The emergence of a variant Omikron, contributed to the increase in the incidence of SARS-CoV-2 infection in the world. This strain has been shown to increase the risk of reinfection as well as infection despite full immunization. With over 37 mutations in the S protein Compared to the original SARS-CoV-2 detected in Wuhan, this variant is more easily transmitted with respiratory drops.
Currently, the Omikron variant is distinguished from other SARS-CoV-2 strains using the method targeted damage to the S protein gene. Due to the presence of a mutation (deletion) in the Omikron S protein gene, standard PCR tests do not detect it. This phenomenon is called SGTF (S-gene target failure) and is used to detect Omikron infections.
Now South African scientists have compared the performance saliva and nasopharyngeal swabs for PCR-based detection of Delta and Omikron variants. Researchers collected saliva and nasopharyngeal swabs from 382 symptomatic, non-hospitalized patients who presented to the Cape Town hospital for SARS-CoV-2 testing between August and December 2021. The samples were checked by RT-PCR.
The positive agreement between saliva and nasopharyngeal swabs was estimated at 71% and 100%. in case of Delta infection. It means that 100 percent infection with the Delta variant can be detected by performing an antigen test from the nasopharynx. In case of variant of the Omikron the results were surprising – 100 percent. the tested samples taken from the saliva detected the pathogen, compared to 86 percent. coming from the nasopharynx.
The results revealed that if infection with the Omikron variant is suspected, it may be better saliva swaband not the nasopharynx. Saliva samples have been shown to contain more viral RNA than nasal samples (in the case of Omikron). This may be due to altered patterns of removal of this variant from the body (more with the mouth and less with the nose). Other evidence suggests that the replication rate of the Omikron variant is significantly higher in the upper respiratory tract than that of the Delta variant.