Looking for a needle in a haystack: nanopore sequencing of a new Simian immunodeficiency virus (SIV) from a chacma baboon (Papio ursinus)

Susan Engelbrecht, from Stellenbosch University, spoke about attempting to sequence simian immunodeficieny virus from chacma baboons. Susan opened by explaining that the SIV virus has a single-stranded RNA genome of approximately 9,500 nucleotides. The viral life cycle involves reverse transcription and integration into the host cell, where it can replicate. One of the unique features of this virus is its extreme genetic variability: closely-related strains may show 45% genetic variability, “making it very difficult to design primers for”. Susan said that in the 1980s, they managed to isolate some of these viruses, and confirmed they had been integrated into the host genome by visualising the cDNA on a Southern blot. She said that she then “waited 30 years… for the MinION” and used the Ligation Sequencing Kit (SQK-LSK109) and the GridION to sequence the low-abundance cDNA viral genome. Despite the number of reads aligning to the viral genome due to the large amount of background host DNA, a consensus sequence was generated which was used for phylogenetic analysis. This showed that the virus clustered with those known to infect the Vervet monkey.