PT - JOURNAL ARTICLE AU - Sureshnee Pillay AU - Jennifer Giandhari AU - Houriiyah Tegally AU - Eduan Wilkinson AU - Benjamin Chimukangara AU - Richard Lessells AU - Yunus Moosa AU - Inbal Gazy AU - Maryam Fish AU - Lavanya Singh AU - Khulekani Sedwell Khanyile AU - Vagner Fonseca AU - Marta Giovanetti AU - Luiz Carols Alcantara AU - Tulio de Oliveira TI - Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic AID - 10.1101/2020.06.10.144212 DP - 2020 Jan 01 TA - bioRxiv PG - 2020.06.10.144212 4099 - http://biorxiv.org/content/early/2020/06/10/2020.06.10.144212.short 4100 - http://biorxiv.org/content/early/2020/06/10/2020.06.10.144212.full AB - The COVID-19 pandemic spread very fast around the world. A few days after the first detected case in South Africa, an infection started a large hospital outbreak in Durban, KwaZulu-Natal. Phylogenetic analysis of SARS-CoV-2 genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. In this manuscript, we outline the obstacles we encountered in order to genotype SARS-CoV-2 in real-time during an urgent outbreak investigation. In this process, we encountered problems with the length of the original genotyping protocol, reagent stockout and sample degradation and storage. However, we managed to set up three different library preparation methods for sequencing in Illumina. We also managed to decrease the hands on library preparation time from twelve to three hours, which allowed us to complete the outbreak investigation in just a few weeks. We also fine-tuned a simple bioinformatics workflow for the assembly of high-quality genomes in real-time. In order to allow other laboratories to learn from our experience, we released all of the library preparation and bioinformatics protocols publicly and distributed them to other laboratories of the South African Network for Genomics Surveillance (SANGS) consortium.Competing Interest StatementThe authors have declared no competing interest.