Transmission of SARS‑CoV‑2 in northern Ghana: insights from whole‑genome sequencing
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Date
2021
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SPRINGER
Abstract
Following the detection of the frst imported case of COVID-19 in the northern sector of Ghana, we molecularly charac terized
and phylogenetically analysed sequences, including three complete genome sequences, of severe acute respiratory
syndrome coronavirus 2 obtained from nine patients in Ghana. We performed high-throughput sequencing on nine samples
that were found to have a high concentration of viral RNA. We also assessed the potential impact that long-distance transport
of samples to testing centres may have on sequencing results. Here, two samples that were similar in terms of viral RNA
concentration but were transported from sites that are over 400 km apart were analyzed. All sequences were compared to
previous sequences from Ghana and representative sequences from regions where our patients had previously travelled. Three
complete genome sequences and another nearly complete genome sequence with 95.6% coverage were obtained. Sequences
with coverage in excess of 80% were found to belong to three lineages, namely A, B.1 and B.2. Our sequences clustered in
two diferent clades, with the majority falling within a clade composed of sequences from sub-Saharan Africa. Less RNA
fragmentation was seen in sample KATH23, which was collected 9 km from the testing site, than in sample TTH6, which was
collected and transported over a distance of 400 km to the testing site. The clustering of several sequences from sub-Saharan
Africa suggests regional circulation of the viruses in the subregion. Importantly, there may be a need to decentralize testing
sites and build more capacity across Africa to boost the sequencing output of the subregion.
Description
This article is published by Springer and is also available at https://doi.org/10.1007/s00705-021-04986-3
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Citation
Archives of Virology (2021) 166:1385–1393 https://doi.org/10.1007/s00705-021-04986-3