Molecular Characterisation of Highly Pathogenic Avian Influenza viruses in Uganda, 2017 Outbreak

Avian influenza (AI) is a viral disease affecting the respiratory, digestive and/or the nervous system of many species of birds. Currently, very little information is available about the prevalence and circulating strains of... [ view full abstract ]

Avian influenza (AI) is a viral disease affecting the respiratory, digestive and/or the nervous system of many species of birds. Currently, very little information is available about the prevalence and circulating strains of avian influenza viruses (AIV) in wild and domestic birds in Uganda. On 3rd January 2017, massive death of wild birds was reported on Lake Victoria, by Fishermen. On 5th January 2017 a team from National Animal Disease Diagnostics and Epidemiology Centre (NADDEC) visited Lutembe Beach where wild birds were dying. In total 08 dead birds were collected and analysed at NADDEC. On 6th January 2017, 27 samples from Masaka district were delivered at NADDEC. I screened the samples using RealTime-PCR, and 12 samples tested positive for Avian Influenza type A. Because primers for sub-typing the viruses were out of stock at the time of outbreak, NADDEC requested Uganda Virus Research Institute (UVRI) to subtype for us, the first batch of 12 positive samples. The results showed that the circulating virus was H5N8. For further confirmation 18 positive samples were shipped to Istituto Zooprofilattico Sperimentale delle Venezie Viale dell’Università 10, 35020 – Legnaro, Padova, Italy. Sanger Sequencing results confirmed that the Virus was Highly Pathogenic influenza Type A, H5N8, clade 2.3.4.4. More samples from Kalangala District (an Island on Lake Victoria), Budaka District (Eastern Uganda), and Kasese district (Western Uganda), have been screened and subtyped at NADDEC and the circulating virus is still the same (H5N8). Investigations are ongoing but our current findings reveal that H5N8 virus is the only subtype circulating and is affecting mainly Wild birds (White winged Terns) and domestic birds (Ducks, Chickens and Turkeys). Next Generation Sequencing is recommended for future sample analysis to determine the circulating strains of Avian Influenza viruses in Uganda and why ducks which are believed to be resistant to avian influenza are dying in large numbers.
Key words: Avian Influenza type A, H5N8, Wild, Domestic, Uganda.