Sponge Whirl-Pak Sampling Method and Droplet Digital RT-PCR Assay for Monitoring of SARS-CoV-2 on Surfaces in Public and Working Environments

Surfaces environmental monitoring of SARS-CoV-2: Loop mediated isothermal amplification (LAMP) and droplet digital PCR (ddPCR) in comparison with standard Reverse-Transcription quantitative polymerase chain reaction (RT-qPCR) techniques

The persistence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on substrates, and the impact of fomites on Coronavirus Disease 19 (COVID-19) transmission, is until now, widely discussed. Consequently, further investigations are required for a correct risk assessment in high-risk facilities such as hospitals, healthcare facilities (HCFs), and long-term care facilities (LTCFs). Therefore, appropriate surveillance and disinfection programs represent the best approach to guarantee the safety of these communities. This study proposes an environmental SARS-CoV-2 surfaces routine monitoring approach in HCF and communities' settings, to provide rapid and effective evaluation of surface hygienic conditions and the effectiveness of applied sanitization measures. Surfaces samples (n = 118) were collected using the SRK® kit (Copan Italia) from 2020 to 2023. Three molecular techniques were compared: Reverse Transcription Loop mediated isothermal AMPlification (RT-LAMP, Enbiotech), Reverse-Transcription quantitative polymerase chain reaction (RT-qPCR) (RT-qPCR, Seegene) and droplet digital PCR (ddPCR, Bio-Rad). For ddPCR, two RNA extraction methods were compared: TRIzol LS (Invitrogen) versus QIAmp Viral Mini kit (QIAGEN), showing how the latter is more suitable for surfaces. Regarding the quantitative ddPCR results, the ROC analysis allowed to reduce the manufacturer cut-off for droplets number (from 3 to 1) for the positive samples. Moreover, a new cut-off for the viral RNA copies' number/μL for each target (N1 and N2) on environmental monitoring was fixed at 2,82. The results obtained using the QIAmp kit, suggested that the N2 target is more stable in the environment and could be most suitable for the virus environmental detection. The percentage of positive samples was similar among the techniques (26% for RT-LAMP, 36% for ddPCR and 23% for RT-qPCR). Using RT-qPCR as reference method, a sensitivity (SE) of 30% for RT-LAMP and 41% for ddPCR was observed. By contrast, specificity (SP) was higher for RT-LAMP (75%) respect to ddPCR (66%). Comparing the faster RT-LAMP with the sensitive ddPCR the 26% and 74% of SE and SP for RT-LAMP, were reported. The low sensitivity for RT-LAMP and ddPCR could be explained with the use of clinical rather than environmental kits, other than the changing in the virus prevalence during the sampling campaign. Although the RT-LAMP requires improvements in term of SE and SP, this research presents an innovative environmental monitoring and prevention method for SARS-CoV-2, that could be extended to other pathogens that are under environmental surveillance.

A 17-month longitudinal surface sampling study carried out on public transport vehicles operating in England during the COVID-19 pandemic identified low levels of SARS-CoV-2 RNA contamination

AIMS

To monitor severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA contamination in vehicles operating in England during the pandemic, to better understand transmission risk of SARS-CoV-2 on public transport.

METHODS AND RESULTS

We collected 1314 surface samples between December 2020 and April 2022 on trains and buses managed by five different transport operators. The presence of SARS-CoV-2 RNA was investigated through reverse transcription polymerase chain reaction (RT-PCR). SARS-CoV-2 RNA was found on 197 (15%) of the 1314 surfaces sampled, including seat head rests, handholds, and air extract grilles, but the levels of RNA recovered on those samples (median value of 23.4, interquartile range: 14.3-35.4, N gene copies per extraction) made the presence of infectious virus at the time of sampling extremely unlikely. However, detection rates varied over time with peaks broadly coinciding with times of high community transmission, when it was more likely that people infected with SARS-CoV-2 were travelling on public transport.

CONCLUSION

During the pandemic, and as in other public spaces, low levels of SARS-CoV-2 RNA were found on surfaces associated with public transport.

Occurrence of Human Viruses on Fomites in the Environment: A Systematic Review and Meta-analysis

Documenting the occurrence of viruses on fomites is crucial in determining the significance of fomite-mediated transmission and the potential use of fomites for environmental disease surveillance. We conducted a systematic review and meta-analysis to compile information on the occurrence of human viruses on fomites in the environment; we identified 134 peer-reviewed papers. We compiled sampling and measurement methods, results, quality control information, and whether virus data were compared with community health data from the papers. We conducted univariate and multivariate analyses to investigate if presence of virus on fomites was associated with virus type (enveloped, nonenveloped), sampling location (healthcare setting, nonhealthcare temporary setting, nonhealthcare nontemporary setting), and area of fomite swabbed (<50, 50-100, >100 cm2). Across 275 data sets from the 134 papers, there was the most data available for Coronaviridae and from fomites at hospitals. Positivity rates, defined as the percent positive fomite samples, were low (median = 6%). Data were available on viruses from 16 different viral families, but data on viruses from 9 families had few (n < 5) data sets. Many human virus families were not identified in this review (11 families). Less than 15% of the data sets reported virus concentrations in externally valid units (viruses per area of surface), and 16% provided a quantitative comparison between virus and health data. Virus type and area swabbed were significant predictors of virus presence on fomites, and the positivity rate of data sets collected from healthcare settings and nonhealthcare nontemporary settings (e.g., individual housing) were significantly higher than those collected in nonhealthcare temporary settings (e.g., restaurants). Data from this review indicates that viruses may be present on fomites, that fomite-mediated virus transmission may occur, and that fomites may provide information on circulation of infectious diseases in the community. However, more quantitative data on diverse viruses are needed, and method reporting needs significant improvements.

Pierre Schneider B, Detrick E. SARS-CoV-2 surveillance with environmental surface sampling in public areas

Contaminated surfaces are one of the ways that coronavirus disease 2019 (COVID-19) may be transmitted. SARS-CoV-2 can be detected on environmental surfaces; however, few environmental sampling studies have been conducted in nonclinical settings. The objective of this study was to detect SARS-CoV-2 RNA on environmental surfaces in public areas in Las Vegas, Nevada. In total, 300 surface samples were collected from high-touch surfaces from high-congregate public locations and from a public health facility (PHF) that was visited by COVID-19 patients. Environmental samples were analyzed with quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) using SARS-CoV-2 specific primers and probes for three target genes. Results showed that 31 out of 300 (10.3%) surface samples tested positive for SARS-CoV-2, 24 at the PHF and 7 in high-congregate public locations. Concentrations ranged from 102 to 106 viral particles per 3 ml sample on a wide variety of materials. The data also showed that the N gene assay had greater sensitivity compared to the S and ORF gene assays. Besides frequently touched surfaces, SARS-CoV-2 was detected in restrooms, on floors and surfaces in contact with floors, as well as in a mop water sample. The results of this study describe the extent and distribution of environmental SARS-CoV-2 contamination in public areas in Las Vegas, Nevada. A method using the N gene PCR assay was developed for SARS-CoV-2 environmental monitoring in public areas. Environmental monitoring with this method can determine the specific sites of surface contamination in the community and may be beneficial for prevention of COVID-19 indirect transmission, and evaluation and improvement of infection control practices in public areas, public health facilities, universities, and businesses.

Evidence of a novel cross-species transmission by ovine papillomaviruses

Ovine papillomavirus (OaPV) comprises four genotypes; OaPV1, OaPV2 and OaPV4 are fibropapillomaviruses within the genus Deltapapillomavirus, whereas OaPV3 is an epitheliotropic virus that belongs to the genus Dyokappapapillomavirus. To date, all of them have been known to infect sheep only. OaPV1, OaPV2 and OaPV4 have been associated with ovine cutaneous and mucosal fibropapillomas, whereas OaPV3 is a key factor in the squamous cell carcinoma pathway of the sheep skin. Whole blood samples obtained from 128 cattle at public slaughterhouses were investigated using droplet digital polymerase chain reaction (ddPCR). ddPCR is a new-generation PCR technique that enables an accurate and absolute quantification of target molecules with high sensitivity and specificity. All OaPVs were detected by identification and quantification of nucleic acids using specific fluorescent probes. Of 128 blood samples, 100 (∼78%) showed OaPV infections. Further, 42, 35 and 23 blood samples showed single, double and triple OaPV infections, respectively. OaPV1 was responsible for 22 single infections, OaPV2 caused 16 single infections and OaPV3 and OaPV4 caused two single infections each. OaPV1 and OaPV2 were the most frequent ovine viruses in dual and triple infections. In many blood samples, both ovine deltapapillomavirus and dyokappapapillomavirus were found to be transcriptionally active, as shown by the detection and quantification of E5 oncogene transcripts for OaPV1, L1 transcripts for OaPV2, E6 and E7 transcripts for OaPV3 and E6 for OaPV4. OaPVs were found in the blood samples from cattle that shared grasslands rich in bracken ferns known to contain immunosuppressant substances. Furthermore, OaPVs were also found in cattle from intensive livestock farming without any contact with sheep. Because OaPV DNA was detected in both grass hay and corn silage, it is conceivable that these feed may be the viral sources.