Scientists find a cryptic SARS-CoV-2 lineage in wastewater


In a recent study posted to the medRxiv* preprint server, researchers in the United States investigated the source of an enigmatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern (VOC)-like spike (S) protein strain detected in wastewater but not in clinical samples.

On 11 January 2022, an uncommon S sequence was identified in metropolitan wastewater; however, the origin of the highly divergent enigmatic SARS-CoV-2 S strain sequence, identified in wastewater but not in clinical samples, is unknown. If the enigmatic strain (ES) sequence was of human origin and transmissible. In that case, it could be a source of future VOCs and a precious tool for predicting SARS-CoV-2 sequences to be incorporated into coronavirus disease 2019 (COVID-19) therapeutics such as vaccines.

Overall, the study findings showed that prolonged shedding from the human gastrointestinal tract (GIT) is the most likely source for evolutionarily advanced SARS-CoV-2 variant sequences detected in wastewater. Therefore, more frequent international wastewater surveillance efforts of sewage lines could probably identify numerous ES.

Considering the massive numbers of Omicron VOC infections, the authors have speculated that several Omicron VOC-derived ES would probably be detected in wastewater shortly. Considering the enormous spread of the Omicron VOC, the counts of prolonged SARS-CoV-2 infections giving rise to multiple ES would also increase, thereby increasing the frequency of detection of several ES. The study findings highlighted that prolonged SARS-CoV-2 infections could give rise to divergent SARS-CoV-2 strains and underscored the need for identifying such COVID-19 cases.