Virus Surveillance Research Articles

Electronic Health Record-Based Algorithm for Monitoring Respiratory Virus-Like Illness.

Viral respiratory illness surveillance has traditionally focused on single pathogens (e.g., influenza) and required fever to identify influenza-like illness (ILI). We developed an automated system applying both laboratory test and syndrome criteria to electronic health records from 3 practice groups in Massachusetts, USA, to monitor trends in respiratory viral-like illness (RAVIOLI) across multiple pathogens. We identified RAVIOLI syndrome using diagnosis codes associated with respiratory viral testing or positive respiratory viral assays or fever. After retrospectively applying RAVIOLI criteria to electronic health records, we observed annual winter peaks during 2015-2019, predominantly caused by influenza, followed by cyclic peaks corresponding to SARS-CoV-2 surges during 2020-2024, spikes in RSV in mid-2021 and late 2022, and recrudescent influenza in late 2022 and 2023. RAVIOLI rates were higher and fluctuations more pronounced compared with traditional ILI surveillance. RAVIOLI broadens the scope, granularity, sensitivity, and specificity of respiratory viral illness surveillance compared with traditional ILI surveillance.

Concurrent Infection with Clade 2.3.4.4b Highly Pathogenic Avian Influenza H5N6 and H5N1 Viruses, South Korea, 2023.

Highly pathogenic avian influenza H5N6 and H5N1 viruses of clade 2.3.4.4b were simultaneously introduced into South Korea at the end of 2023. An outbreak at a broiler duck farm consisted of concurrent infection by both viruses. Sharing genetic information and international surveillance of such viruses in wild birds and poultry is critical.

Current understanding and knowledge gaps regarding wildlife as reservoirs of antimicrobial resistance.

Antimicrobial resistance (AMR) is a serious health issue shared across all One Health domains. Wildlife species represent a key intersection of the animal and environmental domains. They are a relevant but understudied reservoir and route of spread for AMR throughout the environment. Most wildlife AMR research thus far has focused on avian species, terrestrial mammals, and a selection of aquatic and marine species. Pathogens often identified in terrestrial wildlife include enteric zoonotic organisms such as Eschericia coli and Salmonella spp, in addition to nonenterics such as Staphylococci. Resistances have been commonly identified to antimicrobials important in veterinary and human medicine, including β-lactams, tetracyclines, aminoglycosides, and macrolides. Our emerging understanding of the dynamics of AMR distribution across life on Earth provides further opportunities for us to assess the risk it poses to veterinary and human health. Future work will require prioritizing which wildlife most exacerbates and indicates AMR in domestic animals. However, decreasing prices and increasing ease for metagenomic sequencing allows for synergies with expanding wildlife viral disease surveillance. Improved understanding of how wildlife impacts veterinary and human healthcare may increase opportunities for related research funding and global equity in such research. The companion Currents in One Health article by Vezeau and Kahn, JAVMA, June 2024, addresses in further detail the routes of spread of AMR across different animal populations and actions that can be taken to mitigate AMR with special consideration for wildlife sources.

Comprehensive Analysis of Omicron Subvariants: EG.5 Rise, Vaccination Strategies, and Global Impact.

The emergence of new variants of the SARS-CoV-2 virus during the COVID-19 pandemic has prompted significant developments in the understanding, monitoring, and response to these strains. This comprehensive review focuses on two prominent variants of interest (VoI), XBB. 1.5 (Kraken) and XBB.1.16 ("Arcturus"), along with seven variants under observation (VuM), including EG.5. The World Health Organization (WHO) identified these variants in July 2023, highlighting EG.5's noteworthy rise in prevalence. EG.5, also known as "Eris," has exhibited an increased effective reproductive rate, prompting concerns about its contagiousness and immune evasion capabilities. With an altered spike protein in the Receptor-Binding Domain (RBD), EG.5 shares similarities with XBB.1.5 but surpasses it in prevalence, constituting 20% of COVID-19 cases in the United States by late August. EG.5's subvariant, EG.5.1, poses challenges with mutations like Q52H and F456L, contributing to its ability to bypass neutralizing antibodies. The global distribution of SARS-CoV-2 variants presents a dynamic landscape, with XBB.1.16 and other strains gaining prominence. The advent of the BA.2.86 variant further complicates the scenario, with its notable spread in regions lacking robust viral surveillance. A thorough analysis of mutations reveals the evolving nature of the Omicron variant, with distinct amino acid changes characterizing XBB.1.5, XBB.1.16, and EG.5. The WHO designates EG.5 as a "variant of interest" due to its increased contagiousness and potential immune evasion, emphasizing the need for vigilant monitoring. The risk assessment of EG.5 underscores its rapid development and growing prevalence globally. While booster vaccines targeting XBB.1.5 are in development, antiviral medications like nirmatrelvir/ritonavir (Paxlovid) continue to exhibit efficacy. In the context of the evolving variants, the FDA has granted emergency use authorization for updated COVID-19 vaccines targeting circulating strains, reflecting the adaptability of vaccination strategies to address emerging challenges. This comprehensive overview provides a nuanced understanding of the diverse Omicron subvariants, their global impact, and the ongoing efforts to combat their spread through vaccination and therapeutic interventions.

Genetic Comparison of Human Parainfluenza Virus Type 3 Detected in Respiratory Samples from Patients with Encephalopathy and Airway Inflammation in Aichi Prefecture, Japan.

Human parainfluenza virus type 3 (HPIV-3, human respirovirus 3) is the second most frequently detected virus in lower respiratory tract infections in children after human respiratory syncytial virus (HRSV). HPIV-3, similar to related respiratory viruses such as HRSV and influenza virus, may cause encephalopathy; however, the relevance of HPIV-3 as a pathogenic factor in encephalopathy is unknown. We attempted to detect HPIV-1, HPIV-2, HPIV-3, HPIV-4, HRSV, and human metapneumovirus (HMPV) in 136 patients with encephalitis/encephalopathy or suspected encephalitis/encephalopathy during a 6-year period from 2014 to 2019. HPIV-3 was detected in 6 patients, followed by HRSV in 3 patients. The HPIV-3 strains detected were closely related to those detected in a patient with respiratory disease during the same period. Although HPIV-3 is less widely recognized than HRSV as a triggering virus of encephalopathy, our results suggest that HPIV-3 is as important as HRSV. Surveillance of the causative viruses of encephalopathy, including HPIV-3, would help clarify the causes of encephalopathy in Japan, as the cause is currently reported in less than half of cases in Japan.

First Detection of the Jingmen Tick Virus in Amblyomma testudinarium Ticks from the Kanto Region, Japan.

In 2010, Jingmen tick virus (JMTV) was discovered in ticks in China and has been shown to be distributed in several regions worldwide. Recently, cases of JMTV infection in humans have been reported in China and Kosovo, and have attracted much attention as an emerging tick-borne disease. In this study, we detected the JMTV genome in Amblyomma testudinarium ticks collected in Kanagawa Prefecture, Japan, during tick-borne virus surveillance conducted in the Kanto Region. Phylogenetic analysis revealed that the new JMTV strain was closely related to previous strains detected in Japan. This suggests that JMTV may have been maintained during an independent natural transmission cycle in Japan. In addition, unlike other countries and regions, all JMTV strains in Japan were detected only in A. testudinarium ticks, suggesting that this tick species is the primary JMTV vector in Japan. This is the first report of JMTV in the Kanto Region. Further studies are required to elucidate the potential risk of infection with this tick-borne virus in Japan. In particular, the prevalence of JMTV in wild animals should be examined to clarify its geographical distribution, host range, and transmission cycle.

Nowcasting methods to improve the performance of respiratory sentinel surveillance: lessons from the COVID-19 pandemic

Respiratory diseases, including influenza and coronaviruses, pose recurrent global threats. This study delves into the respiratory surveillance systems, focusing on the effectiveness of SARI sentinel surveillance for total and severe cases incidence estimation. Leveraging data from the COVID-19 pandemic in Chile, we examined 2020–2023 data (a 159-week period) comparing census surveillance results of confirmed cases and hospitalizations, with sentinel surveillance. Our analyses revealed a consistent underestimation of total cases and an overestimation of severe cases of sentinel surveillance. To address these limitations, we introduce a nowcasting model, improving the precision and accuracy of incidence estimates. Furthermore, the integration of genomic surveillance data significantly enhances model predictions. While our findings are primarily focused on COVID-19, they have implications for respiratory virus surveillance and early detection of respiratory epidemics. The nowcasting model offers real-time insights into an outbreak for public health decision-making, using the same surveillance data that is routinely collected. This approach enhances preparedness for emerging respiratory diseases by the development of practical solutions with applications in public health.

H9N2: A Mysterious Avian Influenza Virus: A Global Threat for Respiratory Pneumonia

The viral pandemic in India has presented a complex and challenging scenario since 2019, impacting the nation's public health, economy, and social fabric. This abstract provides a concise overview of the key aspects concerning the new virus H9N2. H9N2 is primarily an avian influenza virus, and while it has occasionally infected humans, those cases have generally been limited and the virus has not shown sustained human-to-human transmission. This paper explores the structural components of H9N2, determinant of host tropism, antigenic characteristics, transmission pattern, and symptoms after viral entry, complications, preventive measures, therapeutic measures, research and surveillance and role of Government for prevention and eradication of viral pandemic and measures need to be taken by the government to mitigate economic fallout etc. Special attention is given to the identification of hotspots and the effectiveness of containment measures. The abstract concludes with an exploration of the challenges faced many countries during the viral pandemic during the recent past and the lessons learned in terms of preparedness, response mechanisms, and the need for global cooperation in addressing future pandemics. Paper also serves as a snapshot of the multifaceted impact of the viral pandemic in India, offering insights into the country's response strategies and the broader implications for public health and society.

A capture-recapture modeling framework emphasizing expert opinion in disease surveillance.

In disease surveillance, capture-recapture methods are commonly used to estimate the number of diseased cases in a defined target population. Since the number of cases never identified by any surveillance system cannot be observed, estimation of the case count typically requires at least one crucial assumption about the dependency between surveillance systems. However, such assumptions are generally unverifiable based on the observed data alone. In this paper, we advocate a modeling framework hinging on the choice of a key population-level parameter that reflects dependencies among surveillance streams. With the key dependency parameter as the focus, the proposed method offers the benefits of (a) incorporating expert opinion in the spirit of prior information to guide estimation; (b) providing accessible bias corrections, and (c) leveraging an adapted credible interval approach to facilitate inference. We apply the proposed framework to two real human immunodeficiency virus surveillance datasets exhibiting three-stream and four-stream capture-recapture-based case count estimation. Our approach enables estimation of the number of human immunodeficiency virus positive cases for both examples, under realistic assumptions that are under the investigator's control and can be readily interpreted. The proposed framework also permits principled uncertainty analyses through which a user can acknowledge their level of confidence in assumptions made about the key non-identifiable dependency parameter.

The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research

In recent years, an increasing number of viruses have triggered outbreaks that pose a severe threat to both human and animal life, as well as caused substantial economic losses. It is crucial to understand the genomic structure and epidemiology of these viruses to guide effective clinical prevention and treatment strategies. Nanopore sequencing, a third-generation sequencing technology, has been widely used in genomic research since 2014. This technology offers several advantages over traditional methods and next-generation sequencing (NGS), such as the ability to generate ultra-long reads, high efficiency, real-time monitoring and analysis, portability, and the ability to directly sequence RNA or DNA molecules. As a result, it exhibits excellent applicability and flexibility in virus research, including viral detection and surveillance, genome assembly, the discovery of new variants and novel viruses, and the identification of chemical modifications. In this paper, we provide a comprehensive review of the development, principles, advantages, and applications of nanopore sequencing technology in animal and human virus research, aiming to offer fresh perspectives for future studies in this field.

West Nile virus surveillance using sentinel birds: results of eleven years of testing in corvids in a region of northern Italy.

The natural transmission cycle of West Nile virus (WNV) involves birds as primary hosts and mosquitoes as vectors, but this virus can spread to mammals, human beings included. Asymptomatic infected donors pose a risk to the safety of blood transfusions and organ transplants, as WNV can be transmitted through these medical procedures. Since 2009, the region of Emilia-Romagna in northern Italy has been implementing an integrated surveillance system in order to detect WNV circulation in the environment at an early stage. Here we report the results of the two components of the surveillance system, the active testing of corvids and humans, and demonstrate that bird surveillance alone improves a surveillance system based solely on human case detection. As WNV risk reduction measures are applied on a provincial basis, we assessed the ability of this surveillance system component to detect virus circulation prior to the notification of the first human case for each province. Overall, 99 epidemic seasons were evaluated as a result of 11 years (2013-2023) of surveillance in the nine provinces of the region. In this period, 22,314 corvids were tested for WNV and 642 (2.9%) were found to be infected. WNV was generally first detected in birds in July, with sample prevalence peaks occurring between August and September. During the same period, 469 autochthonous human cases were notified, about 60% of which were reported in August. WNV was detected 79 times out of the 99 seasons considered. The virus was notified in birds 73 times (92.4%) and 60 times (75.9%) in humans. WNV was first or only notified in birds in 57 seasons (72.1%), while it was first or only notified in humans in 22 seasons (27.8%). Active surveillance in corvids generally allows the detection of WNV before the onset of human cases. Failure of virus detection occurred mainly in seasons where the number of birds tested was low. Our results show that active testing of a minimum of 3.8 corvids per 100 km2 provides a satisfactory timeliness in the virus detection, but for early detection of WNV it is crucial to test birds between mid-June and mid-August.

Assessing avian influenza surveillance intensity in wild birds using a One Health lens

Wildlife disease surveillance, particularly for pathogens with zoonotic potential such as Highly Pathogenic Avian Influenza Virus (HPAIV), is critical to facilitate situational awareness, inform risk, and guide communication and response efforts within a One Health framework. This study evaluates the intensity of avian influenza virus (AIV) surveillance in Ontario's wild bird population following the 2021 H5N1 incursion into Canada. Analyzing 2562 samples collected between November 1, 2021, and October 31, 2022, in Ontario, Canada, we identify spatial variations in surveillance intensity relative to human population density, poultry facility density, and wild mallard abundance. Using the spatial scan statistic, we pinpoint areas where public engagement, collaborations with Indigenous and non-Indigenous hunter/harvesters, and working with poultry producers, could augment Ontario's AIV wild bird surveillance program. Enhanced surveillance at these human-domestic animal-wildlife interfaces is a crucial element of a One Health approach to AIV surveillance. Ongoing assessment of our wild bird surveillance programs is essential for strategic planning and will allow us to refine approaches and generate results that continue to support the program's overarching objective of safeguarding the health of people, animals, and ecosystems.

Detection of clade 2.3.4.4b highly pathogenic H5N1 influenza virus in New York City.

Highly pathogenic avian influenza viruses of the H5N1 clade 2.3.4.4b were detected in North America in the winter of 2021/2022. These viruses have spread across the Americas, causing morbidity and mortality in both wild and domestic birds as well as some mammalian species, including cattle. Many surveillance programs for wildlife as well as commercial poultry operations have detected these viruses. In this study, we conducted surveillance of avian species in the urban environment in New York City. We detected highly pathogenic H5N1 viruses in six samples from four different bird species and performed whole-genome sequencing. Sequencing analysis showed the presence of multiple different genotypes. Our work highlights that the interface between animals and humans that may give rise to zoonotic infections or even pandemics is not limited to rural environments and commercial poultry operations but extends into the heart of our urban centers.IMPORTANCEWhile surveillance programs for avian influenza viruses are often focused on migratory routes and their associated stop-over locations or commercial poultry operations, many bird species-including migratory birds-frequent or live in urban green spaces and wetlands. This brings them into contact with a highly dense population of humans and pets, providing an extensive urban animal-human interface in which the general public may have little awareness of circulating infectious diseases. This study focuses on virus surveillance of this interface, combined with culturally responsive science education and community outreach.

Rapid and on-site wireless immunoassay of respiratory virus aerosols via hydrogel-modulated resonators

Rapid and accurate detection of respiratory virus aerosols is highlighted for virus surveillance and infection control. Here, we report a wireless immunoassay technology for fast (within 10 min), on-site (wireless and battery-free), and sensitive (limit of detection down to fg/L) detection of virus antigens in aerosols. The wireless immunoassay leverages the immuno-responsive hydrogel-modulated radio frequency resonant sensor to capture and amplify the recognition of virus antigen, and flexible readout network to transduce the immuno bindings into electrical signals. The wireless immunoassay achieves simultaneous detection of respiratory viruses such as severe acute respiratory syndrome coronavirus 2, influenza A H1N1 virus, and respiratory syncytial virus for community infection surveillance. Direct detection of unpretreated clinical samples further demonstrates high accuracy for diagnosis of respiratory virus infection. This work provides a sensitive and accurate immunoassay technology for on-site virus detection and disease diagnosis compatible with wearable integration.

Seroprevalence and molecular characterization of viral hepatitis and HIV co-infection in the Central African Republic.

The Central African Republic (CAR) is one of the countries with the highest prevalence of viral hepatitis infection in the world. Coinfection with HIV increases the morbidity and mortality beyond that of mono-infection with either hepatitis or HIV. The present study describes the geographic distribution of viral hepatitis infections and molecular characterization of these viruses in the CAR. Out of 12,599 persons enrolled during the fourth Multiple Indicator Cluster Survey of 2010 in the CAR, 10,621 Dried Blood Spot (DBS) samples were obtained and stored at -20°C. Of these DBS, 4,317 samples were randomly selected to represent all regions of the CAR. Serological tests for hepatitis B, D, and C viruses were performed using the ELISA technique. Molecular characterization was performed to identify strains. Of the 4,317 samples included, 53.2% were from men and 46.8% from women. The HBsAg prevalence among participants was 12.9% and that HBc-Ab was 19.7%. The overall prevalence of HCV was 0.6%. Co-infection of HIV/HBV was 1.1% and that of HBV/HDV was 16.6%. A total of 77 HBV, 6 HIV, and 6 HDV strains were successfully sequenced, with 72 HBV (93.5%) strains belonging to genotype E and 5 (6.5%) strains belonging to genotype D. The 6 HDV strains all belonged to clade 1, while 4 recombinants subtype were identified among the 6 strains of HIV. Our study found a high prevalence of HBV, HBV/HDV and HBV/HIV co-infection, but a low prevalence of HCV. CAR remains an area of high HBV endemicity. This study's data and analyses would be useful for establishing an integrated viral hepatitis and HIV surveillance program in the CAR.

Assessment of the USDA Biomass Harvest Trap (USDA-BHT) device as an insect harvest and mosquito surveillance tool.

Insects are a promising source of high-quality protein, and the insect farming industry will lead to higher sustainability when it overcomes scaling up, cost effectiveness, and automation. In contrast to insect farming (raising and breeding insects as livestock), wild insect harvesting (collecting agricultural insect pests), may constitute a simple sustainable animal protein supplementation strategy. For wild harvest to be successful sufficient insect biomass needs to be collected while simultaneously avoiding the collection of nontarget insects. We assessed the performance of the USDA Biomass Harvest Trap (USDA-BHT) device to collect flying insect biomass and as a mosquito surveillance tool. The USDA-BHT device was compared to other suction traps commonly used for mosquito surveillance (Centers for Disease Control and Prevention (CDC) light traps, Encephalitis virus surveillance traps, and Biogents Sentinel traps). The insect biomass harvested in the USDA-BHT was statistically higher than the one harvested in the other traps, however the mosquito collections between traps were not statistically significantly different. The USDA-BHT collected some beneficial insects, although it was observed that their collection was minimized at night. These findings coupled with the fact that sorting time to separate the mosquitoes from the other collected insects was significantly longer for the USDA-BHT, indicate that the use of this device for insect biomass collection conflicts with its use as an efficient mosquito surveillance tool. Nevertheless, the device efficiently collected insect biomass, and thus can be used to generate an alternative protein source for animal feed.

Seasonality of respiratory, enteric, and urinary viruses revealed by wastewater genomic surveillance.

Wastewater surveillance can reveal population-level infectious disease burden and emergent public health threats can be reliably assessed through wastewater surveillance. While molecular methods for wastewater monitoring of microorganisms have traditionally relied on PCR-based approaches, next-generation sequencing (NGS) can provide deeper insights via genomic analyses of multiple diverse pathogens. We conducted a year-long sequencing surveillance of 1,408 composite wastewater samples collected from 12 neighborhood-level access points in the greater Tempe area, Arizona, USA, and show that variation in wastewater viruses is driven by seasonal time and location. The temporal dynamics of viruses in wastewater were influenced cyclically, with the most dissimilarity between samples 23 weeks apart (i.e., winter vs summer, spring vs fall). We identified diverse urinary and enteric viruses including polyomaviruses, astroviruses, and noroviruses, and showed that their genotypes/subtypes shifted across seasons. We show that while wastewater data of certain respiratory viruses like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strongly correlate with clinical case rates, laboratory-reported case incidences were discordant with surges of high viral load in wastewater for other viruses like human coronavirus 229E. These results demonstrate the utility of wastewater sequencing for informing decision-making in public health.IMPORTANCEWastewater surveillance can provide insights into the spread of pathogens in communities. Advances in next-generation sequencing (NGS) methodologies allow for more precise detection of viruses in wastewater. Long-term wastewater surveillance of viruses is an important tool for public health preparedness. This system can act as a public health observatory that gives real-time early warning for infectious disease outbreaks and improved response times.

Geographic Progression of Infant Respiratory Syncytial Virus Associated Bronchiolitis Across the United States Before and Since the Onset of COVID-19: Results From Four Health Systems, 2015-2023.

Respiratory syncytial virus (RSV) is a substantial cause of infant morbidity and mortality due to seasonal peaks of bronchiolitis across the United States. Clinical and viral surveillance plays a pivotal role in helping hospital systems prepare for expected surges in RSV bronchiolitis. Existing surveillance efforts have shown a geographic pattern of RSV positivity across the United States, with cases typically starting in the southeast and spreading north and west. Public health measures implemented due to the COVID-19 pandemic disrupted viral transmission across the nation and altered the expected seasonality of RSV. The impact of these changes on the geographic progression of infant RSV bronchiolitis across the United States has not been described. Here, we used clinical and viral surveillance data from four health care systems located in different regions of the United States to describe the geographic progression of infant RSV bronchiolitis across the country from 2015 to 2023. Prior to widespread circulation of SARS-CoV-2, infant RSV bronchiolitis followed an established geographic pattern associated with seasonal epidemics originating in Florida and spreading north (North Carolina and New York) and later westward (Nevada). Although public health and social measures implemented during the COVID-19 pandemic disrupted the seasonality of RSV disease, infant RSV bronchiolitis epidemics progressed across the nation in a pattern identical to the prepandemic era. Our findings highlight the importance of ongoing clinical and viral surveillance to optimally track the onset of RSV epidemics and allow health care systems to prepare for expected RSV bronchiolitis surges.

Identification and epidemiological study of an uncultured flavivirus from ticks using viral metagenomics and pseudoinfectious viral particles

During their blood-feeding process, ticks are known to transmit various viruses to vertebrates, including humans. Recent viral metagenomic analyses using next-generation sequencing (NGS) have revealed that blood-feeding arthropods like ticks harbor a large diversity of viruses. However, many of these viruses have not been isolated or cultured, and their basic characteristics remain unknown. This study aimed to present the identification of a difficult-to-culture virus in ticks using NGS and to understand its epidemic dynamics using molecular biology techniques. During routine tick-borne virus surveillance in Japan, an unknown flaviviral sequence was detected via virome analysis of host-questing ticks. Similar viral sequences have been detected in the sera of sika deer and wild boars in Japan, and this virus was tentatively named the Saruyama virus (SAYAV). Because SAYAV did not propagate in any cultured cells tested, single-round infectious virus particles (SRIP) were generated based on its structural protein gene sequence utilizing a yellow fever virus-based replicon system to understand its nationwide endemic status. Seroepidemiological studies using SRIP as antigens have demonstrated the presence of neutralizing antibodies against SAYAV in sika deer and wild boar captured at several locations in Japan, suggesting that SAYAV is endemic throughout Japan. Phylogenetic analyses have revealed that SAYAV forms a sister clade with the Orthoflavivirus genus, which includes important mosquito- and tick-borne pathogenic viruses. This shows that SAYAV evolved into a lineage independent of the known orthoflaviviruses. This study demonstrates a unique approach for understanding the epidemiology of uncultured viruses by combining viral metagenomics and pseudoinfectious viral particles.

Repeatability and reproducibility of hunter-harvest sampling for avian influenza virus surveillance in Great Britain

Emerging pathogens can threaten human and animal health, necessitating reliable surveillance schemes to enable preparedness. We evaluated the repeatability and reproducibility of a method developed previously during a single year at one study site. Hunter-harvested ducks and geese were sampled for avian influenza virus at three discrete locations in the UK. H5N1 highly pathogenic avian influenza (HPAIV) was detected in four species (mallard [Anas platyrhynchos], Eurasian teal [Anas crecca], Eurasian wigeon [Mareca penelope] and pink-footed goose [Anser brachyrhynchus]) across all three locations and two non-HPAIV H5N1, influenza A positive detections were made from a mallard and Eurasian wigeon at two locations. Virus was detected within 1-to-4 days of sampling at every location. Application of rapid diagnostic methods to samples collected from hunter-harvested waterfowl offers potential as an early warning system for the surveillance and monitoring of emerging and existing strains of avian influenza A viruses in key avian species.