Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Nov 22;14(12):2601.
doi: 10.3390/v14122601.

Emergence of High Pathogenicity Avian Influenza Virus H5N1 Clade 2.3.4.4b in Wild Birds and Poultry in Botswana

Samantha L Letsholo  1 , Joe James  2 , Stephanie M Meyer  2 , Alexander M P Byrne  2 , Scott M Reid  2 , Tirumala B K Settypalli  3 , Sneha Datta  3 , Letlhogile Oarabile  4 , Obakeng Kemolatlhe  4 , Kgakgamatso T Pebe  4 , Bruce R Mafonko  4 , Tebogo J Kgotlele  1 , Kago Kumile  1 , Boitumelo Modise  1 , Carter Thanda  1 , John F C Nyange  1 , Chandapiwa Marobela-Raborokgwe  1 , Giovanni Cattoli  3 , Charles E Lamien  3 , Ian H Brown  2 , William G Dundon  3 , Ashley C Banyard  2
Affiliations

Emergence of High Pathogenicity Avian Influenza Virus H5N1 Clade 2.3.4.4b in Wild Birds and Poultry in Botswana

Samantha L Letsholo et al. Viruses. .

Abstract

Numerous outbreaks of high-pathogenicity avian influenza (HPAI) were reported during 2020-2021. In Africa, H5Nx has been detected in Benin, Burkina Faso, Nigeria, Senegal, Lesotho, Namibia and South Africa in both wild birds and poultry. Botswana reported its first outbreak of HPAI to the World Organisation for Animal Health (WOAH) in 2021. An H5N1 virus was detected in a fish eagle, doves, and chickens. Full genome sequence analysis revealed that the virus belonged to clade 2.3.4.4b and showed high identity within haemagglutinin (HA) and neuraminidase proteins (NA) for viruses identified across a geographically broad range of locations. The detection of H5N1 in Botswana has important implications for disease management, wild bird conservation, tourism, public health, economic empowerment of vulnerable communities and food security in the region.

Keywords: H5N1; doves; fish eagle; high-pathogenicity; high-pathogenicity avian influenza; mass mortality; poultry.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Samples submitted for diagnostic assessment and geographical distribution of domestic and wild bird carcasses including timeline of detection. The distribution of observed deaths is shown on the map. Cases are coloured according to time of observation as denoted in the key. The size of circle is proportional to the number of cases with larger circles denoting a greater number of observed mortalities as per the key. Positive cases are also noted.
Figure 2
Figure 2
Gross pathological findings. Gross pathological lesions observed from the birds submitted for necropsy and later confirmed for HPAIV H5N1 during winter/spring of 2021. Main gross pathological findings included cyanosis around the hocks and combs. Changes in the abdominal cavity were observed primarily in the liver, spleen and intestines with congestion and oedema being observed. Species examined included chicken (Gallus gallus domesticus), African fish eagle (Haliaeetus vocifer), and African mourning dove (Streptopelia semitorquata). The number of carcasses assessed for each species is indicated at the bottom of the chart. Numbers captured in the chart refer to the number of birds that presented with the lesion. The colour range in the key reflects the frequency of the pathological sign observed from least (light) to highest (dark) frequency.
Figure 3
Figure 3
Maximum-likelihood phylogenetic tree of the HA gene segment. As per the key, H5N1 sequences detected in Botswana between July and September 2021 are highlighted in orange, Eurasian H5N1 sequences detected during 2020 and 2021 are highlighted in blue, and H5N1 sequences detected in Africa between December 2020 and December 2021 are highlighted in purple. Relationships among the Eurasian and African 2020/21 H5 HPAIV strains were inferred by adding the novel sequence data from Botswana to that available on GISAID Epiflu on 25 February 2022. The sequences were then filtered to include only Influenza A virus subtype H5N1 and are rooted to A/Goose/Guangdong/1/1996_|H5N1|_1996-01-01. In September 2022, further H5N1 sequences were added from GISAID for Burkina Faso and from GENBANK for Benin and Lesotho. Sequences were aligned using MAFFT v7.407 and phylogenetic tree inferred using Miyawaki with ultrafast bootstrap node support. Trees were visualised in FigTree v1.4.4.
See this image and copyright information in PMC

References

    1. Adlhoch C., Fusaro A., Gonzales J.L., Kuiken T., Marangon S., Niqueux, Staubach C., Terregino C., Aznar I., Guajardo I.M., et al. Avian influenza overview December 2021–March 2022. EFSA J. 2022;20:e07289. doi: 10.2903/j.efsa.2022.7289. - DOI - PMC - PubMed
    1. Oliver I., Roberts J., Brown C.S., Byrne A.M., Mellon D., Hansen R., Banyard A.C., James J., Donati M., Porter R., et al. A case of avian influenza A(H5N1) in England, January 2022. Eur. Commun. Dis. Bull. 2022;27:2200061. doi: 10.2807/1560-7917.ES.2022.27.5.2200061. - DOI - PMC - PubMed
    1. Pyankova O.G., Susloparov I.M., Moiseeva A.A., Kolosova N.P., Onkhonova G.S., Danilenko A.V., Vakalova E.V., Shendo G.L., Nekeshina N.N., Noskova L.N., et al. Isolation of clade 2.3.4.4b A(H5N8), a highly pathogenic avian influenza virus, from a worker during an outbreak on a poultry farm, Russia, December 2020. Eur. Commun. Dis. Bull. 2021;26:2100439. doi: 10.2807/1560-7917.ES.2021.26.24.2100439. - DOI - PMC - PubMed
    1. Pohlmann A., King J., Fusaro A., Zecchin B., Banyard A.C., Brown I.H., Byrne A.M.P., Beerens N., Liang Y., Heutink R., et al. Has Epizootic Become Enzootic? Evidence for a Fundamental Change in the Infection Dynamics of Highly Pathogenic Avian Influenza in Europe, 2021. mBio. 2022;13:e0060922. doi: 10.1128/mbio.00609-22. - DOI - PMC - PubMed
    1. European Food Safety Authority. European Centre for Disease Prevention and Control and European Union Reference Laboratory for Avian Influenza. Adlhoch C., Fusaro A., Gonzales J.L., Kuiken T., Marangon S., Niqueux É., Staubach C., Terregino C., et al. Avian influenza overview December 2020–February 2021. EFSA J. 2021;19:e06497. doi: 10.2903/j.efsa.2021.6497. - DOI - PMC - PubMed

Publication types