key: cord-0889137-2gan8j84 authors: Manouana, Gédéon Prince; Maloum, Moustapha Nzamba; Bikangui, Rodrigue; Oye Bingono, Sam O'neilla; Ondo, Georgelin Nguema; Honkpehedji, Josiane Yabo; Rossatanga, Elie Gide; Assoumou, Samira Zoa; Pallerla, Srinivas Reddy; Rachakonda, Sivaramakrishna; Ndong, Rodrigue Mintsa; Lekana-Douki, Jean-Bernard; Siawaya, Joël-Fleury Djoba; Borrmann, Steffen; Kremsner, Peter G.; Lell, Bertrand; Velavan, Thirumalaisamy P.; Adegnika, Ayola Akim title: Emergence of B.1.1.318 SARS-CoV-2 viral lineage and high incidence of alpha B.1.1.7 variant of concern in Republic of Gabon date: 2021-11-03 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2021.10.057 sha: 84382991c2e230147b6470ba12a007f2202ba6ba doc_id: 889137 cord_uid: 2gan8j84 Objective Variants of concern (VOCs) associated with relatively high transmissibility appear to be spreading rapidly in Gabon. Therefore, it is imperative to understand the distribution of several variants of concern in the population, which could have implications for transmissibility and vaccine efficacy. Methods Between February and May 2021, SARS-CoV-2 genomes were sequenced using the Oxford nanopore MinION method and the respective genome diversity was elucidated. Phylogenetic analysis was performed and genomes were classified using pangolin lineages. Results The results highlight the increase (46%) of the alpha variant of concern (B.1.1.7) in the Gabonese population over the study period. In addition, an increase (31%) in the B.1.1.318 lineage, which is associated with high transmission and impaired vaccine efficacy (D614G+E484K+Y144del), was detected. Conclusion With the second wave ongoing, our findings highlight the need for surveillance of the SARS-CoV-2 genome in the Republic of Gabon and should provide useful guidance to policy makers in selecting an appropriate vaccine for the population. 2 Emergence of B.1.1.318 SARS-CoV-2 viral lineage and high incidence of alpha B.1.1.7 variant of concern in Republic of Gabon Introduction SARS-CoV-2 Variants of concern (VOC) appear to spread more easily and other emerging variants are also gaining attention as they are known as either "variant of interest" (VOI) or "variant under investigation" (VUI), that increase transmission, warranting further studies. Since the onset of the COVID-19 pandemic, the SARS-CoV-2 genomes have accumulated genetic diversity, leading to increased transmission with altered viral properties (Kraemer et al. 2021 (WHO 2021) . This may be due to factors such as age, demographics, the constant exposure and burden of co-infections (e.g. with helminths) (Velavan et al. 2021 ). The current second wave, which has been ongoing since February 2021, has led to increased SARS-Cov2 genomic surveillance. This study aims to reveal the actual distribution of SARS-CoV-2 variants circulating in the country. The Centre de Recherches Médicales de Lambaréné undertook COVID-19 surveillance between February and May 2021. The study participants were residents living in Lambaréné region. Samples with confirmed Ct values ≤30 were subsequently sequenced using the MinION sequencing platform (Oxford Nanopore Technologies, Oxford, UK). Libraries were prepared according to the nCoV-2019 sequencing protocol (RAPID barcoding,1200bp amplicon) V.3 (Freed et al. 2021 ). Viral genome assembly was performed using the ARTIC pipeline (https://github.com/artic-network/fieldbioinformatics). SARS-CoV-2 genomes (n=74) circulating between February and May 2021 were retrieved from the GISAID for African (n=15) and European (n=14) lineages. Only complete viral genomes were included in the analysis, and different previously represented lineages (n=27) from 29 countries were included. All 74 genomes in the present study were aligned with Wuhan-Hu-1 strain (NC_045512.2) using Multiple Alignment using Fast Fourier Transform The sequenced SARS-COV-2 genomes and their respective genome diversity with distinct viral lineages is summarized in Table1 (Figure 1 ). The observation of an increase in incidence of B. AAA and BL designed the study procedures. GPM performed all experimental procedures. MNM, RB SOOB, GNO, JYH, SZA, EGR, and RMN were involved in sampling procedures and collating the meta data. SRP and SR supported experimental procedures and performed phylogenetic analysis. JBLD, JFDS, SB, BL, and PGK contributed to the study design and patient recruitment. AAA, GPM and TPV analysed the data and wrote the manuscript. Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV-2 Using 1200 Bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding

Identification of SARS-CoV-2 P.1-Related Lineages in Brazil Provides New Insights about the Mechanisms of Emergence of Variants of Concern

MAFFT: A Novel Method for Rapid Multiple Sequence Alignment Based on Fast Fourier Transform Spatiotemporal Invasion Dynamics of SARS-CoV 1.1.7 Emergence Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool Preliminary Genomic Characterisation of an Emergent SARS-CoV-2 Lineage in the UK Defined by a Novel Set of Spike Mutations Genomic Epidemiology -Virological Detection of a SARS-CoV-2 Variant of Concern in South Africa W-IQ-TREE: A Fast Online Phylogenetic Tool for Maximum Likelihood Analysis COVID-19 and Syndemic Challenges in 'Battling the Big Three': HIV, TB and Malaria WHO Coronavirus (COVID-19) Dashboard; Accessed on 25 SARS-CoV-2 Emerging Variants in Africa: View from 1 (N=2) 3 EPI_ISL_1913080; EPI_ISL_2097230 We thank all researchers and staff of CERMEL who are working for COVID-19 diagnosis.The authors gratefully acknowledge the encouragement of the Gabonese Government. We also thank the COPIL committee and the Ministry of Health.The authors TPV and AAA thank the support of PANDORA-ID NET. AAA and MGP are members of CANTAM (EDCTP- The data supporting reported results are available on request. The authors declare no conflict of interest in the submitted work. AIDCO: mobilization of research funds for covid-19 as a public health emergency EDCTP RIA 2020 EF-2961 Informed consent was obtained from all subjects involved in the study.