“Looking for a needle in a haystack: nanopore sequencing of a new Simian immunodeficiency virus (SIV) from a chacma baboon (Papio usrinus)” is the title of Susan Engelbrecht’s 2019 London Calling session. Engelbrecht, from Stellenbosch University in South Africa, spoke about primate lentiviruses and their “extreme genetic variability.” SIV is a retrovirus about 9 kb in length. They have been working on SIV and HIV since the 1980s. One baboon SIV sample was stored in a freezer for thirty years, and the high molecular weight cellular DNA was finally sequenced in 2018! They used the LSK-109 kit and a GridION with FLO-MIN106 flow cells. They used EPI2ME and Geneious Prime to analyze the sequence. They had over 890,000 reads, and of those, thirteen were aligned to the virus. Phylogenetic analyses with BLAST and MEGA helped place the SIV retrovirus in a phylogenetic tree. The virus was most closely related to SIV viruses in South Africa. Two original scientists involved in isolating the cells/virus were still involved in the project. Two newer group members are doing Sanger Sequencing of the virus (integrated) in the cellular DNA. What a fascinating story!
