2025, several Eurasian Blackbird (Turdus merula) deaths were reported on the Isle of Arran in Scotland. Initial investigation included post-mortem examination, where no diagnosis was achieved. Following Orthoflavivirus and avian paramyxovirus testing, Usutu virus RNA was detected in two Blackbirds by reverse transcription-PCR. Phylogenetic analysis identified Usutu virus Africa 3.2 lineage which clustered closely with existing UK detections, indicating geographic expansion rather than a new incursion. Subsequent surveillance confirmed the presence of several potential mosquito vector species.

Rwanda has experienced recurrent Rift Valley fever virus outbreaks in the last decade. In this study, we investigated whether these outbreaks resulted from repeated introductions or sustained local circulation. We generated RVFV whole-genome sequences from livestock samples collected between 2022 and 2025 using Nanopore sequencing. Genomic analyses indicated the outbreaks resulted from sustained local circulation of lineage C rather than repeated introductions, suggesting ongoing transmission likely driven by sporadic spillover. This study underscores the importance of continuous genomic surveillance in endemic settings.

The first cluster of SARS-CoV-2 cases with lineage B.1.1.7 in the state of Michigan was identified through intensive university-led surveillance sampling and targeted sequencing. A collaborative investigation and response was conducted by the local and state health departments, and the campus and athletic medicine COVID-19 response teams, using S-gene target failure screening and rapid genomic sequencing to inform containment strategies. A total of 50 cases of B.1.1.7-lineage SARS-CoV-2 were identified in this outbreak, which was due to three coincident introductions of B.1.1.7-lineage SARS-CoV-2, all of which were genetically distinct from lineages which later circulated in the broader community. This investigation demonstrates the successful implementation of a genomically-informed outbreak response which can be extended to university campuses and other settings at high risk for rapid emergence of new variants.

In November 2025, a traveler from Cuba tested positive for chikungunya virus upon arrival to Mexico. The virus belonged to the East-Central-South-African lineage, clustering with a clade prevalent in Brazil. Ten years after the last chikungunya epidemic in Mexico, strengthened surveillance is required to anticipate transmission of this emergent lineage.

The spread of vector-borne viruses, such as CHIKV, is a significant public health concern in the Americas, with over 120,000 cases and 51 deaths in 2023, of which 46 occurred in Paraguay. Using a suite of genomic, phylodynamic, and epidemiological techniques, we characterized the ongoing large CHIKV epidemic in Paraguay. Article Summary LineGenomic and epidemiological characterization of the ongoing Chikungunya virus epidemic in Paraguay

BackgroundUsutu virus (Orthoflavivirus usutuense, USUV), a neurotropic arthropod-borne RNA virus of the family Flaviviridae, is a zoonotic virus that has spread throughout the European continent over the last three decades, since its emergence in Italy in 1996. However, no cases of USUV have been reported in Portugal so far. Material and methodsIn the scope of an active surveillance program for Orthoflavivirus, we collected growing feather samples from 249 red-legged partridges (Alectoris rufa) hunted in southern Portugal during the 2021-2023 hunting seasons. Samples positive for USUV were subjected to whole genome sequencing and strain characterization. ResultsTwo partridges tested positive for USUV. Phylogenetic analyses of whole and partial genomes assigned the USUV strains to the African 3 lineage, specifically the African 3.1 sub-lineage. ConclusionsOur study confirms, for the first time, the circulation of USUV in wild birds in Portugal. Active surveillance of hunted partridges proved to be a useful, accessible, and cost-effective method for USUV monitoring, further supporting their value as effective sentinels for Orthoflavivirus surveillance. Given the ongoing circulation of USUV and the increasing risk of its spillover to other domestic and wild animals, and humans, additional efforts are needed to improve virus surveillance in Portugal from a One Health perspective.

Four confirmed mpox cases in South Ubangi province, Democratic Republic of the Congo, were linked to documented transboundary transmission from Central African Republic. Viral genome sequencing shows that the MPXV sequences belong to subclade Ia. This demonstrates the borderless nature of mpox and highlights the need for vigilant regional surveillance.

Not all COVID-19 deaths are officially reported and, particularly in low-income and humanitarian settings the magnitude of such reporting gaps remain sparsely characterised. Alternative data sources, including burial site worker reports, satellite imagery of cemeteries and social-media-conducted surveys of infection, may offer solutions. By merging these data with independently conducted, representative serological studies within a mathematical modelling framework, we aim to better understand the range of under-reporting using the example of three major cities: Addis Ababa (Ethiopia), Aden (Yemen) and Khartoum (Sudan) during 2020. We estimate 69% - 100%, 0.8% - 8.0% and 3.0% - 6.0% of COVID-19 deaths were reported in these three settings, respectively. In future epidemics, and in settings where vital registrations systems are absent or limited, using multiple alternative data sources could provide critically-needed, improved estimates of epidemic impact. However, ultimately, functioning vital registration systems are needed to ensure that, in contrast to COVID-19, the impact of future pandemics or other drivers of mortality are reported and understood worldwide. One sentence summaryWe demonstrate the suitability of alternative data sources to assess the under-ascertainment of COVID-19 mortality.

During the ongoing western equine encephalitis virus (WEEV) outbreak in South America, we described three fatal cases in horses from Rio Grande do Sul, Brazil. We sequenced WEEV strains and identified a novel lineage causing these cases. Continued surveillance and horse immunization are needed to mitigate the WEEV burden.

After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Mediterranee Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on [≥]5 hallmark mutations shared by [≥]30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47% and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analysing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from mink farms. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly-introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.

We describe the detection of SARS-CoV-2 (VOC)B.1.1.7 lineage in Oklahoma, USA. Various mutations in the S gene and ORF8 with similarity to the genome of B.1.1.7 lineage were detected in 4 of the 6 genomes sequenced and reported here. The sequences have been made available in GISAID. Presence of novel lineages indicate the need for frequent whole genome sequencing to better understand pathogen dynamics in different geographical locations.

BACKGROUNDOn September 25th, 2022, cholera re-emerged in Haiti. OBJECTIVES/METHODSToxigenic Vibrio cholerae O1 Ogawa were isolated on October 3rd & 4th, 2022, from cholera case patients in Port-au-Prince. The two new genomes were compared with genomes from 2,129 V. cholerae O1 isolated worldwide, including 292 Haitian strains from 2010-2018. RESULTSPhylogenies conclusively show the 2022 strains clustering within the Haitian monophyletic clade dating back to the 2010 outbreak. Strains shared a most recent common ancestor with a 2018 Haitian Ogawa strain isolated from the aquatic ecosystem, and cluster with the Ogawa clade that was circulating in 2015-2016. CONCLUSIONSRe-emergence of cholera in Haiti is the likely result of a spill-over event at the aquatic-human interface related to persistence of V. cholerae O1 in the environment. One-Sentence SummaryWe analyzed the full genome of two V. cholerae strains isolated from Haitian patients infected during the early days of the current 2022 epidemic, with data indicating that they originated from strains that have been circulating undetected at sub-epidemic levels in the aquatic environment.

This article describes the first detections of disease due to natural infection with highly pathogenic avian influenza virus (HPAIv) H5N1 of the Eurasian lineage goose/Guangdong clade 2.3.4.4b in wild terrestrial mammals throughout the United States during 2021-2022. Affected mammalian species include 50 red foxes (Vulpes vulpes), 6 striped skunks (Mephitis mephitis), 4 raccoons (Procyon lotor), 2 bobcats (Lynx rufus), 2 Virginia opossums (Didelphis virginiana), 1 coyote (Canis latrans), 1 fisher (Pekania pennanti), and 1 gray fox (Urocyon cinereoargenteus). Infected mammals primarily exhibited neurological signs. Necrotizing meningoencephalitis, interstitial pneumonia, and myocardial necrosis were the most common lesions; however, species variations in lesion distribution were observed. Genotype analysis of sequences from 48 animals indicates that these cases represent spillover infections from wild birds.

BackgroundWest Nile Virus (WNV) is a zoonotic flavivirus of significant One Health relevance and is classified as a priority pathogen with a high-risk of causing public health emergencies of global concern. WNV is endemic to Africa; however, the availability of genomic sequences from the continent remains limited. MethodsWe review the extent of polymerase chain reaction testing and genomic sequencing of WNV conducted across Africa. Using phylogeographic methods, we map the spatiotemporal spread of the virus across the continent and globally. FindingsOur study shows that WNV has been detected in 39 African countries (including Comoros, Seychelles, and Mauritius), the Canary Islands, and Reunion Island. Publications including molecular data originate from 24 countries; however, genomic sequences are publicly available for only 16 countries. We identify regions with detected viral circulation but lacking molecular surveillance. Further, we list such regions that overlap with Key Biodiversity Areas (sites harbouring significant bird diversity) as they may host high viral circulation, and high human population density that may be susceptible to spillover. InterpretationWe recognise significant knowledge gaps on the true disease burden, molecular epidemiology, and distribution of WNV in Africa. Addressing these gaps requires an integrated One Health surveillance approach which is challenging to establish. We propose three key surveillance needs as potential starting points to improve our understanding of the virus in Africa to strengthen the global public health response to this disease. FundingRockefeller Foundation, the National Institute of Health USA, Institute of Human Virology Nigeria, Global Health EDCTP3 Joint Undertaking, the Health Emergency Preparedness and Response Umbrella Program, managed by the World Bank Group, the Medical Research Foundation, and the Wellcome Trust.

There is growing evidence of cluster transmission and superspreading of SARS-CoV-2, implying heterogeneous dispersion. We discuss the successful containment of COVID-19 local outbreak in Bcharreh, the small town of 4500 inhabitants, in Northern Lebanon. We look at the dynamics of cluster transmission and viral load evolution throughout the outbreak. SARS-CoV-2 PCR test was proposed to all exposed individuals. Persons under investigation that tested negative by PCR were periodically retested. We define: a cluster as more than 3 people with a common suspicious or confirmed SARS-CoV-2 positive contact, clinical cure as the resolution of symptoms, and virologic cure as SARS-CoV-2 PCR Cycle threshold(Ct) >35. We analyzed all obtained Ct into corresponding clusters and performed a time series analysis. A total of 713/871 SARS-CoV-2 PCR tests were performed at Saint George Hospital University Medical Center (SGHUMC) from April 5th 2020 -June 14th 2020. We used the LightMix(R) Modular SARS-CoV-2 (COVID19) E, N, and RdRP-genes (Tib Molbiol, Berlin, Germany). Week one of epidemiologic surveillance began on March 31st when the first case was detected. A strict lockdown was imposed on Bcharreh village 5 days later, on top of the national lockdown. We identified 4 different clusters ranging from 3 to 27 cases and 3 sporadic unrelated cases. Almost 70% of each cluster was diagnosed within 7 days. After 2 weeks, we saw a significant increase in the average initial diagnostic Ct 27.9 to 34.72 (P<0.0001). A total of 73/74 SARS-CoV-2 PCR positive individuals achieved cure (98.6%). We recorded one death of a 90-year-old man with multiple comorbidities. In explosive new epidemics, we can derive from previous experience and not be blinded by it. To safely navigate out of the lockdown, focus on where new transmission is likely to emerge and accordingly target available diagnostic technologies.

Genomic analysis of the monkeypox virus outbreak in Washington State using 109 viral genome sequences collected from July-August 2022 shows low overall genetic diversity, multiple introductions into the state with ongoing community transmission, and potential for coinfection of an individual by multiple strains. BiographyDr. Roychoudhury is Acting Instructor and Director of COVID-19 NGS in the Department of Laboratory Medicine and Pathology at the University of Washington and Associate in the Vaccine and Infectious Disease Division at the Fred Hutchinson Cancer Research Center. Her primary research interests are pathogen genomics and mathematical models of viral evolution and host-pathogen interactions.

Yellow fever virus (YFV) was detected in two distinct geographic locations in Sao Paulo State, Brazil, between September 2024 and February 2025. Phylogenetic analysis of six new genomes revealed a re-introduction in 2022 from Midwest Brazil followed by persistence in Sao Paulo state. Continued surveillance in neotropical primates is required to prevent cases in humans.

Dengue outbreaks in West Africa, linked to urban cycle viruses, pose a significant public health threat. In 2020, a sylvatic Dengue 2 outbreak in Kedougou, southeastern Senegal, resulted in 59 confirmed cases, suggesting these strains may not require additional adaptation but could re-emerge into urban transmission cycles in the region.