Dispersal dynamics and introduction patterns of SARS-CoV-2 lineages in Iran

Abstract

Understanding the dispersal patterns of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) lineages is crucial to public health decision-making, especially in countries with limited access to viral genomic sequencing. This study provides a comprehensive epidemiological and phylodynamic perspective on SARS-CoV-2 lineage dispersal in Iran from February 2020 to July 2022. We explored the genomic epidemiology of SARS-CoV-2 combining 1281 genome sequences with spatial data in a phylogeographic framework. Our analyses shed light on multiple international imports seeding subsequent waves and on domestic dispersal dynamics. Lineage B.4 was identified to have been circulating in Iran, 29 days (95% highest probability density interval: 21-47) before non-pharmaceutical interventions were implemented. The importation dynamics throughout subsequent waves were primarily driven from the country or region where the variant was first reported and gradually shifted to other regions. At the national level, Tehran was the main source of dissemination across the country. Our study highlights the crucial role of continuous genomic surveillance and international collaboration for future pandemic preparedness and efforts to control viral transmission.

Keywords: COVID-19; Iran; SARS-CoV-2; dispersal dynamic; epidemic; genomic epidemiology; pandemic; phylogenetic; preparedness; surveillance; transmission; travel; variants; vigilance.

Figure 1.

Epidemiological landscape of SARS-CoV-2 genomes collected in Iran between 2 February 2020 and 7 July 2022.(a) Histogram of cumulative number of cases accounted per month and white boxes and light blue represent the timeline of lockdown events during the waves in Iran (Our World in Data, Mathieu et al. 2020); (b) Histogram of number of genomes sampled and characterized during waves sampled. The dashed lines correspond to sequences available on GISAID.

Figure 2.

Phylogeographic reconstruction of SARS-CoV-2 lineages responsible for major epidemic waves in Iran. The MCC trees (left panel) are color-coded based on the estimated or sampled region while shapes represent sublineages for Delta and Omicron. The flows of migration among all regions during four waves in Iran are summarized by circular plots, with arrowheads indicating the start and end points (central panel). Bayesian Skygrid plots reconstructed for the Iranian transmission clades (right panel). (a–c): b.4, (d–f): Alpha, and (g–i): Delta.

Figure 3.

Dispersal dynamics among sampled SARS-CoV-2 lineages across five regions in Iran. The discrete phylogeographic reconstruction traces the dispersal history of viral lineages, encompassing the B.4 (a) lineage and the Alpha (b), Delta (c), and Omicron (d) variants. In the discrete reconstructions, we present the number of lineage dispersal movements estimated by MJs between regions (depicted by arrows), extracted from trees sampled in each posterior distribution and color-coded by time interval. The arrow thickness is proportional to the number of MJ events. Only MJ events with an adjusted Bayes factor support higher than 10 are included.