Assessment of inactivation procedures for SARS-CoV-2

Effect of heat inactivation for the detection of severe acute respiratory syndrome-corona virus-2 (SARS-CoV-2) with reverse transcription real time polymerase chain reaction (rRT-PCR): evidence from Ethiopian study

Background

Coronavirus disease 2019 (COVID-19) has been a major public health importance and its specimen needs to be handled safely due to concerns of potential transmissibility to health care workers. Heat inactivation of the sample before nucleic acid isolation might permit safe testing processes. Hence, it is important to assess the effect of heat inactivation on SARS-CoV-2 RT-PCR detection in resource limited settings.

Methods

An experimental study was conducted at Ethiopian Public Health Institute (EPHI) from September 25 to October 15, 2020. A total of 188 Oro-pharyngeal swabs were collected from COVID-19 suspected cases, referred to EPHI for SARS COV-2 testing. One batch of the sample was inactivated at 56 °C heat for 30 min, and the other batch was stored at 4 °C for a similar period of time. RNA extraction and detection were done by DAAN Gene kit protocols. Abbott m2000 RT-PCR was used for amplification and detection. Data analysis was done by using SPSS version 23.0; Chi-square and Pearson correlation test for qualitative and semi-quantitative analysis were used. p-value < 0.05 was considered as statistically significant.

Results

Out of 188 total samples, 119 (63.3%) were positive and 69 (36.7%) were negative in the non-inactivated group. While, 115 (61.2%) of samples were positive and 73 (38.8) were negative in heat inactivated sample batch. Rate of positivity between groups did not have statistically significant difference (p > 0.05). The mean Cycle threshold (Ct) value difference between the two groups of ORF1a/b gene and N gene was 0.042 (95% CI − 0.247–0.331; t = 0.28; p = 0.774) and 0.38 (95% CI 0.097–0.682; t = 2.638; p = 0.010) respectively.

Conclusion

Heat inactivation at 56 °C for 30 min did not affect the qualitative rRT-PCR detection of SARS-CoV-2. However, the finding showed that there was statistically significant Ct value increment after heat inactivation compared to untreated samples. Therefore, false-negative results for high Ct value (Ct > 35) samples were found to be the challenge of this protocol. Hence alternative inactivation methods should be investigated and further studies should be considered.

Preanalytical Issues and Cycle Threshold Values in SARS-CoV-2 Real-Time RT-PCR Testing: Should Test Results Include These?

Since the emergence of SARS-CoV-2 pandemic, clinical laboratories worldwide are overwhelmed with SARS-CoV-2 testing using the current gold standard: real-time reverse-transcription polymerase chain reaction (RT-PCR) assays. The large numbers of suspected cases led to shortages in numerous reagents such as specimen transport and RNA extraction buffers. We try to provide some answers on how strongly preanalytical issues affect RT-PCR results by reviewing the utility of different transport buffer media and virus inactivation procedures and comparing the literature data with our own recent findings. We show that various viral inactivation procedures and transport buffers are available and are less of a bottleneck for PCR-based methods. However, efficient alternative lysis buffers remain more difficult to find, and several fast RT-PCR assays are not compatible with guanidine-containing media, making this aspect more of a challenge in the current crisis. Furthermore, the availability of different SARS-CoV-2-specific RT-PCR kits with different sensitivities makes the definition of a general cutoff level for the cycle threshold (Ct) value challenging. Only a few studies have considered how Ct values relate to viral infectivity and how preanalytical issues might affect viral infectivity and RNA detection. We review the current data on the correlation between Ct values and viral infectivity. The presence of the SARS-CoV-2 viral genome in its own is not sufficient proof of infectivity and caution is needed in evaluation of the infectivity of samples. The correlation between Ct values and viral infectivity revealed an RT-PCR cutoff value of 34 cycles for SARS-CoV-2 infectivity using a laboratory-developed RT-PCR assay targeting the RdRp gene. While ideally each clinical laboratory should perform its own correlation, we believe this perspective article could be a reference point for others, in particular medical doctors and researchers interested in COVID-19 diagnostics, and a first step toward harmonization.

Unlocking the surge in demand for personal and protective equipment (PPE) and improvised face coverings arising from coronavirus disease (COVID-19) pandemic - Implications for efficacy, re-use and sustainable waste management

Currently, there is no effective vaccine for tackling the ongoing COVID-19 pandemic caused by SARS-CoV-2 with the occurrence of repeat waves of infection frequently stretching hospital resources beyond capacity. Disease countermeasures rely upon preventing person-to-person transmission of SARS-CoV2 so as to protect front-line healthcare workers (HCWs). COVID-19 brings enormous challenges in terms of sustaining the supply chain for single-use-plastic personal and protective equipment (PPE). Post-COVID-19, the changes in medical practice will drive high demand for PPE. Important countermeasures for preventing COVID-19 transmission include mitigating potential high risk aerosol transmission in healthcare setting using medical PPE (such as filtering facepiece respirators (FFRs)) and the appropriate use of face coverings by the general public that carries a lower transmission risk. PPE reuse is a potential short term solution during COVID-19 pandemic where there is increased evidence for effective deployment of reprocessing methods such as vaporized hydrogen peroxide (30 to 35% VH2O2) used alone or combined with ozone, ultraviolet light at 254 nm (2000 mJ/cm2) and moist heat (60 °C at high humidity for 60 min). Barriers to PPE reuse include potentially trust and acceptance by HCWs. Efficacy of face coverings are influenced by the appropriate wearing to cover the nose and mouth, type of material used, number of layers, duration of wearing, and potentially superior use of ties over ear loops. Insertion of a nose clip into cloth coverings may help with maintaining fit. Use of 60 °C for 60 min (such as, use of domestic washing machine and spin dryer) has been advocated for face covering decontamination. Risk of virus infiltration in improvised face coverings is potentially increased by duration of wearing due to humidity, liquid diffusion and virus retention. Future sustained use of PPE will be influenced by the availability of recyclable PPE and by innovative biomedical waste management.

Evaluation of Commercially Available Viral Transport Medium (VTM) for SARS-CoV-2 Inactivation and Use in Point-of-Care (POC) Testing

Critical to facilitating SARS-CoV-2 point-of-care (POC) testing is assurance that viruses present in specimens are inactivated onsite prior to processing. Here, we conducted experiments to determine the virucidal activity of commercially available Viral Transport Mediums (VTMs) to inactivate SARS-CoV-2. Independent testing methods for viral inactivation testing were applied, including a previously described World Health Organization (WHO) protocol, in addition to a buffer exchange method where the virus is physically separated from the VTM post exposure. The latter method enables sensitive detection of viral viability at higher viral titre when incubated with VTM. We demonstrate that VTM formulations, Primestore® Molecular Transport Medium (MTM) and COPAN eNAT™ completely inactivate high-titre SARS-CoV-2 virus (>1 × 107 copies/mL) and are compatible with POC processing. Furthermore, full viral inactivation was rapidly achieved in as little as 2 min of VTM exposure. We conclude that adding certain VTM formulations as a first step post specimen collection will render SARS-CoV-2 non-infectious for transport, or for further in-field POC molecular testing using rapid turnaround GeneXpert platforms or equivalent.

Rapid Review of SARS-CoV-1 and SARS-CoV-2 Viability, Susceptibility to Treatment, and the Disinfection and Reuse of PPE, Particularly Filtering Facepiece Respirators

In the COVID-19 pandemic caused by SARS-CoV-2, hospitals are often stretched beyond capacity. There are widespread reports of dwindling supplies of personal protective equipment (PPE), particularly N95-type filtering facepiece respirators (FFRs), which are paramount to protect frontline medical/nursing staff, and to minimize further spread of the virus. We carried out a rapid review to summarize the existing literature on the viability of SARS-CoV-2, the efficacy of key potential disinfection procedures against the virus (specifically ultraviolet light and heat), and the impact of these procedures on FFR performance, material integrity, and/or fit. In light of the recent discovery of SARS-CoV-2 and limited associated research, our review also focused on the closely related SARS-CoV-1. We propose a possible whole-of-PPE disinfection solution for potential reuse that could be rapidly instituted in many health care settings, without significant investments in equipment.