Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2020 Jun 9:36:80.
doi: 10.11604/pamj.2020.36.80.23723. eCollection 2020.

Genome sequencing and the diagnosis of novel coronavirus (SARS-COV-2) in Africa: how far are we?

Muki Shey  1   2 , Joseph Chukwudi Okeibunor  3 , Ali Ahmed Yahaya  3 , Belinda Louise Herring  3 , Oyewale Tomori  3 , Sheick Omar Coulibaly  3 , Hieronyma Nelisiwe Gumede-Moeletsi  3 , Jason Mathiu Mwenda  3 , Zabulon Yoti  3 , Charles Shey Wiysonge  4   5 , Ambrose Otau Talisuna  3
Affiliations
Review

Genome sequencing and the diagnosis of novel coronavirus (SARS-COV-2) in Africa: how far are we?

Muki Shey et al. Pan Afr Med J. .

Abstract

The coronavirus disease (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) has become a pandemic. There is currently no vaccine or effective treatment for COVID-19. Early diagnosis and management is key to favourable outcomes. In order to prevent more widespread transmission of the virus, rapid detection and isolation of confirmed cases is of utmost importance. Real time reverse transcriptase polymerase chain reaction (RT-PCR) is currently the "gold standard" for the detection of SARS-COV-2. There are several challenges associated with this test from sample collection to processing and the longer turnaround time for the results to be available. More rapid and faster diagnostic tests that may produce results within minutes to a few hours will be instrumental in controlling the disease. Serological tests that detect specific antibodies to the virus may be such options. In this review, we extensively searched for studies that compared RT-PCR with serological tests for the diagnosis of COVID-19. We extracted the data from the various selected studies that compared the different tests and summarised the available evidence to determine which test is more appropriate especially in Africa. We also reviewed the current evidence and the challenges for the genome sequencing of SARS-COV-2 in Africa. Finally, we discuss the relevance of the different diagnostic tests and the importance of genome sequencing in identifying potential therapeutic options for the control of COVID-19 in Africa.

Keywords: COVID-19; RT-PCR; SARS-COV-2; antibody test; genome sequencing; rapid diagnostic test (RDT); serology test.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

References

    1. WHO. African countries move from COVID-19 readiness to response as many confirm cases. 2020. Accessed on 21 May 2020.
    1. CDC. Interim guidelines for collecting, handling and testing clinical specimens from persons for coronavirus disease 2019 (COVID-19) 2020 Accessed on 29 April 2020.
    1. Liu J, Xiao Y, Shen Y, Shi C, Chen Y, Shi P, et al. Detection of SARS-CoV-2 by RT-PCR in anal from patients who have recovered from coronavirus disease 2019. J Med Virol. 2020 Apr 14; doi: 10.1002/jmv.25875. - DOI - PMC - PubMed
    1. Zhang W, Du RH, Li B, Zheng XS, Yang XL, Hu B, et al. Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes. Emerg Microbes Infect. 2020;9(1):386–389. - PMC - PubMed
    1. Li Y, Yao L, Li J, Chen L, Song Y, Cai Z, et al. Stability issues of RT-PCR testing of SARS-CoV-2 for hospitalized patients clinically diagnosed with COVID-19. J Med Virol. 2020 Mar 26; doi: 10.1002/jmv.25786. - DOI - PMC - PubMed