Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Mar 6;3(3):e0001593.
doi: 10.1371/journal.pgph.0001593. eCollection 2023.

Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique

Nalia Ismael  1   2 , Stephanie van Wyk  3   4 , Houriiyah Tegally  3   4 , Jennifer Giandhari  3   4 , James Emmanuel San  3   4 , Monika Moir  3   4 , Sureshnee Pillay  3   4 , Christian Utpatel  5 , Lavanya Singh  3   4 , Yeshnee Naidoo  3   4 , Upasana Ramphal  3   4 , Nédio Mabunda  1 , Nuro Abílio  1 , Paulo Arnaldo  1 , Joicymara Xavier  3   4   6 , Daniel Gyamfi Amoako  7   8 , Josie Everatt  7 , Yajna Ramphal  3   4 , Arisha Maharaj  3   4 , Leonardo de Araujo  5 , Ugochukwu J Anyaneji  3   4 , Derek Tshiabuila  3   4 , Sofia Viegas  1 , Richard Lessells  3   4 , Susan Engelbrecht  2 , Eduardo Gudo  1 , Ilesh Jani  1 , Stefan Niemann  5   9 , Eduan Wilkinson  3   4 , Túlio de Oliveira  3   4
Affiliations

Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique

Nalia Ismael et al. PLOS Glob Public Health. .

Abstract

Mozambique reported the first case of coronavirus disease 2019 (COVID-19) in March 2020 and it has since spread to all provinces in the country. To investigate the introductions and spread of SARS-CoV-2 in Mozambique, 1 142 whole genome sequences sampled within Mozambique were phylogenetically analyzed against a globally representative set, reflecting the first 25 months of the epidemic. The epidemic in the country was marked by four waves of infection, the first associated with B.1 ancestral lineages, while the Beta, Delta, and Omicron Variants of Concern (VOCs) were responsible for most infections and deaths during the second, third, and fourth waves. Large-scale viral exchanges occurred during the latter three waves and were largely attributed to southern African origins. Not only did the country remain vulnerable to the introductions of new variants but these variants continued to evolve within the borders of the country. Due to the Mozambican health system already under constraint, and paucity of data in Mozambique, there is a need to continue to strengthen and support genomic surveillance in the country as VOCs and Variants of interests (VOIs) are often reported from the southern African region.

PubMed Disclaimer

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Schematic representation of the progression and milestones occurring during the COVID-19 pandemic in Mozambique (March 2020- April 2022).
The number of reported COVID-19 cases milestones were illustrated in blue, the total deaths milestones are illustrated in red, the first detection of new variants are illustrated in black, and other key milestones such as local transmission and vaccination rollout are illustrated in orange.
Fig 2
Fig 2. SARS-CoV-2 epidemiological dynamics in Mozambique.
(A) Schematic illustration of genomic and epidemiological data. Changes in the daily reported COVID-19 cases are indicated in blue, the cumulative death count associated with COVID-19 disease in orange, and the estimated Re values are indicated in purple. (B) Geographic map of Mozambique illustrating the origin and count genome sequences generated in this study (The map for Mozambique was accessed using the software packages used for mapping, GADM, https://gadm.org/download_country.html). Genome sequences without information on the province from which it originated were omitted from this graph.
Fig 3
Fig 3. Lineage and phylogenetic analysis.
(A) Phylogenetic tree of SARS-CoV-2 sequences representing global and Mozambique subsets during the first 25 months of the pandemic. Taxa obtained from Mozambique are illustrated with circles and the lines represent taxa from the global dataset. (B) Lineage through time plots illustrate the change in genetic diversity of sequenced genomes sampled in Mozambique throughout the study period.
Fig 4
Fig 4. SARS-CoV-2 import and export events inferred for Mozambique.
The bar charts illustrate the average number of SARS-CoV-2 introduction events (top), and the average number of export events (bottom).
See this image and copyright information in PMC

References

    1. Shu Y, McCauley J. GISAID: Global initiative on sharing all influenza data -from vision to reality. Euro Surveill. 2017;22: 30494. doi: 10.2807/1560-7917.ES.2017.22.13.30494 - DOI - PMC - PubMed
    1. Masood N, Malik SS, Raja MN, Mubarik S, Yu C. Unraveling the Epidemiology, Geographical Distribution, and Genomic Evolution of Potentially Lethal Coronaviruses (SARS, MERS, and SARS CoV-2). Front Cell Infect Microbiol. 2020;10: 499. doi: 10.3389/fcimb.2020.00499 - DOI - PMC - PubMed
    1. Naqvi AAT, Fatima K, Mohammad T, Fatima U, Singh IK, Singh A, et al.. Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach. Biochim Biophys Acta Mol Basis Dis. 2020;1866: 165878. doi: 10.1016/j.bbadis.2020.165878 - DOI - PMC - PubMed
    1. Cantón R, De Lucas Ramos P, García-Botella A, García-Lledó A, Gómez-Pavón J, González Del Castillo J, et al.. New variants of SARS-CoV-2. Rev Esp Quimioter. 2021;34: 419–428. doi: 10.37201/req/071.2021 - DOI - PMC - PubMed
    1. Otto SP, Day T, Arino J, Colijn C, Dushoff J, Li M, et al.. The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic. Curr Biol. 2021;31: R918–R929. doi: 10.1016/j.cub.2021.06.049 - DOI - PMC - PubMed

LinkOut - more resources