# A clue to clarify the origin of Omicron

## TL;DR

This study suggests that the Omicron variant of SARS-CoV-2 may have originated in urban rodents before spreading to humans.

## Contribution

The study provides evidence that Omicron may have transitioned between humans and rodents, offering a new hypothesis for its origin.

## Key findings

- Omicron variants BA.5.2 and BA.5.1.17 were identified in rodent fecal samples from Mexico City in late 2020.
- The findings suggest Omicron may have emerged from a combination of silent spread and mouse-to-human transmission.
- Rodents may have harbored Omicron a year before its official emergence in humans.

## Abstract

This study utilized faecal samples from synanthropic rodents collected during September–December of 2020 from a public park in southern Mexico City, previously identified as positive for SARS-CoV-2, to perform molecular identification of the viral variant. Typing was successful for two Mus musculus and one Rattus norvegicus, revealing Omicron variants BA.5.2 (from a rat) and BA.5.1.17 (from mice). Additionally, confirmation from a reference centre and Global Initiative on Sharing All Influenza Data (GISAID) analysis verified the presence of the Omicron variant. By considering three primary hypotheses regarding Omicron's origin and integrating these findings with concurrent events in Mexico during the initial wave of SARS-CoV-2, it is reasonable to suggest that the variant’s emergence may stem from a combination of a ‘silent spread’ (indicating circulation among populations with limited viral monitoring and sequencing) and a ‘mouse origin’ (where the progenitor of Omicron transitioned from humans to mice, acquiring mutations that enhanced its ability to infect that host, before re-emerging in humans). Consequently, our results indicate that Omicron was present in urban rodents a year prior to its official emergence, amplified by the conditions existing during the first wave of COVID-19 in Mexico.