The constant mutation of new strains that are more contagious or pathogenic is one of the main reasons why the COVID-19 pandemic has persisted and brought serious disasters to the world.
It is generally believed that the mutation of the new crown virus is mainly point mutation, and the incidence of recombinant mutation is low, but the recombinant variant may produce a more contagious and pathogenic strain.
Recombinant variation is defined as the exchange of genetic material between two different viral variants that leads to the creation of new variants with new characteristics.
So far, α and δ variants have been confirmed, δ and o (Aomi Keron), as well as Aomi Keron subsymbial BA.1 and BA.2 recombinant variants.
Among them, due to the high pathogenicity of δ variants, the high infectivity of o variants and the immune evasion capacity of O variants, new variants produced by delta-omicron recombination are expected to produce more "bad" variants, and the potential impact on vaccine and treatment effectiveness may also be greater, so it is more interesting.
Prior to this, the δ-o restructuring had been confirmed in the UK and France.
However, it has been suggested that these recombinant variants may be caused by laboratory contamination, sequencing errors, or co-infection.
The PURPOSE of the CDC National Strain Surveillance Program is to identify, characterize, and monitor new variants of the coronavirus. The program has so far identified 1.8 million new coronavirus genomes from the United States.
Scientists have identified a total of nine delta-omicron recombinant sequences from the genomes of the 1.8 million new coronaviruses.
The analysis found that these recombinant sequences contained both δ and o variants characteristic mutations, especially between the spike protein amino acids 158 and 339 sequences from δ-associated mutations to ο-related mutations.
In the figure, orange represents amino acid substitution associated with the Delta variant, and purple represents amino acid substitution associated with the Omicron variant; the hue corresponds to the proportion containing Omicron or Delta-related sequences. A gray box indicates an amino acid substitution that is common to the Omicron and Delta sequences; a white box indicates no variation relative to the earliest original strain; and a black box indicates a substitution that is generally uncommon for Delta or Omicron sequences.
To rule out the possibility that the recombinant came from laboratory contamination or sequencing errors, the scientists repeatedly read the raw data of the identified recombination sequence using various sequencing strategies to confirm that the recombination originated from natural infection.
In addition, scientists fragment the recombination sequence at specific locations within the predicted recombination site. By comparing the sequence of fragments with the reference sequences of the delta and omicron variants, it was observed that the first fragment belonged to the delta branch and the remaining fragments belonged to the omicron branch.
Further sequencing analysis also confirmed that in recombinant variants, characteristic δ mutations occur simultaneously with different lambda mutations.
The spike proteins translated by these genes also showed heterozygous sequences containing amino acids characteristic of the delta and omicron variants.
In summary, the scientists repeatedly confirmed the 9 delta-omicron recombinant sequences found in the United States after complex tests.
Although there has been no significant increase in the number of cases in the United States where these recombinant variants have been detected, these recombinant variants may not have had a significant impact on the outbreak so far.
Of course, scientists acknowledge that due to the lack of identification information to detect the inclusion of these recombinant genomes, it is not yet possible to determine their epidemiological link.
Given the potential public health implications of recombinant variants, scientists recommend continuous genomic monitoring of new recombinant variants for rapid detection and surveillance.