Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil

Abstract

Recombination events have been described in the Coronaviridae family. Since the beginning of the SARS-CoV-2 pandemic, a variable degree of selection pressure has acted upon the virus, generating new strains with increased fitness in terms of viral transmission and antibody scape. Most of the SC2 variants of concern (VOC) detected so far carry a combination of key amino acid changes and indels. Recombination may also reshuffle existing genetic profiles of distinct strains, potentially giving origin to recombinant strains with altered phenotypes. However, co-infection and recombination events are challenging to detect and require in-depth curation of assembled genomes and sequencing reds. Here, we present the molecular characterization of a new SARS-CoV-2 recombinant between BA.1.1 and BA.2.23 Omicron lineages identified in Brazil. We characterized four mutations that had not been previously described in any of the recombinants already identified worldwide and described the likely breaking points. Moreover, through phylogenetic analysis, we showed that the newly named XAG lineage groups in a highly supported monophyletic clade confirmed its common evolutionary history from parental Omicron lineages and other recombinants already described. These observations were only possible thanks to the joint effort of bioinformatics tools auxiliary in genomic surveillance and the manual curation of experienced personnel, demonstrating the importance of genetic, and bioinformatic knowledge in genomics.

Keywords: SARS-CoV-2; XAG; genomic surveillance; omicron; recombinant; variants.

FIGURE 1

Schematic representation of recombination points. Schematic of the SARS-CoV-2 genome (upper panel) and positions where possible recombination points occur in the XAG, XG, XL, XN, XQ, and XR recombinants (lower panel).

FIGURE 2

Detection of recombinant XAG in Brazil. (A) Until June 2022, 186 sequences were detected in 10 states of Brazil: 107 sequences in Rio Grande do Sul (RS), 7 in Paraná (PR), 17 in Santa Catarina (SC), 34 in São Paulo (SP), 3 in Espírito Santo (ES), 2 in Minas Gerais (MG), 5 in Rio de Janeiro (RJ), 2 in Distrito Federal (DF), 2 in Pernambuco (PE), and 3 in Ceará (CE). The XAG recombinant was detected in other countries such as Argentina, Austria, Canada, Chile, Colombia, Denmark, France, Germany, India, Israel, Japan, Luxembourg, Mexico, New Zealand, Peru, Portugal, Scotland, Switzerland, and USA. (B) The number of XAG sequences submitted to GISAID between March and June in Brazil and worldwide.

FIGURE 3

Phylogenetic analysis. The multiple alignment was used in IQ-Tree for estimating the Maximum-Likelihood phylogeny. Bootstrap analyzes were made using SH-like approximate likelihood ratio test with 1,000 replicates. (A) Phylogenetic tree reconstructed with the first fragment of the beginning of the genome up to 6,512 nt position (considered the probable recombination breakpoint), with characteristics like Omicron BA.1 (Model: TIM + F + I). (B) Phylogenetic tree reconstructed with the second fragment after the 6,512 nt position, the genomic section likely derived from Omicron BA.2/BA.2.23 (Model: TIM + F + R3). (C) Phylogenetic tree reconstructed with the complete genome of XAG genome, other available recombinant lineages and parental BA.1 and BA.2 lineages (Model: TIM + F + R3). A dataset with representative sequences of the following lineages was used: Omicron BA.1, BA.2, BA.2.23, XF (Delta/Omicron BA.1), XL (Omicron BA.1/BA.2), XG (Omicron BA.1/BA.2), XN (Omicron BA.1/BA.2), XQ (Omicron BA.1/BA.2), XR (Omicron BA.1/BA.2), and XAG (Omicron BA.1/BA.2).

FIGURE 4

Molecular characterization of recombinant XAG. Alignment of sequences from Omicron subvariants BA.1 and BA.2, which originated the recombination that generated the XAG recombinant showed four distinct markers (in red) of this recombinant at positions (A) 2,857 (C/T), (B) 5,585 (C/A), (C) 12,334 (A/G), and (D) 17,502 (C/T). The mutation at positions 2,857 and 17,502 generate synonymous mutations and the mutation at position 5,585 (L1774I) is exclusive to this recombinant.