Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study

Abstract

Background: From the start of the SARS-CoV-2 outbreak, global sequencing efforts have generated an unprecedented amount of genomic data. Nonetheless, unequal sampling between high-income and low-income countries hinders the implementation of genomic surveillance systems at the global and local level. Filling the knowledge gaps of genomic information and understanding pandemic dynamics in low-income countries is essential for public health decision making and to prepare for future pandemics. In this context, we aimed to discover the timing and origin of SARS-CoV-2 variant introductions in Mozambique, taking advantage of pandemic-scale phylogenies.

Methods: We did a retrospective, observational study in southern Mozambique. Patients from Manhiça presenting with respiratory symptoms were recruited, and those enrolled in clinical trials were excluded. Data were included from three sources: (1) a prospective hospital-based surveillance study (MozCOVID), recruiting patients living in Manhiça, attending the Manhiça district hospital, and fulfilling the criteria of suspected COVID-19 case according to WHO; (2) symptomatic and asymptomatic individuals with SARS-CoV-2 infection recruited by the National Surveillance system; and (3) sequences from SARS-CoV-2-infected Mozambican cases deposited on the Global Initiative on Sharing Avian Influenza Data database. Positive samples amenable for sequencing were analysed. We used Ultrafast Sample placement on Existing tRees to understand the dynamics of beta and delta waves, using available genomic data. This tool can reconstruct a phylogeny with millions of sequences by efficient sample placement in a tree. We reconstructed a phylogeny (~7·6 million sequences) adding new and publicly available beta and delta sequences.

Findings: A total of 5793 patients were recruited between Nov 1, 2020, and Aug 31, 2021. During this time, 133 328 COVID-19 cases were reported in Mozambique. 280 good quality new SARS-CoV-2 sequences were obtained after the inclusion criteria were applied and an additional 652 beta (B.1.351) and delta (B.1.617.2) public sequences were included from Mozambique. We evaluated 373 beta and 559 delta sequences. We identified 187 beta introductions (including 295 sequences), 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 (including 494 sequences), with 49 transmission groups and 171 unique introductions, mostly from the UK, India, and South Africa, between April and November, 2021.

Interpretation: The timing and origin of introductions suggests that movement restrictions effectively avoided introductions from non-African countries, but not from surrounding countries. Our results raise questions about the imbalance between the consequences of 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.

Funding: European and Developing Countries Clinical Trials, European Research Council, Bill & Melinda Gates Foundation, and Agència de Gestió d'Ajuts Universitaris i de Recerca.

Figure 1

SARS-CoV-2 waves in Mozambique and cumulative total cases Public calamity status began on Sept 7, 2020, replacing the State of emergency. Movement restrictions included: no travel and limited internal movement; during the state of emergency, travels were allowed with mandatory quarantine in Mozambique. Measures were gradually alleviated by April and by the end of May, 2021, when internal movement and restricted social events were permitted.

Figure 2

Number of sequenced beta and delta samples per region in Mozambique The map includes 280 samples from this study all taken in Manhiça district, represented with a lighter colour in the Maputo region, in the south of the country, and the Mozambique samples from Global Initiative on Sharing Avian Influenza Data.

Figure 3

Sample inclusion and sequencing criteria (A) and Mozambique and GISAID enrichment of the eTree and subtree pruning results (B) GISAID=Global Initiative on Sharing Avian Influenza Data. UShER=Ultrafast Sample placement on Existing tRees. Low coverage samples are samples with low sequencing quality. Non-index samples are sequences from a second sample from the same patient.

Figure 4

SARS-CoV-2 introductions in Mozambique (A) Circos plot for beta variant. (B) Dot plot for beta variant. (C) Circos plot for delta variant. (D) Dot plot for delta variant. The circos plots indicate the origin of the introductions to Mozambique and the contribution of each country or region. For beta, 74% of introductions came from South Africa, 19% from other African countries, 5% from Europe, and 2% from Asia. For delta, 36% of introductions came from the UK, 28% from India, 27% from South Africa, 1% from Portugal, and 7% from other countries. Dot plots display introduction periods for transmission groups and unique sequences. Density plots indicate introductions distribution. Public calamity status began on Sept 7, 2020, right after the State of emergency. Movement restrictions included: no travel and limited internal movement. During the state of emergency, travels were allowed with mandatory quarantine in Mozambique. Measures were gradually alleviated by April 2 and by May 26, 2021, when internal movement and restricted social events were permitted.