key: cord-0815292-6s0ibhm3
authors: Lin, Lei; Zhang, Juling; Rogers, James; Campbell, Allan; Zhao, Jianjun; Harding, Doris; Sahr, Foday; Liu, Yongjian; Wurie, Isata
title: The dynamic change of SARS-CoV-2 variants in Sierra Leone
date: 2022-01-06
journal: Infect Genet Evol
DOI: 10.1016/j.meegid.2022.105208
sha: db3f057d6b7e012862fcc4e49c5d4f8f02fe0825
doc_id: 815292
cord_uid: 6s0ibhm3

Since the beginning of the SARS-CoV-2 pandemic, the emergence of multiple new variants posed an increased risk to global public health. The aim of this study is to investigate SARS-CoV-2 variants and possible transmission of variants of concern (VOCs) in Sierra Leone. A total of 65 nasal swab samples were collected from COVID-19 cases in Sierra Leone, among which 24 samples were collected during the second wave and 41 samples were collected during the third wave. Nanopore sequencing generated 54 SARS-CoV-2 whole genomes. The second COVID-19 wave was mainly caused by R.1 lineage while the third COVID-19 wave was dominated by B.1.617.2 lineage (Delta variant). The phylogenetic analysis suggested multiple introductions of SARS-CoV-2 Delta variant into Sierra Leone and subsequent local transmission in this country. Our findings highlight the importance of genomic surveillance of SARS-CoV-2 variants and the urgent need for implementation of strengthened public health and social measures (PHSM) to control the spread of virus variants.

public health and social measures or available diagnostics, vaccines, therapeutics [5] [6] [7] .

In addition, variants of interest (VOIs) are defined as variants with specific genetic changes that are predicted or known to affect virus characteristics and identified to cause apparent epidemiological impacts to suggest an emerging risk to global public health. According to the data from WHO, there are four currently designated VOCs (Alpha, Beta, Gamma and Delta) and four currently designated VOIs (Eta, Iota, Kappa and Lambda). The number of countries reporting VOCs continues to increase. 

Increased household secondary attacks rates with Variant of Concern SARS-CoV-2 index cases

Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at

Detection of a SARS-CoV-2 variant of concern in South Africa

Risk of hospitalisation associated with infection with SARS-CoV-2 lineage B.1.1.7 in Denmark: an observational cohort study

Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization

Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence

Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area

Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7

mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants

Predicted dominance of variant Delta of SARS-CoV-2 Credit Author Statement Lei Lin: Conceptualization, Methodology

Resources, Investigation Jianjun Zhao: Software, Formal analysis Doris Harding: Resources, Investigation Foday Sahr: Resources, Investigation

Conceptualization, Original draft preparation, Review & Editing Isata Wurie: Conceptualization, Supervision

The authors declare that they have no competing interests.All authors have no financial and personal relationships with other people or