A partial sequence of SARS-CoV-2 (RdRp region) with a length of 486 bp (15321bp to 15806bp) was generated. Sanger sequencing (ABI 3130 xl) using specific primer targeting the RdRp region was done.
#COVID 19 GENOME SEQUENCE ANALYSIS FULL#
A full genome of SARS-CoV-2 was assembled with a length of 29,759 bp and mean coverage depth of 20X (Figure 1).Īt the Centre for Human Virology and Genomics, NIMR, RT-qPCR was carried out using the assay designed by BGI China to confirm the presence of SARS-CoV-2 viral RNA with a Ct value of 26, targeting the high conservative region in 2019-nCoV genome. Metagenomic sequencing libraries were prepared from total RNA as previously described (Matranga et al., 2016) and sequenced using one of the two Illumina MiSeqs in the sequencing platform of ACEGID. RT-qPCR was repeated at ACEGID using the assay designed by the US CDC and confirmed the presence of SARS-CoV-2 viral RNA (Ct values of 28, 29, and 30 for N1, N2 and N3 viral gene targets, respectively), with no NTC amplification. On the 1st of March 2020, a clinical specimen, specifically, a sputum specimen resuspended in 500µL of viral transport medium (VTM), was sent to ACEGID, Redeemer’s University, Nigeria, and Centre for Human Virology and Genomics, Nigerian Institute of Medical Research for sequencing and molecular characterization.Īt ACEGID, viral RNA was extracted using the QiAmp viral RNA mini kit (Qiagen). The case was diagnosed by the Centre for Human and Zoonotic Virology (CHAZVY), College of Medicine University of Lagos/Lagos University Teaching Hospital (LUTH), part of the Laboratory Network of the NCDC.
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On the 27th of February 2020, Nigeria confirmed its first case of COVID-19 at the Infectious Disease Hospital in Yaba, Lagos.
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The Nigerian Centre for Disease Control (NCDC), the African Centre of Excellence for the Genomics of Infectious Disease (ACEGID) at Redeemer’s University, Ede, Nigeria (RUN), the Centre for Human Virology and Genomics (CHVG), Nigerian Institute of Medical Research (NIMR), the Centre for Human and Zoonotic Virology (CHAZVY), College of Medicine University of Lagos/ Lagos University Teaching Hospital (LUTH), the Lagos State Ministry of Health Bio-Safety Level 3 (BSL-3) Bio-Bank facility and partners report the first genome sequence of SARS-CoV-2 from Africa, from the first confirmed case of COVID-19 in Nigeria.