Detection of SARS-CoV-2 in Nigeria: laboratory preparedness and report of index case

INTRODUCTION: Heightened surveillance of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) 2019 outbreak in Wuhan, China activated several collaborative laboratory drills on its detection by health institutions in Nigeria. We hereby detail the laboratory detection and confirmation of the novel SARS-CoV-2 virus of the index case imported into Nigeria. METHODS: viral RNA from sputum sample of the index case was tested for SARS-CoV-2 envelope (E) and RNA dependent RNA polymerase (RdRp) genes using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Genetic analysis using a partial sequence of RdRp gene was used for laboratory confirmation, evolutionary inferences, and relatedness to previous strains of betacoronaviruses in Nigeria. RESULTS: both qRT-PCR for the E and RdRp genes indicated the presence of the SARS-CoV-2 RNA by showing cycle threshold (ct) values of 20.27 and 25.26 respectively. On successful completion of the sequencing run, data aligned with >98% similarity of the 2019 circulating strain of Coronavirus SARS-CoV-2. Evolutionary algorithms revealed that the sequence (RdRp gene) of the outbreak circulating strains were more conserved unlike previous coronavirus outbreaks. Data showed that some coronaviruses belonging to the BetaCoV genus had earlier been reported in bats and camels in Nigeria indicating the possibility of sero-protection in exposed populations. CONCLUSIONS: pre-laboratory drills prompted early diagnosis and confirmation of SARS-CoV-2 index case in Nigeria initiating rapid case-definition, contact tracing, and successful epidemiological management of the outbreak. Rapid sequencing of the viral genome during strategic points of the outbreak curve and making libraries of new variants for improved vaccine development are recommended.