Environment surveillance to detect COVID-19 outbreaks early

A recent study was posted to the medRxiv* preprint server investigated whether environmental samples could serve as early indicators for detecting severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in large communities.

SARS-CoV-2 caused the coronavirus disease 2019 pandemic (COVID-19), which has had an unprecedented impact on public health, society, economies, and cultures. It has been difficult to manage and control the pandemic, made more difficult by the evolution and limited testing of the virus, particularly among asymptomatic people.

SARS-CoV-2 is released into the environment (as particles) by infected individuals while they travel. These viral genomic footprints may survive for several days or even weeks. SARS-CoV-2 can be contracted through contact with contaminated surfaces or inhalation of aerosols. It is possible to determine the genomic footprints of the environment samples and make tailored management decisions. This is both cost-effective and noninvasive.

Study: COVID-19 Prediction by Genomic Footprint SARS-CoV-2 Surface Swab, and Wastewater Samples. Image Credit: FOTOGRIN / Shutterstock

The study

The Present studyResearchers measured SARS-CoV-2 levels in water, soil, and air samples at a University of Miami student dormitory for three months from March to May 2021. The dormitory houses approximately 500 students. It also has high traffic access and wastewater points. The wastewater drains into a designated maintenance hole from the dorm. The authors collected air, surface (elevator buttons, door bars, and handles), and wastewater samples between 8 – 9 AM on weekdays and 10 – 11 AM on weekends. In addition, the student population was randomly screened for COVID-19 once or three times per week during the study period.

250 ml wastewater samples were collected every day as grab or composite sample. A sonde computed pH and temperature, salinity and dissolved oxygen. To capture all floors of air samples, vacuum pumps were connected to an air impactor. The polyester swab was used to collect surface samples by scraping the high contact surfaces with a unidirectional scrapping motion.

All samples were infected with heat-inactivated HCoV–OC43 (human Coronavirus) as an RNA recovery controller. The second-generation volcano quantitative polymerase chain reactions (V2GqPCR) was used to quantify OC43 and the SARS-2N3 gene. SARS-CoV-2, OC43 concentrations were expressed in genomic copies (gc), per surface area wiped, wastewater volume, and air.

Findings

Between March 2nd and May 25th, 2021, approximately 445 environmental samples were collected. These included 165 air-,166 surface swab and 114 wastewater samples. SARS-CoV-2, which was detected in all sample types, was detected in 140 samples (31.5%) over the study period. 50 samples of air were tested for the virus, with a mean level of 14.8 gc/m.³19.9% of surface swab sample at 16.5 gc/m³. The authors detected SARS CoV-2 in 57 wastewater samples with a mean concentration 1390 gc/L. The average concentration of SARS-CoV-2 in wastewater samples was higher than the detection limit in composite samples than in grab samples. However, statistically, this difference was not significant.

Distribution of SARS-CoV-2’s one-day lagged average in surface and air samples relative to SARS-CoV-2 wastewater samples, March-May 20,21 (wastewater concentration at x-axis).

The researchers compared wastewater samples against surface swab samples. SARS-CoV-2 detected on 36 of 78 matched day was consistent across all three types of samples. On many other days, SARS-CoV-2 was detected only in surface swab or air samples. On 44 days of the study period, COVID-19 tests were performed at an average rate of 2.3 students per day.

On 11 days, positive cases were identified. SARS-CoV-2 was detected in surface swab samples and in air samples on six days and seven days respectively in wastewater samples during the 11 days that cases were clinically confirmed. SARS-CoV-2 was detected in surface swab and air samples for five days, and wastewater samples for four days. This is when students were found to have positive COVID-19. SARS-CoV-2 positive cases prediction was 100% when a 1-day moving average of any type of sample was used. This indicates that SARS-CoV-2 can be detected in other types of sample types if one fails.

Conclusions

This study revealed that SARS-CoV-2 was detected in air, wastewater, and surface samples. It is possible to trace viral genomic footprints in the ambient environment. The results also showed that confirmed COVID-19 infection could be predicted by detecting SARS-2 in the environment samples in the dormitory.

Notably, SARS-CoV-2 can be detected in different sample types, so it is possible to increase environmental surveillance efficacy by sampling all three specimens. Consistent environmental sampling could be used to guide timely and appropriate interventions in order to decrease viral transmission.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.