ETIDIOH - NEW

Abstract Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus that causes acute respiratory disease after transmission via close contact with camels . In contrast to the incidence of MERS-CoV human infections in the Middle East , MERS-CoV infections in the Horn of Africa have been rarely reported despite the high number of camels and common camel–human interactions in the area. Whether passive cross-sectional sampling misses active human cases is a significant gap in our understanding of MERS-CoV epidemiology and its impact in the Horn of Africa. To address this gap, we conducted a prospective cross-sectional study at Laisamis Catholic Hospital in northern Kenya’s camel pastoralist community . A total of 942 patients with acute respiratory symptoms were enrolled over 18 months (August 2022–February 2024); 54% of these individuals reported frequent contact with camels and consumption of camel products. Testing via reverse transcriptase – polymerase chain reaction ...

Abstract Recently, cats have emerged as potential incidental hosts for avian and human influenza A viruses (IAVs), including the highly pathogenic avian influenza (HPAI) H5N1 virus. Following an unprecedented outbreak of H5N1 HPAI in cats in Poland in June 2023, we conducted a cross-sectional epidemiological study to assess the seroprevalence of IAV, especially H5Nx , infections in domestic cats. Eight hundred thirty-five serum samples collected in June 2023 were tested using a competitive ELISA for antibodies to IAV nucleoprotein. Positive or doubtful samples were further screened for H5-specific antibodies. The overall seropositivity for IAV was 8.5% (CI 95%: 6.8%, 10.6%; 71/835 cats), and 23/68 IAV-seropositive cats (33.8%) were also seropositive for H5 antigen . Multivariable analysis identified young age (≤8 years) and male sex as significant risk factors for H5 seropositivity, while non-H5-IAV seropositivity was more common in cats aged ≥12 years. These findings suggest different...

Abstract Background :  The experience of the COVID-19 pandemic has differed across continents. We hypothesized that regional differences in SARS-CoV-2 immunity might explain this observation. We therefore established the WWW Consortium in Ghana , W Africa; Jamaica , W Indies ; and W London . Here, we describe the extent to which antibody immunity differs between these geographic locations.  Methods :  The WWW Consortium harmonises across the HERITAGE (Accra, Ghana), WINDFall (Kingston, Jamaica) and Legacy (London, UK) studies, establishing sharing frameworks for samples , metadata, and data; related permissions and oversight; and associated physical and cloud infrastructure. With centralised testing, we performed serological assessments across all three locations at two snapshots in 2024 (April 1st - August 18th; August 19th - December 31st) using high-throughput live virus neutralization and anti-nucleocapsid IgG, including n=763 individuals.  Findings :  We fo...

Abstract We conducted genomic surveillance of seasonal influenza during the 2022-2023 northern hemisphere flu season on a large university setting in Southwest Arizona USA to understand the diversity, evolution, and spread within a local environment and how it relates to national data. Through high-throughput sequencing and bioinformatics, we identified 100 positive samples (19%) from 516 clinical swabs collected at the student health clinic. We observed a dominance of subtype A(H3N2) which was consistent nationally for the 2022-2023 season. However, we found stark differences when examining subtype-specific H3 clades , which included an early dominance of clade 2a.3a.1 variants contrasting from country-level data in which 2b variants were most abundant. These variants might have contributed to the early seasonal peak on campus which lagged national trends by one month. We used phylodynamics to understand the timing, source, and impact of clade-specific introductions on campus and obse...

Abstract Highly pathogenic avian influenza (HPAI) viruses with H5 hemagglutinin (HA) genes (clade 2.3.4.4b) are causing an ongoing panzootic in wild birds . Circulation of these viruses is associated with spillover infections in multiple species of mammals , including a large, unprecedented outbreak in American dairy cattle . Before widespread on-farm testing, there was an unmet need for genomic surveillance. Infected cattle can shed high amounts of HPAI H5N1 viruses in milk , allowing detection in pasteurized retail dairy samples. Over a 2-month sampling period in one Midwestern city , we obtained dairy products processed in 20 different states. Here we demonstrate that a tiled-amplicon sequencing approach produced over 90% genome coverage at greater than 20x depth from 5 of 13 viral RNA positive samples, with higher viral copies corresponding to better sequencing success. The sequences clustered phylogenetically within the rest of the cattle outbreak sequences reported. A combination...

  {Excerpt} Time Period: June 01, 2025 - June 07, 2025 - H5 Detection :  4 sites ( 1.1% ) - No Detection :  370 sites ( 98.9% ) - No samples in last week :  73 sites (...) Source: US Centers for Disease Control and Prevention,  https://www.cdc.gov/bird-flu/h5-monitoring/index.html ____

Abstract Neuroinvasive arboviruses such as tick-borne encephalitis virus (TBEV), West Nile virus (WNV), Usutu virus (USUV), and Toscana virus (TOSV) have (re-)emerged with increasing incidence and geographic range . We analyzed the epidemiology of arboviral infections in Croatia during the 2024 transmission season. A total of 154 patients with neuroinvasive diseases (NID), 1596 horses , 69 dead birds , and 7726 mosquitoes were tested. Viral RNA was detected using RT-qPCR. IgM/IgG-specific antibodies were detected using commercial ELISA or IFA, with confirmation of cross-reactive samples by virus neutralization test. RT-qPCR-positive samples were Sanger sequenced. Arboviral etiology was confirmed in 33/21.42% of patients with NID. WNV was most frequently detected (17/11.03%), followed by TBEV (10/6.49%), USUV (5/3.24%), and TOSV (1/0.64%). WNV infections were reported in regions previously known as endemic, while in one continental county, WNV was recorded for the first time. USUV infec...

{Excerpt} After the spread of SARS-CoV-2 JN.1, its subvariants, such as KP.3 (JN.1.11.1.3)1 and KP.3.1.1 (JN.1.11.1.3.1.1),2 and XEC (a recombinant lineage of two JN.1 subvariants),3 emerged and rapidly spread globally. Subsequently, LP.8.1 (JN.1.11.1.1.1.3.8.1),4 a descendant lineage of KP.1.1.3 (JN.1.11.1.1.1.3), accounts for approximately 30% of all global infections as of April, 2025 , as per data from Nextstrain. Thereafter, NB.1.8.1 (XDV.1.5.1.1.8.1), a descendant lineage of XDV , has started to spread worldwide. XDV is a recombinant lineage of XDE (a recombinant lineage of GW.5.1 [XBB.1.19.1.5.1] and FL.13.4 [XBB.1.9.1.13.4]) and JN.1. NB.1.8.1 has acquired seven spike substitutions and 23 non-spike substitutions compared with JN.1 (appendix pp 15–16). Compared with the XEC spike protein, the NB.1.8.1 spike bears four substitutions : G184S, K478I, A435S, and L1104V (appendix pp 15–16). We estimated the relative effective reproduction number (Re) of NB.1.8.1 using a Bayesian mult...

  {Excerpt} Time Period: May 25, 2025 - May 31, 2025 - H5 Detection :  10 sites ( 2.5% ) - No Detection :  389 sites ( 97.5% ) - No samples in last week :  52 sites (...) Source: US Centers for Disease Control and Prevention,  https://www.cdc.gov/nwss/rv/wwd-h5.html ____

Abstract Nationwide surveillance of avian influenza viruses (AIVs) in live poultry markets across China has occurred since 2014, providing a resource for AIV prevalence and genetic diversity studies . Here we report that 3,237 of 18,425 samples from poultry were AIV positive (17.57%) between 2019 and 2023, with H9N2 being the dominant subtype . We developed an automated phylogeny-based nomenclature system to classify genetic clades of the dominant H9N2 lineage, the BJ94 lineage. Using this model, we found that ten haemagglutinin (HA) sub-subclades cocirculated in poultry and showed antigenic variation. In addition, 99.46% and 96.17% of H9N2 AIVs in 2021–2023 possessed human-receptor binding-related HA-L226 and human MxA-resistance-related NP-N52 mutations , respectively. H9N2 strains with these two mutations preferred human-type receptors and increased replication in human cells in vitro, regardless of the presence of PB2-V/K/E627. Moreover, H9N2 AIVs containing HA-L226, PB2-V/K627 and...

Abstract Free-ranging white-tailed deer (WTD) are highly susceptible to the SARS-CoV-2 virus . Through an opportunistic sampling of WTD in northeast Ohio, USA , during January–March 2023 , we identified 6 SARS-CoV-2 lineages from 36 sequences using the pangolin lineages tool, including the B.1.1.7 lineage (Alpha variant) and BQ.1.1, BQ.1.1.63, BQ.1.1.67, BQ.1.23, and XBB.1.5.35 lineages ( Omicron variant ). The Alpha variant, introduced by a single human-to-deer transmission event , was detected in 5 WTD in January 2023, more than 1 year after the most recent detection of the Alpha variant in humans in Ohio (August 2021). A genetically similar B.1.1.7 lineage virus from WTD in a nearby county in Pennsylvania was positioned with our Ohio deer transmission cluster, suggesting deer-to-deer transmission . The persistence of the Alpha variant in WTD in Ohio warrants continued surveillance to monitor if WTD can become a reservoir for displaced SARS-CoV-2 variants. Source: US Centers for Dise...

Abstract We confirmed influenza A virus (IAV) by PCR in serum from 18 cows on 3 affected dairy farms in California, USA . Our findings indicate the presence of viremia and might help explain IAV transmission dynamics and shedding patterns in cows. An understanding of those dynamics could enable development of IAV mitigation strategies. Source: US Centers for Disease Control and Prevention,  https://wwwnc.cdc.gov/eid/article/31/7/25-0134_article ____

  {Excerpt} Time Period: May 18, 2025 - May 24, 2025 -- H5 Detection :  17 sites ( 5.0% ) - No Detection :  322 sites ( 95.0% ) - No samples in last week :  116 sites (...) Source: US Centers for Disease Control and Prevention,  https://www.cdc.gov/bird-flu/h5-monitoring/index.html ____

Abstract Avian influenza viruses (AIVs) pose a growing global health threat , particularly in low- and middle-income countries (LMICs), where limited surveillance capacity and under-resourced healthcare systems hinder timely detection and response. Migratory birds play a significant role in the transboundary spread of AIVs, yet data from key regions along migratory flyways remain sparse. To address these surveillance gaps, we conducted a study between December 2021 and February 2023 using fresh bird guano collected across 10 countries in the Global South . Here, we show that remote, uninhabited regions in previously unsampled areas harbor a high diversity of AIV strains , with H5N1 emerging as the most prevalent . Some of these H5N1 samples also carry mutations that may make them less responsive to the antiviral drug oseltamivir . Our findings documented the presence of AIVs in several underrepresented regions and highlighted critical transmission hotspots where viral evolution may be ...

Abstract Background Avian influenza, a significant threat to public health , requires monitoring for the development of control strategies. This study aims to analyze the spatiotemporal distribution of avian influenza virus in the external environment of Xinjiang from 2021 to 2023, to enhance understanding of its transmission patterns and provide a scientific basis for public health response measures. Methods A total of 3913 avian-related environmental samples were collected from nine monitoring areas in Xinjiang . Sample types included poultry drinking water, meat cutting boards, cage surfaces, feces, and wastewater. Real-time RT-PCR was used to detect nucleic acid for H5, H7, and H9 subtypes. Data were statistically analyzed using Excel and SPSS, and spatial distribution was visualized through Kriging interpolation using ArcGIS. Results Among the collected samples, 810 tested positive , with an overall positivity rate of 20.70%. The H9 subtype was predominant , accounting for 85.43% ...

{Excerpt} Time Period: May 11, 2025 - May 17, 2025 -- H5 Detection :  18 sites ( 4.5% ) -- No Detection :  381 sites ( 95.5% ) -- No samples in last week :  59 sites (...) Source: US Centers for Disease Control and Prevention,  https://www.cdc.gov/bird-flu/h5-monitoring/index.html ____

  {Excerpt} Time Period: April 27, 2025 - May 03, 2025 -- H5 Detection :  8 sites ( 2.0% ) - No Detection :  402 sites ( 98.0% ) - No samples in last week :  67 sites (...) Source: US Centers for Disease Control and Prevention,  https://www.cdc.gov/bird-flu/h5-monitoring/index.html ____

Abstract Background The prevalence and transmission of avian influenza viruses (AIVs) in the live poultry market (LPM) is a serious public health concern . This study was to investigate the prevalence of different subtypes of avian influenza viruses in environment of LPM, and to analyze the differences and seasonality of the nucleic acid positive rate (NAPR) of A type, H5, H7, and H9 subtypes in feces, sewage, drinking water, breeding cages, and chopping boards . Methods Feces, breeding cages swabs, drinking water, sewage and chopping boards swabs were collected from live poultry market during 2019–2023 from southern and northern China . Real-time PCR was used to screen for virus subtypes. Viruses were isolated, and deep sequencing was performed to obtain whole-genome sequences. Chi-square test was used for statistical analysis of categorical variable, GraphPad Prism software were used to construct graphs. Results A total of 64,599 environmental samples were collected from live poultry...

{Excerpt} Time Period: April 27, 2025 - May 03, 2025 - H5 Detection :  8 sites ( 2.0% ) - No Detection :  402 sites ( 98.0% ) - No samples in last week :  67 sites (...) Source: US Centers for Disease Control and Prevention,  https://www.cdc.gov/bird-flu/h5-monitoring/index.html ____

Abstract Low pathogenic H9N2 avian influenza viruses have become widespread in wild birds and poultry worldwide, raising concerns about their potential to spark pandemics or their role in enhancing the virulence and infectivity of H5Nx viruses through genetic reassortment . Therefore, influenza monitoring studies, including those of H9N2 viruses, are crucial for understanding, evaluating, and mitigating the risks associated with avian infections, and have broader implications for global public health. Although H9N2 viruses are not considered enzootic in Kazakhstan , they have been repeatedly detected in wild waterfowls and domestic poultry . In this study, all eight gene segments of influenza A/H9N2 viruses isolated in various regions of Kazakhstan between 2014 and 2020 were sequenced and analyzed. Molecular characterization revealed the presence of genetic markers associated with mammalian infectivity and disease potential . Furthermore, their predicted receptor binding site sequences...