Influenza D virus (IDV) was first isolated in 2011 in Oklahoma, USA from pigs presenting with influenza-like symptoms. IDV is known to mainly circulate in ruminants, especially cattle. In Africa, there is limited information on the epidemiology of IDV, although the virus has likely circulated in the region since 2012. In the present study, we investigated the seropositivity of IDV among domestic ruminants and swine in West and East Africa from 2017 to 2020. Serum samples were analyzed using the hemagglutination inhibition (HI) assay. Our study demonstrated that IDV is still circulating in Africa, with variations in seropositivity among countries and species. The highest seropositivity was detected in cattle (3.9 to 20.9%). Our data highlights a need for extensive surveillance of IDV in Africa in order to better understand the epidemiology of the virus in the region.

Avian influenza viruses (AIVs) of the H9N2 subtype have become widespread in Western Africa since their first detection in 2017 in Burkina Faso. However, the genetic characteristics and diffusion patterns of the H9N2 virus remain poorly understood in Western Africa, mainly due to limited surveillance activities. In addition, Mali, a country considered to play an important role in the epidemiology of AIVs in the region, lacks more comprehensive data on the genetic characteristics of these viruses, especially the H9N2 subtype. To better understand the genetic characteristics and spatio-temporal dynamics of H9N2 virus within this region, we carried out a comprehensive genetic characterization of H9N2 viruses collected through active surveillance in live bird markets in Mali between 2021 and 2022. We also performed a continuous phylogeographic analysis to unravel the dispersal history of H9N2 lineages between Northern and Western Africa. The identified Malian H9N2 virus belonged to the G1 lineage, similar to viruses circulating in both Western and Northern Africa, and possessed multiple molecular markers associated with an increased potential for zoonotic transmission and virulence. Notably, some Malian strains carried the R-S-N-R motif at their cleavage site, mainly observed in H9N2 strains in Asia. Our continuous phylogeographic analysis revealed a single and significant long-distance lineage dispersal event of the H9N2 virus to Western Africa, likely to have originated from Morocco in 2015, shaping the westward diffusion of the H9N2 virus. Our study highlights the need for long-term surveillance of H9N2 viruses in poultry populations in Western Africa, which is crucial for a better understanding of virus evolution and effective management against potential zoonotic AIV strain emergence.

Mali is a country where little information is known about the circulation of avian influenza viruses (AIVs) in poultry. Implementing risk-based surveillance strategies would allow early detection and rapid control of AIVs outbreaks in the country. In this study, we implemented a multi-criteria decision analysis (MCDA) method coupled with geographic information systems (GIS) to identify risk areas for AIVs occurrence in domestic poultry in Mali. Five risk factors associated with AIVs occurrence were identified from the literature, and their relative weights were determined using the analytic hierarchy process (AHP). Spatial data were collected for each risk factor and processed to produce risk maps for AIVs outbreaks using a weighted linear combination (WLC). We identified the southeast regions (Bamako and Sikasso) and the central region (Mopti) as areas with the highest risk of AIVs occurrence. Conversely, northern regions were considered low-risk areas. The risk areas agree with the location of HPAI outbreaks in Mali. This study provides the first risk map using the GIS-MCDA approach to identify risk areas for AIVs occurrence in Mali. It should provide a basis for designing risk-based and more cost-effective surveillance strategies for the early detection of avian influenza outbreaks in Mali.

Natural infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been documented in over 60 animal species, some distantly related. Several marine mammals have been predicted as highly susceptible to SARS-CoV-2 infection based on the homology of their ACE2 receptors to those of humans. To assess potential exposure of marine mammals to SARS-CoV-2, we conducted an opportunistic survey from 2020 to 2025 and tested 1,808 swabs and 378 serum samples from 21 marine mammal species in the United States. All the swabs tested by RT-qPCR were negative, indicating the absence of active infection. A low level of SARS-CoV-2 neutralizing antibodies was detected in three pinniped species, including Phoca vitulina (harbor seal, 13.6%, 95% CI: 5.2–27.4%), Zalophus californianus (California sea lion, 7%, 95% CI: 1.9–17.0%), and Halichoerus grypus (grey seal, 3.7%, 95% CI: 0.5–12.7%). These findings represent the first serological evidence of SARS-CoV-2 exposure in marine mammals in the United States, highlighting the need for continued monitoring of these populations and further research on SARS-CoV-2 transmission dynamics in wildlife.

Natural infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been documented in over 60 animal species, some distantly related. Several marine mammals have been predicted as highly susceptible to SARS-CoV-2 infection based on the homology of their ACE2 receptors to those of humans. To assess potential exposure of marine mammals to SARS-CoV-2, we conducted an opportunistic survey from 2020 to 2025 and tested 1,808 swabs and 378 serum samples from 21 marine mammal species in the United States. All the swabs tested by RT-qPCR were negative, indicating the absence of active infection. A low level of SARS-CoV-2 neutralizing antibodies was detected in three pinniped species, including Phoca vitulina (harbor seal, 13.6%, 95% CI: 5.2–27.4%), Zalophus californianus (California sea lion, 7%, 95% CI: 1.9–17.0%), and Halichoerus grypus (grey seal, 3.7%, 95% CI: 0.5–12.7%). These findings represent the first serological evidence of SARS-CoV-2 exposure in marine mammals in the United States, highlighting the need for continued monitoring of these populations and further research on SARS-CoV-2 transmission dynamics in wildlife.

Since its emergence in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected a wide range of animal species, including wildlife. Although SARS-CoV-2 infection has been widely reported in wildlife, particularly in white-tailed deer (WTD; Odocoileus virginianus) across the United States, data on viral circulation in New England wildlife remain limited. Here, we investigated active SARS-CoV-2 infection and serological evidence of previous exposure in free-ranging wildlife from New England and Virginia. We examined samples from 1646 animals representing 29 wildlife species, collected through wildlife rehabilitation centers, clinics, and hunter harvests in New England and Virginia between 2022 and 2025. SARS-CoV-2 RNA was detected in three WTD from Massachusetts and Vermont. Phylogeographic analysis showed that the Vermont WTD SARS-CoV-2 sequences were closely related to contemporaneous human SARS-CoV-2 sequences from the same region, consistent with a possible human-to-deer spillover event. Serological screening by ELISA detected SARS-CoV-2 reactive samples in nine individuals from three species, including Eastern cottontail (Sylvilagus floridanus), Eastern coyote (Canis latrans), and raccoon (Procyon lotor), providing putative evidence of prior SARS-CoV-2 exposure. However, neutralizing antibodies against the SARS-CoV-2 Omicron variant were detected in only a single Eastern cottontail. Overall, these findings indicate sporadic SARS-CoV-2 detection and limited serological evidence of prior exposure among wildlife sampled in New England and Virginia, and highlight the importance of continued surveillance to detect spillover events, monitor viral evolution, and assess the potential risks associated with wildlife reservoirs.