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Genomic Surveillance of SARS-CoV-2 in Mozambique Using Pandemic-Scale Phylogenies
20 Pages Posted: 27 Sep 2022
More...Abstract
Background: Since the SARS-CoV-2 outbreak, sequencing efforts from virtually all countries have led to an unprecedented amount of genome data from the virus. Even so, unequal sampling between Global North and South hinders the implementation of global genomic surveillance systems.
Methods: UShER is able to reconstruct a phylogeny with millions of sequences by efficient sample placement in a tree. We used this tool to understand the dynamics of Beta and Delta waves in Mozambique, maximising the use of available genomic data. We reconstructed two phylogenies with ~7.6 million sequences to which we added Beta and Delta samples. Thanks to pandemic-scale phylogenies, we identified the timing of introduction events of the variants in the country and their potential geographic origin.
Findings: We identified 187 Beta introductions, divided in 42 transmission groups and 145 unique introductions, mostly from South Africa, between August 2020 and July 2021. For Delta, we identified 220 introductions, with 49 transmission groups and 171 unique introductions, mostly from the United Kingdom, India and South Africa, between April 2021 and November 2021.
Interpretation: The high number of introductions and their origins suggests that movement restrictions effectively avoided imports from non-African countries, but not from surrounding countries. Our results raise questions about the imbalance between economic cost, imposed by these restrictions, and health benefits. This new understanding of pandemic dynamics in Mozambique can be used to inform public health interventions to control the spread of new variants in the country.
Funding Information: This publication was produced by MozCovid which is part of the EDCTP2 programme supported by the European Union (grant number RIA2020EF-3005-MozCOVID). This work was also supported by the CHAMPS project which is funded by the Bill & Melinda Gates Foundation under the Grant OPP1126780 to Robert Breiman, subcontract SC00003286), the European Research Council under the European Union’s Horizon 2020 Research and Innovation Program Grant 101001038 (TB-RECONNECT), the European Commission – NextGenerationEU (Regulation EU 2020/2094), through CSIC's Global Health Platform (PTI Salud Global), and the Departament d’Universitats i Recerca de la Generalitat de Catalunya (AGAUR; 2017 SGR 664). In addition, this work was funded by the Ministerio de Ciencia e Innovación (Spanish Government) Project PID2019-104477RB-I00. CISM is supported by the Government of Mozambique and the Spanish Agency for International Development (AECID). ISGlobal is a member of the CERCA Programme, Generalitat de Catalunya (http://cerca.cat/en/suma/). We also acknowledge support from the Spanish Ministry of Science and Innovation through the “Centro de Excelencia Severo Ochoa 2019-2023” Program (CEX2018-000806-S).
Declaration of Interests: We declare no competing interests.
Ethics Approval Statement: Informed written consent was obtained from all participants. The study was approved by Centro de Investigação em Saúde de Manhiça (CISM) institutional ethics committee and the Mozambican Ministry of Health National Bioethics Committee (Approval No. 80/CNBS/2020).
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