key: cord-0954518-qtobzqiy
authors: Abe, Haruka; Ushijima, Yuri; Bikangui, Rodrigue; Zoa‐Assoumou, Samira; Ondo, Georgelin Nguema; Manouana, Gédéon Prince; More, Ayong; Skarwan, Emilio; Yali‐Assy‐Oyamli, Yoric; Ndeboko, Bénédicte; Myrabelle Avome Houechenou, Rotimi; Djoba Siawaya, Joel Fleury; Lell, Bertrand; Adegnika, Ayola Akim; Yasuda, Jiro
title: Unrecognized introduction of SARS‐CoV‐2 variants of concern to Central Africa: Import and local transmission of B.1.1.7 in Gabon in the very early stage of the variant spread to the African continent
date: 2021-07-09
journal: J Med Virol
DOI: 10.1002/jmv.27164
sha: 588fbb0f439746a210d8767d42dc2e9fd9a6b148
doc_id: 954518
cord_uid: qtobzqiy

The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variant of concern with higher infectivity has already resulted in the enormous increase in infection cases worldwide. We report an unrecognized introduction of the variant B.1.1.7 in Gabon in December 2020, which was the initial phase of the variant introduction to Africa. The B.1.1.7 variant was also detected in a hospitalized patient in January 2021, indicating a rapid spread of the variant in Gabon since its first detection. Phylogenetic analysis revealed that the detected B.1.1.7 variants originated from the distinct regions, strongly suggesting that the B.1.1.7 variant had been repeatedly introduced to Gabon since December 2020. These results provide insights on the unrecognized risks of infections with variants of concern, and show the necessity to conduct continuous genomic monitoring for immediate alert and control of novel SARS‐CoV‐2 variant infections.

The emergence of the variants of concern (VOC) of the severe acute isolates. 3 Furthermore, B.1.1.7 infections have been indicated to lead to 40%-80% higher mortality rates than non-VOC infections. 4 As of April 22, 2021, a cumulative total of 4 467 666 confirmed COVID-19 cases with 118 937 deaths (mortality rate 2.7%) have been reported in Africa. 5 The Africa Centres for Disease Control and Prevention warned that the rising COVID-19 mortality rates across the continent have exceeded the current global average of 2.1%. 6 The continuous introduction of VOCs has been a concern to cause increased cases and mortality in Africa. African and European lineages: shared substitutions in the S and N genes, whereas different substitution patterns in the ORF1ab region (Table 1) . Thus, the B.1.1.7 strains AP360 and JE08 might have been independently introduced into Gabon within a short period.

Concerning the B.1.351 lineage, the AP264 strain formed a cluster with European strains, indicating an import event from Europe to Gabon ( Figure 1C ). As B.1.351 strains of other Central African countries were located independently in the lineage, it is unlikely that B.1.351 strains were transmitted among neighboring countries in Central Africa (e.g., via land transportation). Amino acid substitutions were highly conserved within the cluster to which the AP264 strain belonged (Table 2) . has already exceeded the number in 2020 (64 deaths) in Gabon, 9 possibly reflecting the rapid spread of VOC strains. In Gabon, preventive vaccination against SARS-CoV-2 was initiated in March 2021. 10 As the impact of VOCs on clinical significance and vaccination efficacy remains unclear, it is necessary to establish a borderless genomic surveillance system to combine epidemiological information with the genetic characteristics of SARS-CoV-2 in Central Africa.

World Health Organization

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies

Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7

Africa Centres for Disease Control and Prevention

First evidence for continuous circulation of hepatitis A virus subgenotype IIA in Central Africa

Multiplex PCR method for MinION and Illumina sequencing of zika and other virus genomes directly from clinical samples

World Health Organization. Coronavirus (COVID-19) Dashboard-Gabon

Africa Centres for Disease Control and Prevention. COVID-19 Vaccination Dashboard-Gabon

Unrecognized introduction of SARS-CoV-2 variants of concern to Central Africa: import and local transmission of B.1.1.7 in Gabon in the very early stage of the variant spread to the African continent

We thank all the researchers and staff of Centre de recherches 

The authors declare that there are no conflict of interests. 

The data that support the findings of this study are openly available in GISAID (https://www.gisaid.org/), accession numbers EPI_ISL_1760554-1760556. The supplementary material that supports the detailed methods of this study is available.