First molecular detection of influenza D virus in cattle from commercial farm in Nigeria, Sub-Saharan Africa

Objective: To carrry out molecular surveillance of influenza D virus (IDV) in cattle in Lagos, Nigeria. Methods: Prospective epidemiological investigation was initiated in a large commercial farm market where animals in open pens were reared, sold, and butchered under poor hygienic conditions without adequate biosecurity measures. A total of 80 nasopharyngeal swabs were collected from cattle between October and November 2021. The samples were extracted using an RNA purification kit (NIMR). RNA extracts were amplified following a two-step PCR using FIREScript RT cDNA synthesis kit (Solis Biodyne, Estonia), followed by PCR OneTaq Quick-load 2X master-mix (NEB, UK) in a Rotor-Gene thermocycler (Qiagen, Germany). Amplicons were detected using a 1.5% Gel electrophoresis. Results: In total, 32.5% (26/80) IDV was detected in cattle. Sick animals showed higher burden of IDV with 65.4% (17/26) than 34.6% (9/26) in a healthy population, including 88.2% (15/17) cattle with diarrhoea and 11.8% (2/17) with nausea having IDV. An incidence of 69.2% (18/26) by sex was recorded in bull, which was more than twice compared to 30.7% (8/26) in cow. Age prevalence showed 62.2% (18/26), the highest detection in cattle of four years old, followed by 23.1% (6/26) in five years old, while the lowest 7.7% (2/26) was recorded in three years old. Conclusions: To the best of our knowledge, this study presents the first molecular detection of IDV in Nigeria and West Africa sub-region. It underscores the need for continuous surveillance of IDV at the animal-human interface.