SARS-CoV-2 RNA found to be present in various environmental surface samples

By Tarun Sai LomteNov 29 2022Reviewed by Aimee Molineux

In a recent study published in PLOS ONE, researchers conducted environmental surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ribonucleic acid (RNA).

Background

SARS-CoV-2 spreads among humans through air, respiratory droplets, and contact with animals and contaminated surfaces. An animal study indicated fomites as a potential transmission route for SARS-CoV-2, wherein fomite exposure caused a milder clinical course than intranasal/aerosol exposure among animals. A mathematical modeling study concluded that surface disinfection and hand hygiene were critical measures for preventing coronavirus disease 2019 (COVID-19) via environmental transmission.

SARS-CoV-2 may persist for days on different surfaces, such as cardboard, plastics, copper, stainless steel, masks, and skin, depending on the relative humidity and temperature of the surfaces. Environmental monitoring of SARS-CoV-2 has been a pivotal aspect of public health surveillance. Nevertheless, COVID-19 environmental surveillance has been limited at large, congregated travel destinations.

About the study

In the present study, researchers performed the environmental surface sampling of SARS-CoV-2 RNA in select high-traffic public places and a public health facility (PHF) in Las Vegas, the United States (US). Three hundred surface samples were collected between December 7, 2020, and April 22, 2021. from frequently touched surfaces in public locations, such as post offices, gas stations, car washes, shopping malls, and grocery store restrooms.

PHF samples were collected from surfaces frequently touched by COVID-19 patients and staff, such as faucets, door locks, copy machines, chairs, and tables. Sampling was performed using sterile foam-tipped applicators immersed in 3ml of viral transport medium. Viral RNA was extracted and subject to quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis.

The nucleocapsid (N) gene of SARS-CoV-2 was used for nucleic acid amplification. Mean cycle threshold (Ct) values were used to analyze amplification results. Additionally, positive samples were verified by qRT-PCR of spike and open-reading frame (ORF) gene markers. Negative specimens were analyzed using an internal positive control PCR to rule out false negatives.

Findings

The authors collected 150 samples from public locations and 150 from the PHF. Overall, 31 were positive for SARS-CoV-2 RNA. Of these, 24 PHF samples and seven specimens from high-traffic public areas were positive for viral RNA. The seven positive specimens were collected from a handrail, door handle, elevator buttons, crosswalk pedestrian push buttons, sinks, toilet seats, and doorknobs of restrooms.

The Ct values ranged between 25.8 and 38.4. The lowest and highest number of viral RNA copies were 697/sample and 7.8 million/sample, respectively, collected from a clothes locker and restroom sink in the PHF. The PHF restroom floor sample also had a high RNA concentration, indicating that viral RNA quantity increases in sites where patients’ secretions and respiratory fluids exist.

SARS-CoV-2 RNA was detected on plastic, rubber, steel, wood, vinyl, ceramic, metal, and artificial leather surfaces and in mop water. Ten positive specimens with the lowest Ct values were selected for comparing the N gene PCR assay with ORF and spike gene PCR assays. Among these, the N gene assay yielded the lowest Ct value, while the ORF gene assay yielded the highest Ct value.

One-way analysis of variance (ANOVA) showed significant differences between the average Ct values of the three assays. It revealed that the N gene assay was more sensitive than the ORF/S gene assay. The detection limit was 86 – 860 SARS-CoV-2 RNA copies/sample, equivalent to 3 to 33 RNA copies/cm².

Conclusions

The positivity rate of SARS-CoV-2 detection in samples from the PHF and select public places was 10.3%. More frequently, SARS-CoV-2 was detected on commonly touched surfaces, such as plastics, rubber, and stainless steel. All samples collected from the PHF floor surface, including the objects in contact with the floor (staff shoes), were positive for viral RNA.

Moreover, SARS-CoV-2 RNA was found in mop water containing detergent for cleaning. The highest concentration of viral RNA was detected in samples obtained from public and PHF restrooms. Notably, it could not be verified whether the virus was viable or infectious. Although the swab sampling technique successfully detected viral RNA, the collection efficiency was unknown.

Taken together, the study demonstrated the distribution and extent of SARS-CoV-2 contamination in public places and the PHF in Las Vegas. The high concentrations of viral RNA detected in public/PHF restrooms warrant frequent cleaning, hand washing policies, and implementation of hands-free controls limiting contact, such as automatic soap/water dispensers.