# Cryptic transmission of a SARS-CoV-2 variant detected by wastewater surveillance in Panama

## TL;DR

Wastewater surveillance in Panama detected a SARS-CoV-2 variant that was not identified through clinical testing, showing its importance for tracking undetected viral spread.

## Contribution

Demonstrates the effectiveness of wastewater surveillance in identifying undetected SARS-CoV-2 variants in Panama.

## Key findings

- Wastewater surveillance detected the Omicron sublineage JN.1.16.1 in Panama, which was not found through clinical testing.
- 36 wastewater samples and 822 clinical samples were analyzed, showing wastewater surveillance can detect variants earlier.
- The study emphasizes the need to continue genomic surveillance programs beyond the pandemic.

## Abstract

The COVID-19 pandemic highlighted the critical role of viral genomic surveillance, prompting numerous countries to enhance their monitoring systems for acute respiratory infections (ARIs), especially influenza-like illnesses (ILIs). Given the significance of asymptomatic cases in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, cases often undetected by the ILI surveillance, a more comprehensive approach was essential to track the circulation of SARS-CoV-2 variants in the population. In response, many countries swiftly adopted wastewater surveillance, which allowed the early detection of SARS-CoV-2 variants before they were identified through molecular characterization from confirmed clinical cases. In this report, we detail the implementation of SARS-CoV-2 wastewater genomic surveillance in Panama during the first half of 2024. Wastewater samples were collected monthly in duplicate at two collection points from three districts of Panama city metropolitan area for testing by SARS-CoV-2 RT-qPCR, and positive samples were analyzed by next-generation sequencing to identify sublineages. A total of 36 wastewater samples and 822 samples obtained through the clinical surveillance were analyzed for molecular detection and sequencing. Sublineages detected by wastewater surveillance were compared to those detected by clinical surveillance for the same period of time. Wastewater surveillance allowed the identification of the Omicron sublineage JN.1.16.1 in the capital city and its surroundings, which was not detected by the clinical surveillance in the country, despite its global circulation. This highlights the critical need to sustain both genomic surveillance programs beyond the pandemic in countries like Panama that serve as pivotal exchange hubs.