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. 2022 Sep 14;12(9):2219.
doi: 10.3390/diagnostics12092219.

Molecular Characterization of Whole-Genome SARS-CoV-2 from the First Suspected Cases of the XE Variant in the Lazio Region, Italy

Martina Rueca  1 , Emanuela Giombini  1 , Giulia Gramigna  1 , Cesare Ernesto Maria Gruber  1 , Lavinia Fabeni  1 , Angela Corpolongo  1 , Valentina Mazzotta  1 , Luisella Corso  2 , Ornella Butera  1 , Maria Beatrice Valli  1 , Fabrizio Carletti  1 , Stefano Pignalosa  2 , Francesco Vairo  1 , Emanuele Nicastri  1 , Andrea Antinori  1 , Enrico Girardi  1 , Francesco Vaia  1 , Fabrizio Maggi  1 , Sars CoV-Lazio Surveillance Study Group
Affiliations

Molecular Characterization of Whole-Genome SARS-CoV-2 from the First Suspected Cases of the XE Variant in the Lazio Region, Italy

Martina Rueca et al. Diagnostics (Basel). .

Abstract

We report two cases of SARS-CoV-2 recombinant variant XE detected in nasopharyngeal swabs (NPS) of hospitalized patients with no evident epidemiological link in Lazio, Central Italy. Whole-Genome Sequencing (WGS) performed on an Ion Torrent GSS5 platform according to Italian flash surveys showed genomes corresponding to the PANGOLIN unclassified lineage and the Nextclade XE clade. Further analyses were then carried out to investigate more deeply the genetic characteristics of these XE-like sequences. When phylogenetic trees, by using IQ-TREE, were built splitting the genome into two regions according to the putative XE recombination site, the upstream and downstream regions were seen to be clustered near BA.1 and BA.2 sequences, respectively. However, our XE-like sequences clustered separately, with a significant bootstrap, from the classified European and Italian XE strains, although the recombination site between BA.1 and BA.2 was identified at the nucleotide site 11556 by RDP4 software, consistent with the putative XE breakpoint. These findings show the risk of the introduction of novel recombinant variants of SARS-CoV-2 and the existence of XE-like strains, phylogenetically separated, that could make their exact taxonomy difficult. It follows the need for continued SARS-CoV-2 surveillance by WGS.

Keywords: COVID-19; Nextclade; PANGOLIN; SARS-CoV-2; XE; recombination; whole-genome sequencing.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
The phylogenetic tree is constructed by the maximum likelihood method and based on the whole-genome sequences. Nodes supported with bootstrap values ≥80 are marked with black dots. Sequences from suspected XE cases are reported in red and indicated with an arrow.
Figure 2
Figure 2
The phylogenetic tree is constructed by the maximum likelihood method and based on the XE recombination site: genomic elements from 266 to 11,500 nucleotides. Nodes supported with bootstrap values ≥80 are marked with black dots. Sequences from suspected XE cases are reported in red and indicated with an arrow.
Figure 3
Figure 3
The phylogenetic tree is constructed by the maximum likelihood method and based on the XE recombination site: genomic element from 11,501 to 29,500. Untranslated regions are excluded from the analysis. Nodes supported with bootstrap values ≥80 are marked with black dots. Sequences from suspected XE cases are reported in red and indicated with an arrow.
See this image and copyright information in PMC

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