Isolation and characterization of SARS-CoV-2 in Kenya

Abstract

The emergence of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) from Wuhan, China, in December 2019 raised a global health concern that eventually became a pandemic affecting almost all countries worldwide. The respiratory disease has infected over 530 million people worldwide, with over 950,000 deaths recorded. This has led scientists to focus their efforts on understanding the virus to develop effective means to diagnose, treat, prevent, and control this pandemic. One of the areas of focus is isolation of this virus, which plays a crucial role in understanding the viral dynamics in the laboratory. In this study, we report the isolation and detection of locally circulating SARS-CoV-2 in Kenya. The isolates were cultured on Vero Cercopithecus cell line (CCL-81) cells, RNA extraction conducted from the supernatants, and reverse transcriptase-polymerase chain reaction (RT-PCR). Genome sequencing was done to profile the strains phylogenetically and identify novel and previously reported mutations. Vero CCL-81 cells were able to support the growth of SARS-CoV-2 in vitro, and mutations were detected from the two isolates sequenced (001 and 002). These virus isolates will be expanded and made available to the Kenya Ministry of Health and other research institutions to advance SARS-CoV-2 research in Kenya and the region. Author SummaryThe Coronavirus disease 2019 (COVID-19) pandemic is caused by a type of coronavirus that emerged in Wuhan, China in December 2019 and later spread to almost all countries. Many countries are still finding ways to contain it. The virus has been studied in many ways to investigate its origin, infectivity, and evolution. Different variants of the virus have emerged and spread, causing a lot of concern as to whether the pandemic will end soon. Significant studies have proven the ability of the virus to grow in the laboratory using cell lines that offer the necessary conditions. Therefore, this study sought to find out the growth of the virus in specific monkey cell line and the variant circulating within the Kenyan population. We found that the selected cell lines supported viral growth outside a human host system. In addition, the circulating virus was found to have evolved to enhance its survival mechanism. This is the first study in Kenya to report this viruss isolation, culture, and identification in monkey kidney cells. These cells supported the growth of the virus in the laboratory and analysing the genome of the growth products showed the virus was related to previously reported strains with multiple changes in its whole DNA sequence.