Biosafety Requirements for Autopsies of Patients with COVID-19: Example of a BSL-3 Autopsy Facility Designed for Highly Pathogenic Agents

Unlocking the potential of in silico approach in designing antibodies against SARS-CoV-2

Antibodies are naturally produced safeguarding proteins that the immune system generates to fight against invasive invaders. For centuries, they have been produced artificially and utilized to eradicate various infectious diseases. Given the ongoing threat posed by COVID-19 pandemics worldwide, antibodies have become one of the most promising treatments to prevent infection and save millions of lives. Currently, in silico techniques provide an innovative approach for developing antibodies, which significantly impacts the formulation of antibodies. These techniques develop antibodies with great specificity and potency against diseases such as SARS-CoV-2 by using computational tools and algorithms. Conventional methods for designing and developing antibodies are frequently costly and time-consuming. However, in silico approach offers a contemporary, effective, and economical paradigm for creating next-generation antibodies, especially in accordance with recent developments in bioinformatics. By utilizing multiple antibody databases and high-throughput approaches, a unique antibody construct can be designed in silico, facilitating accurate, reliable, and secure antibody development for human use. Compared to their traditionally developed equivalents, a large number of in silico-designed antibodies have advanced swiftly to clinical trials and became accessible sooner. This article helps researchers develop SARS-CoV-2 antibodies more quickly and affordably by giving them access to current information on computational approaches for antibody creation.

A Standardized Protocol for the Safe Retrieval of Infectious Postmortem Human Brain for Studying Whole-Brain Pathology

ABSTRACT

We describe a safe and standardized perfusion protocol for studying brain pathology in high-risk autopsies using a custom-designed low-cost infection containment chamber and high-resolution histology. The output quality was studied using the histological data from the whole cerebellum and brain stem processed using a high-resolution cryohistology pipeline at 0.5 μm per pixel, in-plane resolution with serial sections at 20-μm thickness. To understand the pathophysiology of highly infectious diseases, it is necessary to have a safe and cost-effective method of performing high-risk autopsies and a standardized perfusion protocol for preparing high-quality tissues. Using the low-cost infection containment chamber, we detail the cranial autopsy protocol and ex situ perfusion-fixation of 4 highly infectious adult human brains. The digitized high-resolution histology images of the Nissl-stained series reveal that most of the sections were free of processing artifacts, such as fixation damage, freezing artifacts, and osmotic shock, at the macrocellular and microcellular level. The quality of our protocol was also tested with the highly sensitive immunohistochemistry staining for specific protein markers. Our protocol provides a safe and effective method in high-risk autopsies that allows for the evaluation of pathogen-host interaction, the underlying pathophysiology, and the extent of the infection across the whole brain at microscopic resolutions.

New autopsy technique in COVID-19 positive dead bodies: opening the thoracic cavity with an outlook to reduce aerosol spread

AIMS

After the advent of the COVID-19 pandemic, most countries have modified some of their health-related regulations. However, this has not been in the case of the postmortem of deceased because it has a legal aspect. Thus, the healthcare providers knowingly or unknowingly faced the threat of COVID-19 exposure from those dead bodies. To introduce an autopsy technique that reduces the droplet spreads, especially in those mortuaries where the biosafety mechanism is not highly equipped.

METHODS

The validity of the new incision was achieved through the calculation of the Scale Content Validity Index (SCVI) taking inputs from 17 forensic specialists. The subjects for the new technique were selected from the patients who were RTPCR positive for COVID-19 or clinically or radiologically showing features of COVID-19.

RESULTS

The dissection procedure was finalised by achieving the SCVI at 0.92. The chest cavity was approached through the abdominal cavity by opening the diaphragm and dissecting out the contents of the chest using a long blade knife.

CONCLUSIONS

The advantage of this approach is that the autopsy surgeon and pathologists do not have to open the chest cavity by dissecting the Sternum, and hence the chance of droplet infection becomes almost nil. This technique is complete, simple, less time-consuming and conducive for sample collection, and even reduces the possibility of body fluid seepage following a postmortem examination.

Virucidal activity of three standard chemical disinfectants against Ebola virus suspended in tripartite soil and whole blood

Proper disinfection and inactivation of highly pathogenic viruses is an essential component of public health and prevention. Depending on environment, surfaces, and type of contaminant, various methods of disinfection must be both efficient and available. To test both established and novel chemical disinfectants against risk group 4 viruses in our maximum containment facility, we developed a standardized protocol and assessed the chemical inactivation of the two Ebola virus variants Mayinga and Makona suspended in two different biological soil loads. Standard chemical disinfectants ethanol and sodium hypochlorite completely inactivate both Ebola variants after 30 s in suspension at 70% and 0.5% v/v, respectively, concentrations recommended for disinfection by the World Health Organization. Additionally, peracetic acid is also inactivating at 0.2% v/v under the same conditions. Continued vigilance and optimization of current disinfection protocols is extremely important due to the continuous presence of Ebola virus on the African continent and increased zoonotic spillover of novel viral pathogens. Furthermore, to facilitate general pandemic preparedness, the establishment and sharing of standardized protocols is very important as it allows for rapid testing and evaluation of novel pathogens and chemical disinfectants.

Inactivation of Bacteriophage ɸ6 and SARS-CoV-2 in Antimicrobial Surface Tests

Due to the COVID-19 pandemic, researchers have focused on new preventive measures to limit the spread of SARS-CoV-2. One promising application is the usage of antimicrobial materials on often-touched surfaces to reduce the load of infectious virus particles. Since tests with in vitro-propagated SARS-CoV-2 require biosafety level 3 (BSL-3) laboratories with limited capacities and high costs, experiments with an appropriate surrogate like the bacteriophage ɸ6 are preferred in most studies. The aim of this study was to compare ɸ6 and SARS-CoV-2 within antiviral surface tests. Different concentrations of copper coatings on polyethylene terephthalate (PET) were used to determine their neutralizing activity against ɸ6 and SARS-CoV-2. The incubation on the different specimens led to similar inactivation of both SARS-CoV-2 and ɸ6. After 24 h, no infectious virus particles were evident on any of the tested samples. Shorter incubation periods on specimens with high copper concentrations also showed a complete inactivation. In contrast, the uncoated PET foils resulted only in a negligible reduced inactivation during the one-hour incubation. The similar reduction rate for ɸ6 and SARS-CoV-2 in our experiments provide further evidence that the bacteriophage ɸ6 is an adequate model organism for SARS-CoV-2 for this type of testing.

Minimally Invasive Tissue Sampling via Post Mortem Ultrasound: A Feasible Tool (Not Only) in Infectious Diseases-A Case Report

In the past years the number of hospital autopsies have declined steadily, becoming almost excluded from medical training. Medicolegal (forensic) autopsies account for almost all autopsies, whereas hospital autopsies are becoming increasingly rare. Minimally invasive tissue sampling (MITS) using post mortem ultrasound offers the opportunity to increase the number of post mortem examinations in a clinical and even forensic context. MITS is a needle-based post mortem procedure that uses (radiological) imaging techniques to examine major organs of the body, acquire tissue samples and aspirate fluid from the body cavities or hollow organs. In this study, MITS was used to determine the presence of other co-existing diseases in a deceased infected 97-year-old woman with severe acute respiratory syndrome coronavirus 2. The examination of her body was carried out using ultrasound as an imaging tool and to gather ultrasound-guided biopsies as conventional autopsy was rejected by the next of kin. Ultrasound and histology identified an intravesical mass leading to an obstruction of the urinary outlet resulting in bilateral hydronephrosis and purulent pyelonephritis, which was unknown during her lifetime. Histopathological examination revealed the tumor mass to be a squamous cell carcinoma. This study has shown that MITS can be used to determine the cause of death and the presence of concomitant diseases in the infectious deceased.

Antiviral Activity of Zinc Oxide Nanoparticles against SARS-CoV-2

The highly contagious SARS-CoV-2 virus is primarily transmitted through respiratory droplets, aerosols, and contaminated surfaces. In addition to antiviral drugs, the decontamination of surfaces and personal protective equipment (PPE) is crucial to mitigate the spread of infection. Conventional approaches, including ultraviolet radiation, vaporized hydrogen peroxide, heat and liquid chemicals, can damage materials or lack comprehensive, effective disinfection. Consequently, alternative material-compatible and sustainable methods, such as nanomaterial coatings, are needed. Therefore, the antiviral activity of two novel zinc-oxide nanoparticles (ZnO-NP) against SARS-CoV-2 was investigated in vitro. Each nanoparticle was produced by applying highly efficient "green" synthesis techniques, which are free of fossil derivatives and use nitrate, chlorate and sulfonate salts as starting materials and whey as chelating agents. The two "green" nanomaterials differ in size distribution, with ZnO-NP-45 consisting of particles ranging from 30 nm to 60 nm and ZnO-NP-76 from 60 nm to 92 nm. Human lung epithelial cells (Calu-3) were infected with SARS-CoV-2, pre-treated in suspensions with increasing ZnO-NP concentrations up to 20 mg/mL. Both "green" materials were compared to commercially available ZnO-NP as a reference. While all three materials were active against both virus variants at concentrations of 10-20 mg/mL, ZnO-NP-45 was found to be more active than ZnO-NP-76 and the reference material, resulting in the inactivation of the Delta and Omicron SARS-CoV-2 variants by a factor of more than 10⁶. This effect could be due to its greater total reactive surface, as evidenced by transmission electron microscopy and dynamic light scattering. Higher variations in virus inactivation were found for the latter two nanomaterials, ZnO-NP-76 and ZnO-NP-ref, which putatively may be due to secondary infections upon incomplete inactivation inside infected cells caused by insufficient NP loading of the virions. Taken together, inactivation with 20 mg/mL ZnO-NP-45 seems to have the greatest effect on both SARS-CoV-2 variants tested. Prospective ZnO-NP applications include an antiviral coating of filters or PPE to enhance user protection.

Autopsy Study of Testicles in COVID-19: Upregulation of Immune-Related Genes and Downregulation of Testis-Specific Genes

CONTEXT

Infection by SARS-CoV-2 may be associated with testicular dysfunction that could affect male fertility.

OBJECTIVE

Testicles of fatal COVID-19 cases were investigated to detect virus in tissue and to evaluate histopathological and transcriptomic changes.

METHODS

Three groups were compared: (a) uninfected controls (subjects dying of trauma or sudden cardiac death; n = 10); (b) subjects dying of COVID-19 (virus-negative in testes; n = 15); (c) subjects dying of COVID-19 (virus-positive in testes; n = 9). SARS-CoV-2 genome and nucleocapsid antigen were probed using RT-PCR, in situ hybridization, and immunohistochemistry (IHC). Infiltrating leukocytes were typed by IHC. mRNA transcripts of immune-related and testis-specific genes were quantified using the nCounter method.

RESULTS

SARS-CoV-2 was detected in testis tissue of 9/24 (37%) COVID-19 cases accompanied by scattered T-cell and macrophage infiltrates. Size of testicles and counts of spermatogenic cells were not significantly different among groups. Analysis of mRNA transcripts showed that in virus-positive testes immune processes were activated (interferon-alpha and -gamma pathways). By contrast, transcription of 12 testis-specific genes was downregulated, independently of virus positivity in tissue. By IHC, expression of the luteinizing hormone/choriogonadotropin receptor was enhanced in virus-positive compared to virus-negative testicles, while expression of receptors for androgens and the follicle-stimulating hormone were not significantly different among groups.

CONCLUSION

In lethal COVID-19 cases, infection of testicular cells is not uncommon. Viral infection associates with activation of interferon pathways and downregulation of testis-specific genes involved in spermatogenesis. Due to the exceedingly high numbers of infected people in the pandemic, the impact of virus on fertility should be further investigated.

A Systematic Review of Lung Autopsy Findings in Elderly Patients after SARS-CoV-2 Infection

Although COVID-19 may cause various and multiorgan diseases, few research studies have examined the postmortem pathological findings of SARS-CoV-2-infected individuals who died. Active autopsy results may be crucial for understanding how COVID-19 infection operates and preventing severe effects. In contrast to younger persons, however, the patient's age, lifestyle, and concomitant comorbidities might alter the morpho-pathological aspects of the damaged lungs. Through a systematic analysis of the available literature until December 2022, we aimed to provide a thorough picture of the histopathological characteristics of the lungs in patients older than 70 years who died of COVID-19. A thorough search was conducted on three electronic databases (PubMed, Scopus, and Web of Science), including 18 studies and a total of 478 autopsies performed. It was observed that the average age of patients was 75.6 years, of which 65.4% were men. COPD was identified in an average of 16.7% of all patients. Autopsy findings indicated significantly heavier lungs, with an average weight of the right lung of 1103 g, while the left lung mass had an average weight of 848 g. Diffuse alveolar damage was a main finding in 67.2% of all autopsies, while pulmonary edema had a prevalence of between 50% and 70%. Thrombosis was also a significant finding, while some studies described focal and extensive pulmonary infarctions in 72.7% of elderly patients. Pneumonia and bronchopneumonia were observed, with a prevalence ranging from 47.6% to 89.5%. Other important findings described in less detail comprise hyaline membranes, the proliferation of pneumocytes and fibroblasts, extensive suppurative bronchopneumonic infiltrates, intra-alveolar edema, thickened alveolar septa, desquamation of pneumocytes, alveolar infiltrates, multinucleated giant cells, and intranuclear inclusion bodies. These findings should be corroborated with children's and adults' autopsies. Postmortem examination as a technique for studying the microscopic and macroscopic features of the lungs might lead to a better knowledge of COVID-19 pathogenesis, diagnosis, and treatment, hence enhancing elderly patient care.

Applicability and usefulness of the Declaration of Helsinki for forensic research with human cadavers and remains

Bodies of deceased persons and human remains and their specimens (i.e., organs, bones, tissues, or biological samples) are essential in forensic research but ad hoc worldwide-recognized ethical standards for their use are still lacking. Such standards are needed both to avoid possible unethical practices and to sustain research in the forensic field. Pending consensus within the forensic science community regarding this topic, with this article we aim to stimulate a debate as to the applicability and usefulness of the Declaration of Helsinki in the field of forensic research involving human cadavers and remains. Considering the fundamental differences compared to clinical research involving human beings and the different moral obligations involved, we focus on the risks, burdens, and benefits of research, ethics committee approval, and informed consent requirements. The Declaration of Helsinki framework allows forensic researchers to focus on substantial ethical principles promoting the consistency, integrity, and quality of research. Consensus regarding ethical standards and the adoption of national and supranational laws that clearly regulate the use of human cadavers and remains, including those from autopsies, continues to be of primary importance for the forensic science community.

Predicting In Vitro and In Vivo Anti-SARS-CoV-2 Activities of Antivirals by Intracellular Bioavailability and Biochemical Activity

Cellular drug response (concentration required for obtaining 50% of a maximum cellular effect, EC₅₀) can be predicted by the intracellular bioavailability (F _ic) and biochemical activity (half-maximal inhibitory concentration, IC₅₀) of drugs. In an ideal model, the cellular negative log of EC₅₀ (pEC₅₀) equals the sum of log F _ic and the negative log of IC₅₀ (pIC₅₀). Here, we measured F _ic's of remdesivir, favipiravir, and hydroxychloroquine in various cells and calculated their anti-SARS-CoV-2 EC₅₀'s. The predicted EC₅₀'s are close to the observed EC₅₀'s in vitro. When the lung concentrations of antiviral drugs are higher than the predicted EC₅₀'s in alveolar type 2 cells, the antiviral drugs inhibit virus replication in vivo, and vice versa. Overall, our results indicate that both in vitro and in vivo antiviral activities of drugs can be predicted by their intracellular bioavailability and biochemical activity without using virus. This virus-free strategy can help medicinal chemists and pharmacologists to screen antivirals during early drug discovery, especially for researchers who are not able to work in the high-level biosafety lab.

Host and microbiome features of secondary infections in lethal covid-19

Secondary infections contribute significantly to covid-19 mortality but driving factors remain poorly understood. Autopsies of 20 covid-19 cases and 14 controls from the first pandemic wave complemented with microbial cultivation and RNA-seq from lung tissues enabled description of major organ pathologies and specification of secondary infections. Lethal covid-19 segregated into two main death causes with either dominant diffuse alveolar damage (DAD) or secondary pneumonias. The lung microbiome in covid-19 showed a reduced biodiversity and increased prototypical bacterial and fungal pathogens in cases of secondary pneumonias. RNA-seq distinctly mirrored death causes and stratified DAD cases into subgroups with differing cellular compositions identifying myeloid cells, macrophages and complement C1q as strong separating factors suggesting a pathophysiological link. Together with a prominent induction of inhibitory immune-checkpoints our study highlights profound alterations of the lung immunity in covid-19 wherein a reduced antimicrobial defense likely drives development of secondary infections on top of SARS-CoV-2 infection.

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Covid-19 autopsy cohort complemented with microbial cultivation and deep sequencing

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Major death causes stratify into DAD and secondary pneumonias

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Prototypical bacterial and fungal agents are found in secondary pneumonias

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Macrophages and C1q stratify DAD subgroups and indicate immune impairment in lungs

Resilience and Protection of Health Care and Research Laboratory Workers During the SARS-CoV-2 Pandemic: Analysis and Case Study From an Austrian High Security Laboratory

The SARS-CoV-2 pandemic has highlighted the interdependency of healthcare systems and research organizations on manufacturers and suppliers of personnel protective equipment (PPE) and the need for well-trained personnel who can react quickly to changing working conditions. Reports on challenges faced by research laboratory workers (RLWs) are rare in contrast to the lived experience of hospital health care workers. We report on experiences gained by RLWs (e.g., molecular scientists, pathologists, autopsy assistants) who significantly contributed to combating the pandemic under particularly challenging conditions due to increased workload, sickness and interrupted PPE supply chains. RLWs perform a broad spectrum of work with SARS-CoV-2 such as autopsies, establishment of virus cultures and infection models, development and verification of diagnostics, performance of virus inactivation assays to investigate various antiviral agents including vaccines and evaluation of decontamination technologies in high containment biological laboratories (HCBL). Performance of autopsies and laboratory work increased substantially during the pandemic and thus led to highly demanding working conditions with working shifts of more than eight hours working in PPE that stressed individual limits and also the ergonomic and safety limits of PPE. We provide detailed insights into the challenges of the stressful daily laboratory routine since the pandemic began, lessons learned, and suggest solutions for better safety based on a case study of a newly established HCBL (i.e., BSL-3 laboratory) designed for autopsies and research laboratory work. Reduced personal risk, increased resilience, and stress resistance can be achieved by improved PPE components, better training, redundant safety measures, inculcating a culture of safety, and excellent teamwork.

Pre-analytical sample stabilization by different sampling devices for PCR-based COVID-19 diagnostics

The outbreak of the SARS-CoV-2 pandemic created an unprecedented requirement for diagnostic testing, challenging not only healthcare workers and laboratories, but also providers. Quantitative RT-PCR of various specimen types is considered the diagnostic gold standard for the detection of SARS-CoV-2, both in terms of sensitivity and specificity. The pre-analytical handling of patient specimens is a critical factor to ensure reliable and valid test results. Therefore, the effect of storage duration and temperature on SARS-CoV-2 RNA copy number stability was examined in various commercially available specimen collection, transport and storage devices for naso/oropharyngeal swabs and saliva. The swab specimen transport and storage devices tested showed no significant alteration of viral RNA copy numbers when stored at room temperature, except for one system when stored for up to 96 h. However, at 37 °C a significant reduction of detectable RNA was found in 3 out of 4 of the swab solutions tested. It was also found that detectability of viral RNA remained unchanged in all 7 saliva devices as well as in unstabilized saliva when stored for 96 h at room temperature, but one device showed marked RNA copy number loss at 37 °C. All tested saliva collection devices inhibited SARS-CoV-2 infectivity immediately, whereas SARS-CoV-2 remained infectious in the swab transport systems examined, which are designed to be used for viral or bacterial growth in cell culture systems.

SARS-CoV2 neutralizing activity of ozone on porous and non-porous materials

The COVID-19 pandemic has generated a major need for non-destructive and environmentally friendly disinfection methods. This work presents the development and testing of a disinfection process based on gaseous ozone for SARS-CoV-2-contaminated porous and non-porous surfaces. A newly developed disinfection chamber was used, equipped with a CeraPlas™ cold plasma generator that produces ozone during plasma ignition. A reduction of more than log 6 of infectious virus could be demonstrated for virus-contaminated cotton and FFP3 face masks as well as glass slides after exposure to 800 ppm ozone for 10-60 min, depending on the material. In contrast to other disinfectants, ozone can be produced quickly and cost-effectively, and its environmentally friendly breakdown product oxygen does not leave harmful residues. Disinfection with ozone could help to overcome delivery difficulties of personal protective equipment by enabling safe reuse with further applications, thereby reducing waste generation, and may allow regular disinfection of personal items with non-porous surfaces.

Minimally Invasive Tissue Sampling as an Alternative to Complete Diagnostic Autopsies in the Context of Epidemic Outbreaks and Pandemics: The Example of Coronavirus Disease 2019 (COVID-19)

Background

Infectious diseases’ outbreak investigation requires, by definition, conducting a thorough epidemiological assessment while simultaneously obtaining biological samples for an adequate screening of potential responsible pathogens. Complete autopsies remain the gold-standard approach for cause-of-death evaluation and characterization of emerging diseases. However, for highly transmissible infections with a significant associated lethality, such as COVID-19, complete autopsies are seldom performed due to biosafety challenges, especially in low-resource settings. Minimally invasive tissue sampling (MITS) is a validated new approach based on obtaining postmortem samples from key organs and body fluids, a procedure that does not require advanced biosafety measures or a special autopsy room.

Methods

We aimed to review the use of MITS or similar procedures for outbreak investigation up to 27 March 2021 and their performance for evaluating COVID-19 deaths.

Results

After a literature review, we analyzed in detail the results of 20 studies conducted at international sites, whereby 216 COVID-19–related deaths were investigated. MITS provided a general and more granular understanding of the pathophysiological changes secondary to the infection and high-quality samples where the extent and degree of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–related damage could be evaluated.

Conclusions

MITS is a useful addition in the investigation and surveillance of infections occurring in outbreaks or epidemics. Its less invasive nature makes the tool more acceptable and feasible and reduces the risk of procedure-associated contagion, using basic biosafety measures. Standardized approaches protocolizing which samples should be collected—and under which exact biosafety measures—are necessary to facilitate and expand its use globally.

Mapping Biological Risks Related to Necropsy Activities: Old Concerns and Novel Issues for the Safety of Health Professionals

Nowadays only a few studies on biological and environmental risk among healthcare workers are available in literature. The present study aims to assess the health operator's risk of contact with microorganisms during necropsy activities, to evaluate the efficiency of current protections, to identify possible new sources of contact, and to point out possible preventive measures. In addition, considering the current pandemic scenario, the risk of transmission of SARS-CoV-2 infection in the dissection room is assessed. The objectives were pursued through two distinct monitoring campaigns carried out in different periods through sampling performed both on the corpses and at the environmental level.

The Experience of the Fight Against COVID-19 in Clinical Laboratory Departments from Chengdu, China

Objective

In order to fight against coronavirus disease 2019 (COVID-19) better and to share our experience as a reference for clinical laboratory departments.

Methods

This was a retrospective study conducted in the clinical laboratory department of Chengdu Women's and Children's Central Hospital in Chengdu, China, from April 2020 to January 2021. The number of nucleic acid and antibody testing specimens of suspected COVID-19 cases was analyzed. The key points of suspected-case sample processing and detection in the clinical laboratory department were summarized. The laboratory was directly involved in the sample processing and testing of suspected cases, the release of reports, and the transfer of specimens to the fever clinic.

Results

The number of COVID-19 nucleic acid test specimens in our laboratory ranged from 102 to 2170 per day, and the number of antibody test specimens ranged from 24 to 391 per day. There were four main considerations in the treatment and detection of suspected-case specimens in the clinical laboratory: biosafety management in clinical laboratory departments, measures to ensure the health of the staff, the eight time points for processing suspected-case samples (turn-around time), and key points for the detection of suspected case specimens.

Conclusion

The laboratory developed a protective process for COVID-19 antibody and nucleic acid detection during the pandemic. At present, the detection of COVID-19 antibodies and nucleic acids in the clinical laboratory department is orderly, and there have been no cases of laboratory infection.

Rapid Antigen Test for Postmortem Evaluation of SARS-CoV-2 Carriage

Detecting severe acute respiratory syndrome coronavirus 2 in deceased patients is key when considering appropriate safety measures to prevent infection during postmortem examinations. A prospective cohort study comparing a rapid antigen test with quantitative reverse transcription PCR showed the rapid test’s usability as a tool to guide autopsy practice.