SARS-CoV-2 variant from India to Marseille: The still active role of ports in the introduction of epidemics.

Dear Editor,

A recent variant of SARS-CoV-2 named B.1.617 has spread to several countries from India [1]. The mutations found in the Indian variant in its spike are identified as E484Q, L452R, E154K and P681R. Amino acid 484 is changed in the South African variant B.1.351 and in the Brazilian variant P1 while L452R was already detected in a Californian variant. The association in a single variant of these mutations supposed to reduce recognition by antibodies and impact on attachment to the ACE2 receptor that has caused this strain to be classified as a variant of interest by the WHO due to a strong potential to cause epidemics [2].

We report herein the case of an Indian sailor coming to Marseille, south-east France, to embark as a crew member which illustrates the role of ports in the historical introduction of epidemics. This patient from Goa embarked at New Delhi airport, passed through Amsterdam airport and landed at Marseille airport on April 26, 2021. Tested SARS-CoV-2-negative 72 hours before boarding, he was detected positive upon arrival at Marseille by an antigen test. A new nasopharyngeal swab was performed for confirmation on April 27 and sent to our institute [3]. qRT-PCR was positive at Ct 17 and direct sequencing [4] confirmed the “Indian Variant” nature of this strain (Fig. 1 , Supplementary Figure S1). On April 28, characteristic CPEs were seen in culture (Supplementary Figure S2) and the strain sub-cultured for subsequent sero-neutralization analysis on the sera of local patients carrying antibodies (vaccinated and convalescent). So far, five B.1.617 cases were documented in France (https://www.nouvelle-aquitaine.ars.sante.fr/communique-de-presse-coronavirus-point-de-situation-en-nouvelle-aquitaine-au-30-avril-2021; https://solidarites-sante.gouv.fr/actualites/presse/communiques-de-presse/article/premieres-detections-de-cas-de-contamination-au-variant-b-1-617-du-sars-cov-2).

Fig. 1

Phylogeny reconstruction based on the SARS-CoV-2 full-length genomes.

The Marseille-IHU-9101 genome, indicated by a white bold font and a black background, is classified in Nextstrain clade 20A and Pangolin lineage B.1.617.2. It has been deposited in the GISAID database (https://www.gisaid.org/) [8] (No. EPI_ISL_1825677). Its best BLASTn hits (n = 30 selected) in GISAID have been obtained from samples collected recently (not earlier than the March 19, 2021) in India, Singapore, the USA, and Western Europe (England, Italy, Belgium, Germany, Greece). This genome is strongly clustered (bootstrap value, 100%) with these most similar sequences in a subcluster of lineage B.1.617.2, and is clustered (bootstrap value, 88%) with one sequence obtained from a sample collected in England the same day than the present case-patient.

The SARS-CoV-2 phylogenetic tree is based on the full-length SARS-CoV-2 genomes. The 30 sequences with the highest BLAST scores recovered from the GISAID database (https://www.gisaid.org/) [8] were incorporated in the phylogeny reconstruction, being indicated by a black bold font. Additional sequences included the genome of the Wuhan-Hu-1 isolate and genomes obtained in our institute and classified as predominant variants. Nucleotide alignments were performed using the MUSCLE software (http://www.ebi.ac.uk/Tools/msa/muscle/). Evolutionary history was inferred using the MEGAX software (http://www.megasoftware.net/) using the neighbor-joining method and the Kimura 2-parameter method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree; the scale bars indicate the number of nucleotide substitutions per site. Bootstrap values > 50% are indicated on the tree. Pangolin lineages determined using the Pangolin COVID-19 Lineage Assigner https://pangolin.cog-uk.io/) are indicated.

This case perfectly illustrates the role played by ports such as Marseille in the entry of epidemics of distant origin. Indeed, for 2000 years this port has faced the arrival of epidemic agents, in particular plague, cholera, yellow fever. The history of these epidemics and the strategies put in place to fight them, including creation of our institute, have been recently reviewed [5]. For many years, merchant navy crews have mainly come from countries with low labor costs, in particular the Indian subcontinent, and the case of this sailor continues to illustrate this historical characteristic by the fact that it is an area of mixing of populations. It also raises the question of the lack of real control over transfers of people from areas where variants of concern are circulating. This patient had been tested before boarding and was able to transit unchecked to Marseille where, fortunately, civil security checks as many travelers as possible but without being exhaustive. It is very probable that similar situations will occur, illustrating the extreme difficulty of controlling the introduction of new epidemic variants in regions which are traditionally areas of intense transit. Ensuring effective detection of these cases is however critical, especially for crew members destined, as was the case with this sailor, to embark on cruise ships in order to avoid a repetition of the Diamond Princess episode [6].