The confirmed case fatality rate for the coronavirus disease 2019 (COVID-19) in Ghana has dropped from a peak of 2% in March to be consistently below 1% since May 2020. Globally, case fatality rates have been linked to the strains/clades of circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within a specific country. Here we present 46 whole genomes of SARS-CoV-2 circulating in Ghana, from two separate sequencing batches: 15 isolates from the early epidemic (March 12–April 1 2020) and 31 from later time-points ( 25–27 May 2020). Sequencing was carried out on an Illumina MiSeq system following an amplicon-based enrichment for SARS-CoV-2 cDNA. After genome assembly and quality control processes, phylogenetic analysis showed that the first batch of 15 genomes clustered into five clades: 19A, 19B, 20A, 20B, and 20C, whereas the second batch of 31 genomes clustered to only three clades 19B, 20A, and 20B. The imported cases (6/46) mapped to circulating viruses in their countries of origin, namely, India, Hungary, Norway, the United Kingdom, and the United States of America. All genomes mapped to the original Wuhan strain with high similarity (99.5–99.8%). All imported strains mapped to the European superclade A, whereas 5/9 locally infected individuals harbored the B4 clade, from the East Asian superclade B. Ghana appears to have 19B and 20B as the two largest circulating clades based on our sequence analyses. In line with global reports, the D614G linked viruses seem to be predominating. Comparison of Ghanaian SARS-CoV-2 genomes with global genomes indicates that Ghanaian strains have not diverged significantly from circulating strains commonly imported into Africa. The low level of diversity in our genomes may indicate lower levels of transmission, even for D614G viruses, which is consistent with the relatively low levels of infection reported in Ghana.

加纳 2019 年冠状病毒病 (COVID-19) 确诊病死率已从 3 月份 2% 的峰值下降至 2020 年 5 月以来一直低于 1%。在全球范围内，病死率与毒株/进化枝有关特定国家内流行的严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2)。在这里，我们展示了在加纳流行的 SARS-CoV-2 全基因组，来自两个独立的测序批次：15 个分离株来自早期流行病（2020 年 3 月 12 日至 4 月 1 日），31 个分离株来自后期时间点（2020 年 5 月 25 日至 27 日） 。对 SARS-CoV-2 cDNA 进行基于扩增子的富集后，在 Illumina MiSeq 系统上进行测序。经过基因组组装和质量控制过程后，系统发育分析显示，第一批 15 个基因组聚类为 5 个进化枝：19A、19B、20A、20B 和 20C，而第二批 31 个基因组仅聚类为 3 个进化枝 19B、20A、和20B。输入病例 (6/46) 与其原籍国（即印度、匈牙利、挪威、英国和美利坚合众国）的流行病毒相对应。所有基因组均与原始武汉毒株具有高度相似性（99.5-99.8%）。所有进口菌株都映射到欧洲超进化枝 A，而 5/9 的本地感染个体携带来自东亚超进化枝 B 的 B4 进化枝。根据我们的序列分析，加纳似乎有 19B 和 20B 作为两个最大的流行进化枝。根据全球报告，D614G 相关病毒似乎占主导地位。加纳 SARS-CoV-2 基因组与全球基因组的比较表明，加纳毒株与通常输入非洲的流行毒株没有显着差异。 我们基因组的低水平多样性可能表明传播水平较低，即使对于 D614G 病毒也是如此，这与加纳报告的相对较低的感染水平一致。