SARS-CoV-2 genomic surveillance of migrants arriving to Europe through the Mediterranean routes

Abstract

Background: The implementation genomic-based surveillance on emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in low-income countries, which have inadequate molecular and sequencing capabilities and limited vaccine storage, represents a challenge for public health. To date, there is little evidence on molecular investigations of SARS-CoV-2 variants in areas where they might emerge. We report the findings of an experimental SARS-CoV-2 molecular surveillance programme for migrants, refugees, and asylum seekers arriving to Europe via Italy through the Mediterranean Sea.

Methods: We descriptively analysed data on migrants collected at entry points in Sicily from February 2021 to May 2022. These entry points are integrated with a network of laboratories fully equipped for molecular analyses, which performed next-generation sequencing and used Nextclade and the Pangolin coronavirus disease 2019 (COVID-19) tools for clade/lineage assignment.

Results: We obtained 472 full-length SARS-CoV-2 sequences and identified 12 unique clades belonging to 31 different lineages. The delta variant accounted for 43.6% of all genomes, followed by clades 21D (Eta) and 20A (25.4% and 11.4%, respectively). Notably, some of the identified lineages (A.23.1, A.27, and A.29) predicted their introduction into the migration area. The mutation analysis allowed us to identify 617 different amino acid substitutions, 156 amino acid deletions, 7 stop codons, and 6 amino acid insertions. Lastly, we highlighted the geographical distribution patterns of some mutational profiles occurring in the migrants' countries of origin.

Conclusions: Genome-based molecular surveillance dedicated to migrant populations from low-resource areas may be useful for forecasting new epidemiological scenarios related to SARS-CoV-2 variants or other emerging pathogens, as well as for informing the updating of vaccination strategies.

Figure 1

Geographic map showing the main routes documented among the convenience sample of migrants who arrived in Italy by the Mediterranean Sea (February 2021 to May 2022).

Figure 2

Flowchart describing the selection procedure for next-generation sequencing. rt-RT-PCR – real-time reverse transcription polymerase chain reaction.

Figure 3

Nextclade phylogenetic tree of SARS-CoV2 genomes compared to reference sequences retrieved from GISAID, according to identified clades. Branches with coloured dots refer to sequences obtained from the convenience sample of migrants.

Figure 4

Description of the SARS-CoV2 clades and lineages identified in the convenience sample of migrants, according to Nextclade and the Pangolin COVID-19 tools. Values plotted on top of each bar indicate the number of SARS-CoV-2 strains belonging to each lineage.

Figure 5

Monthly distribution of the SARS-CoV-2 lineages detected during the experimental molecular surveillance.

Figure 6

Genomic location and frequency distribution of top 40 non-synonymous mutations found in SARS-CoV-2 genomes sampled in the migrant subjects.

Figure 7

Distribution of the 15 most prevalent SARS-CoV-2 non-synonymous substitutions detected in the convenience sample of migrants by geographic macro-area of origin.