Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil

Abstract

With the coexistence of multiple lineages and increased international travel, recombination and gene flow are likely to become increasingly important in the adaptive evolution of SARS-CoV-2. These processes could result in genetic introgression and the incipient parallel evolution of multiple recombinant lineages. However, identifying recombinant lineages is challenging, and the true extent of recombinant evolution in SARS-CoV-2 may be underestimated. This study describes the first SARS-CoV-2 Deltacron recombinant case identified in Brazil. We demonstrate that the recombination breakpoint is at the beginning of the Spike gene. The 5' genome portion (circa 22 kb) resembles the AY.101 (Delta), and the 3' genome portion (circa 8 kb nucleotides) is most similar to the BA.1.1 (Omicron). Furthermore, evolutionary genomic analyses indicate that the new strain emerged after a single recombination event between lineages of diverse geographical locations in December 2021 in South Brazil. This Deltacron, AYBA-RS, is one of the dozens of recombinants described in 2022. The submission of only four sequences in the GISAID database suggests that this lineage had a minor epidemiological impact. However, the recent emergence of this and other Deltacron recombinant lineages (XD, XF, and XS) suggests that gene flow and recombination may play an increasingly important role in the COVID-19 pandemic. We explain the evolutionary and population genetic theory that supports this assertion, concluding that this stresses the need for continued genomic surveillance. This monitoring is vital for countries where multiple variants are present, as well as for countries that receive significant inbound international travel.

Keywords: AYBA-RS; Brazil; COVID-19; Deltacron; SARS-CoV-2 genomes; adaptive landscape; gene flow; genetic introgression; recombinant; recombination; severe acute respiratory syndrome coronavirus 2.

Figure A1

Mutational patterns of the Brazilian and the XS recombinants (Nextclade’s output). The Brazilian recombinant was initially identified as an XS lineage, although the portion between the positions 1 and 20,000 diverged from the XS archetype.

Figure A2

Origin of the Brazilian Deltacron samples. Map of Brazil showing where the Brazilian Deltacron samples were collected (yellow points) with their respective collection dates. GISAID accession numbers are in parentheses.

Figure A3

Recombination detection in the genome sequence of Brazil/RS-FIOCRUZ-8390/2022 (Sc2rf output). The analysis indicated that the 5′ region (positions 1–21,845) came from Delta, and the 3′ region (positions 21,846–29,903) came from an Omicron.

Figure A4

Nucleotide assignatures of each lineage. Heatmap showing the frequency of nucleotide mutations in each lineage. We utilized the blastn top-hits sequences for each parental lineage AY.101 (n = 20) and BA.1.1 (n = 19). Mutation frequencies of AYBA-RS were computed from the four sequences found in Brazil. Asterisk—exclusive mutation of AYBA-RS.

Figure A5

Phylogenetic history of genomic segments of the Brazilian Deltacron. (A) The 5′ segment (coordinates 1–21,769) of the Brazilian recombinant grouped to the Brazilian AY.101 genomes. (B) The 3′ segment (coordinates 21,770–29,903) of the Brazilian recombinant grouped to BA.1.1 genomes from diverse geographical locations. Ultrafast bootstrap values of the main branches are close to the nodes.

Figure 1

Mutation profiles of the AYBA-RS and the Delta and Omicron variants. The AYBA-RS recombinant presents a similar mutational pattern among the four Brazilian samples, where the first ~22 kb (5′ segment) resembles the Delta variant, and the last ~8 kb (3′ segment) the Omicron variant. Vertical colored lines represent nucleotide substitutions, with Wuhan/2019 as the reference. The legend depicts the characteristic mutations of each parental sequence and of the recombinants. The SARS-CoV-2 genome map and their respective coordinates are shown at the bottom.

Figure 2

Comparison of the recombination patterns of the AYBA-RS Deltacron and the Deltacrons XD, XF, and XS. Similarity values between the recombinant and the Delta and Omicron parental sequences within a window length of 20 nucleotides along the genome. The legend describes the reference of each comparison. The recombination breakpoints, i.e., points where the lines cross over each other, are distinct for each of the recombinants, and this supports our conclusion of their independent evolution. Recombination plots generated with HybridCheck [29]. Sequences analysed in this plot: Brazil/RS-FIOCRUZ-8390/2022 (AYBA-RS), Brazil/SC-FIOCRUZ-43556-R2/2021 (Delta) and USA/CA-OC-FG-228571/2021 (Omicron) as its parental sequences; France/HDF-IPP54794/2022 (XD), Sweden/37524448XXP/2021 (Delta) and Finland/P-1301/2022 (Omicron) as its parental sequences; England/PHEC-YYN8J41/2022 (XF), South Africa/NHLS-UCT-GS-AF27/2021 (Delta) and South Africa/NICD-N28358/2022 (Omicron) as its parental sequences; USA/CO-CDC-FG-248528/2022 (XS), Latvia/3410639/2021 (Delta) and USA/CA-CDC-FG-223742/2021 (Omicron) as its parental sequences. Similarity at the y-axis refers to percentage sequence similarity at polymorphic sites only. The SARS-CoV-2 genome map and their respective coordinates are shown at the bottom.

Figure 3

The evolution of Deltacron variants (XD, XF, XS and AYBA-S) in relation to that of their parental variants (Delta and Omicron). (A)—Phylogenetic network of Deltacron sequences built with SplitsTree (NeighborNet method, RootedEqualAngle on Wuhan/WH01/2019). The loops in this network are consistent with recombinant evolution. (B)—Haplotype network of Deltacron sequences made with pegas (haploNet method). The number of SNPs is in parentheses (Table A5); the AYBA-RS is within an ellipse. In both analyses, Delta (AY.101, AY.4, B.1.617.2) and Omicron (BA.1, BA.1.1) sequences were used as references. Nodes are coloured according to the variant type.

Figure 4

Density plot of the frequencies of AY.101 (Delta) and BA.1.1 (Omicron) lineages circulating in Brazil between June 2021 and June 2022. Both lineages co-circulated mainly in December 2021 in South Brazil. The colour of the lineages is shown in the legend.