This study outlines the processes involved in setting up genomic sequencing in order to investigate the previously mentioned hospital outbreak in South Africa. On 15 March 2020, South Africa declared a state of emergency, and on 27 March, a countrywide lockdown was implemented, which included grounding most of the international flights. On 9 March 2020, another returned traveler from Europe started a large chain of infection in a hospital in Durban, KwaZulu-Natal. On 5 March 2020, the first COVID-19 case was reported in KwaZulu-Natal, South Africa, from a traveler from Italy.

This can then be used to trace the path of transmission within a population and to possibly identify the probable source, potentially leading to an improved public health response. Genomic sequencing can be used to rapidly and accurately identify the transmission routes of the pathogen. These outbreaks require urgent testing and tracing, identification of the causative agent, and epidemiological investigations to allow for appropriate infection control and for clusters of patients to be identified. Localized outbreaks are common when SARS-CoV-2 is introduced in a new geographic area. Despite widespread attempts to contain the virus in China, within a few months, the outbreak had reached and affected 215 countries and territories around the world, including all countries in Africa. This virus was labeled severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and defined as the causal agent of Coronavirus Disease 2019 (COVID-19).

In late December 2019, a mysterious viral pneumonia which had infected a number of people in Wuhan, China, was attributed to a new coronavirus. In order to allow other laboratories to learn from our experience, all of the library preparation and bioinformatics protocols are publicly available at protocols.io and distributed to other laboratories of the Network for Genomics Surveillance in South Africa (NGS-SA) consortium. A simple bioinformatics workflow for the assembly of high-quality genomes in near-real time was also fine-tuned. Furthermore, the new protocols increased the success rate of sequencing whole viral genomes.

Despite this, three different library preparation methods for Illumina sequencing were set up, and the hands-on library preparation time was decreased from twelve to three hours, which enabled the outbreak investigation to be completed in just a few weeks. This included problems with the length of the original genotyping protocol, unavailability of reagents, and sample degradation and storage. This manuscript outlines the obstacles encountered in order to genotype SARS-CoV-2 in near-real time during an urgent outbreak investigation. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes can be used to trace the path of transmission within a hospital. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). The COVID-19 pandemic has spread very fast around the world.

Geneious prime 2020