The “Wolf” Is Indeed Coming: Recombinant “Deltacron” SARS-CoV-2 Detected
Liang Wang, George F. Gao
Abstract
On March 9, 2022, researchers from the Institut Pasteur used the global data science initiative GISAID (1-3) to release a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome (ID: EPI_ISL_10819657) from an isolated virus and announced that it was the first solid evidence for a recombinant strain from 2 types of variants of concern (VOCs) of SARS-CoV-2 (lineage AY.4 and BA.1, belonging to Delta and Omicron, respectively). Complementary to the original data submitters' full analysis, we would like to comment on this case in context of our experience in coronavirus evolution and the further perspective of this finding on the course of the pandemic. As announced, this novel strain has high genomic similarity to viruses belonging to lineage AY.4, except for the region encoding the spike (S) gene, which is more similar to those from lineage BA.1 (Figure Therefore, this novel strain uses Delta as its genomic backbone and then replaces a large portion of original S gene with the ortholog from Omicron. A total of 36 amino acid changes were found in the S protein compared to the prototype of SARS-CoV-2 (Figure Among 36 amino acid mutations, 27 were found in BA.1, 5 mutations were found in AY.4, and 4 mutations were found in both AY.4 and BA.1. However, it was not the first case of a recombination event identified in SARS-CoV-2. A previous study has documented that inter-lineage recombination events have been found in SARS-CoV-2 and then some recombinants caused further community transmission (4). However, these inter-lineage recombination events only occurred in some loci of the genome. No recombination events involving large genomic fragments (like "Deltacron") have been found in SARS-CoV-2 before.