Genetic Detection and Characterization of Influenza Viruses in Selected Wildlife and Humans at High-risk Interface in Laikipia County.

Abstract

Incidences of emerging and re-emerging zoonotic infectious diseases increase especially at the livestock-wildlife-human overlap, an interface commonly found in Kenya. Such overlaps intensify during the dry season and prolonged drought. This is especially true for Laikipia County, populated by dense wildlife and many pastoralists; hence detection, and characterization of influenza viruses in bats, rodents, Olive baboons, and human sample was carried out at this high-risk interface. 1497 oral and rectal swab samples in TRIzol were collected during the wet and dry season which coincide with the month of May and September respectively. This was done from 2017 to 2018 in olive baboons (Papio anubis), bats (Chaerephon spp), rodents (Mus musculus) and humans. Oral and rectal/fecal samples in TRIzol were analyzed using gene specific primers directed to conserved regions of polymerase protein 1 gene of influenza viruses; sequencing and sequence analysis was done on PCR positive samples. Nine samples were positive for influenza virus but only seven samples (approx. 0.6%) were sequenced successfully (one oral swab from human, five orals swabs from baboons and one rectal sample from bat). Nucleotide and aminoacid sequence similarity searches (through BLASTn, BLASTp) of the diagnostic 400-bp PB1 amplicons derived from bat, Olive baboons and human samples were very similar to each other and were closely related to influenza type A sequences as the most significant matches (>95%). Phylogenetic analyses of these viruses revealed a close relation between non-human primates and human influenza virus sequences (76 -78% nucleotide and amino acid sequence similarity). Bat influenza virus sequence (KEAB0224) was genetically distinct and appeared as an outgroup in all phylogenetic trees suggesting the Bat virus was more ancient compared to the human. Distinct clustering of the detected Bat influenza virus when compared to viral sequences available in the database could be due to this being the first-time influenza virus is being detected in bat and non-human primates in Laikipia County. Hence further work on influenza virus diversity in Kenya, as well as on the ecology and behavior of susceptible species, is needed to understand the origins and evolution