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Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study
Francisco José Martínez-Martínez1, Arsenia J Massinga2, Áuria De Jesus2
1Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain.
The Lancet. Global Health
|May 18, 2023
Summary
Genomic surveillance in Mozambique revealed numerous introductions of SARS-CoV-2 beta and delta variants, primarily from South Africa and the UK. Travel restrictions limited non-African introductions but not regional spread, impacting public health strategies.
Area of Science:
- Genomic epidemiology
- Viral evolution and surveillance
- Public health policy
Background:
- Global SARS-CoV-2 sequencing efforts are extensive but unequally distributed, with low-income countries having significant knowledge gaps.
- Understanding pandemic dynamics in underrepresented regions is crucial for effective global and local public health decision-making.
- Genomic surveillance in Mozambique is essential for tracking variant introductions and informing pandemic response.
Purpose of the Study:
- To determine the timing and origin of SARS-CoV-2 variant introductions in Mozambique.
- To analyze the effectiveness of movement restrictions on limiting variant spread.
- To leverage pandemic-scale phylogenies for understanding local transmission dynamics.
Main Methods:
- Retrospective observational study in southern Mozambique analyzing respiratory symptomatic patients.
- Inclusion of data from hospital-based surveillance (MozCOVID), national surveillance, and public genomic databases (GISAID).
- Phylogenetic analysis using Ultrafast Sample placement on Existing tRees (UShER) on approximately 7.6 million SARS-CoV-2 sequences.
Main Results:
- Identified 187 introductions of the beta (B.1.351) variant, primarily from South Africa (August 2020–July 2021).
- Identified 220 introductions of the delta (B.1.617.2) variant, with origins including the UK, India, and South Africa (April–November 2021).
- New sequences from Mozambique included 280 SARS-CoV-2, 373 beta, and 559 delta variants.
Conclusions:
- Movement restrictions were effective against non-African introductions but not against spread from neighboring countries.
- Findings highlight the need to re-evaluate the balance between restriction consequences and public health benefits.
- This study provides critical insights into Mozambique's pandemic dynamics to guide future public health interventions against new variants.
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