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Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe

Our take —

This study, available as a preprint and thus not yet peer-reviewed, analyzed SARS-CoV-2 sequences belonging to the B.1.620 lineage. The authors find that this is a particularly diverse lineage with several mutations associated with antibody-induced immunity, and find evidence for local transmission of this lineage in Lithuania and other parts of Europe (including Germany, France, and Belgium). When available, the authors also used travel history metadata to conclude that this lineage likely originated in Cameroon or a nearby country in central Africa, despite limited sequencing there. This work highlights the need for global genomic surveillance to limit SARS-CoV-2 spread everywhere, as well as the importance of keeping and sharing travel history information as part of routine surveillance efforts. Evaluation of the effectiveness of existing COVID-19 vaccines against the B.1.620 lineage will be critical to understand the potential impact of these mutations on public health outcomes.

Study design

Other

Study population and setting

This study was an analysis of all publicly available whole genome sequences of SARS-CoV-2 belonging to lineage B.1.620 as of April 29, 2021 (85 sequences, after quality filtering). The authors were interested in this lineage because of the large number of mutations found in sequences belonging to it, including several mutations that have been found individually in other variants of concern, but never together. Because this lineage was found in a large cluster in Lithuania, the authors analyzed the 85 B.1.620 sequences alongside the other lineages observed there. And, because several B.1.620 cases turned out to be in travelers returning from Cameroon, the analysis also included other sequences from Cameroon showing high similarity to the B.1.620 lineage. The 85 B.1.620 sequences and 141 Lithuanian and Cameroonian sequences were subsequently combined with 150 randomly selected global sequences to understand B.1.620 in the context of global diversity.

Summary of Main Findings

The authors found that B.1.620 lineage carries several mutations and deletions that have been previously observed in other variants of concern individually, but never together. The majority of these mutations have been shown in other studies to likely escape antibody-mediated immunity. The authors also found compelling evidence for local transmission of B.1.620 in Lithuania and other parts of Europe, including Germany and France. However, a large number of cases were among travelers returning from Cameroon (7 out of 85 B.1.620 sequences) or Central African Republic (6 out of 85), which borders Cameroon. The authors concluded that these findings suggested a central African origin of the B.1.620 lineage, and detection of the lineage in neighboring countries suggests that the lineage may be circulating widely in Central Africa, despite limited genomic surveillance and detection.

Study Strengths

The study uses sophisticated phylogeographic techniques to estimate the likely origin of B.1.620 in Central Africa. This was enabled by collection of detailed travel histories of several sequenced European cases.

Limitations

As the authors themselves point out, the study is limited by the lack of metadata (specifically travel history) for the majority of B.1.620 sequences. Furthermore, limited genomic surveillance in parts of Central Africa means that the authors were not able to define the extent and geographic coverage of B.1.620 circulation in the region.

Value added

This study highlights the importance of global genomic surveillance of SARS-CoV-2. In particular, the authors describe how lack of surveillance makes it difficult to reconstruct the order of mutations that occurred during the evolution of the B.1.620 lineage, which limits our ability to understand how viral mutations affect fitness. The authors also highlight a new lineage (B.1.620) with mutations seen in other variants of concern and ensured that these sequences are categorized correctly in public databases.

This review was posted on: 28 May 2021