Genomic Analysis and Lineage Identification of SARS-CoV-2 Strains in Migrants Accessing Europe Through the Libyan Route

Abstract

Many African countries, representing the origin of the majority of refugees, asylum-seekers, and other migrants, toward regions bordering on the Mediterranean area, are experiencing sustained local transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Sicily is one of the main entry gates of migrants crossing into Europe. We conducted a pilot study, based on the full-genome sequencing of SARS-CoV-2 strains isolated from migrants coming to Sicily by crossing the Mediterranean Sea, with the aim to investigate the viral genome polymorphism and to describe their genetic variations and the phylogenetic relationships. On June 21, a nongovernmental organization vessel rescued 210 migrants crossing the Mediterranean Sea from Libya to Sicily. Of them, 13.4% tested positive for SARS-CoV-2. Eighteen whole genome sequences were obtained to explore viral genetic variability. All but one of the sequences clustered with other viral African strains within the lineage A, whereas only one intermixed among B.1 lineage genomes. Our findings documented that most of the investigated migrants acquired SARS-CoV-2 infection before landing in Sicily. However, SARS-CoV-2 transmission during travel or in overcrowded Libyan immigrant camps and/or illegal transport boats could not be ruled out. SARS-CoV-2 molecular surveillance on migrants arriving in Europe through the Sicilian gate may improve the knowledge of global SARS-CoV-2 transmission dynamic also in light of the emergence of new variants.

Keywords: Mediterranean Sea; NGS; SARS-CoV-2; asylum-seeker; migrant; molecular surveillance.

Figure 1

Phylogenetic analysis highlighting the selected clade extrapolated from the whole tree and focusing on the 17 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from migrants (reported in red) belonging to lineage A. These genomes appeared related in a subclade with four genomes from Mali (ML, Mali highlighted in blue: EPI_ISl_487450; EPI_ISL_487447; EPI_ISL_487452; EPI_ISL_487457), one from Bangladesh (BD, Bangladesh reported in dark green: MT502774), two from Benin (Benin, BJ reported in fuchsia: EPI_ISL_476830 and EPI_ISL_476831), two from Nigeria (NG, Nigeria reported in light violet: EPI_ISL_487107; EPI_ISL_455423), six from Sierra Leone (SL, Sierra Leone reported in ocra yellow: EPI_ISL_512816, EPI_ISL_512817, EPI_ISL_512819, EPI_ISL_512820, EPI_ISL_512821, MT872492), three from Tunisia (TN, Tunisia reported in gray: MT955171, EPI_ISL_458286, EPI_ISL_463001), two from Egypt (EG, Egypt highlighted in light green: EPI_ISL_483035 and 483036), and one from Gabon (GA, Gabon reported in black: EPI_ISL_539573). SARS-CoV-2 genomes from other countries can be found externally located to this subclade. An ISO alpha-2 code (www.iso.org) was used at the end of the taxon names to refer to each country. An asterisk along the branches represents an aLRT–aBayes support ≥0.99 (Bayesian-like transformation of aLRT available from Phyml software) for the clade subtending that branch.

Figure 2

Phylogenetic analysis highlighting the selected clade extrapolated from the whole tree and including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain EPI_ISL_582768 (highlighted in red) intermixed among other SARS-CoV-2 B–B.1 lineage genomes. This strain appeared intermixed among other genomes from different countries and more proximal to strains from Egypt (EPI_ISL_526975), Greece (EPI_ISL_487370), Germany (EPI_ISL_406862), and Uganda (EPI_ISL_451195). The ISO alpha-2 codes (www.iso.org) were used at the end of the taxon names to refer to each country. An asterisk along the branches represents an aLRT–aBayes support ≥0.99 (Bayesian-like transformation of aLRT available from Phyml software) for the clade subtending that branch.