SARS-CoV-2 viral load and replication in postmortem examinations

SARS-CoV-2 superinfection in CD14+ monocytes with latent human cytomegalovirus (HCMV) promotes inflammatory cascade

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 2019 (COVID-19), has posed significant challenges to global health. While much attention has been directed towards understanding the primary mechanisms of SARS-CoV-2 infection, emerging evidence suggests co-infections or superinfections with other viruses may contribute to increased morbidity and mortality, particularly in severe cases of COVID-19. Among viruses that have been reported in patients with SARS-CoV-2, seropositivity for Human cytomegalovirus (HCMV) is associated with increased COVID-19 risk and hospitalization. HCMV is a ubiquitous beta-herpesvirus with a seroprevalence of 60-90 % worldwide and one of the leading causes of mortality in immunocompromised individuals. The primary sites of latency for HCMV include CD14+ monocytes and CD34+ hematopoietic cells. In this study, we sought to investigate SARS-CoV-2 infection of CD14+ monocytes latently infected with HCMV. We demonstrate that CD14+ cells are susceptible and permissive to SARS-CoV-2 infection and detect subgenomic transcripts indicative of replication. To further investigate the molecular changes triggered by SARS-CoV-2 infection in HCMV-latent CD14+ monocytes, we conducted RNA sequencing coupled with bioinformatic differential gene analysis. The results revealed significant differences in cytokine-cytokine receptor interactions and inflammatory pathways in cells superinfected with replication-competent SARS-CoV-2 compared to the heat-inactivated and mock controls. Notably, there was a significant upregulation in transcripts associated with pro-inflammatory response factors and a decrease in anti-inflammatory factors. Taken together, these findings provide a basis for the heightened inflammatory response, offering potential avenues for targeted therapeutic interventions among HCMV-infected severe cases of COVID-19. SUMMARY: COVID-19 patients infected with secondary viruses have been associated with a higher prevalence of severe symptoms. Individuals seropositive for human cytomegalovirus (HCMV) infection are at an increased risk for severe COVID-19 disease and hospitalization. HCMV reactivation has been reported in severe COVID-19 cases with respiratory failure and could be the result of co-infection with SARS-CoV-2 and HCMV. In a cell culture model of superinfection, HCMV has previously been shown to increase infection of SARS-CoV-2 of epithelial cells by upregulating the human angiotensin-converting enzyme-2 (ACE2) receptor. In this study, we utilize CD14+ monocytes, a major cell type that harbors latent HCMV, to investigate co-infection of SARS-CoV-2 and HCMV. This study is a first step toward understanding the mechanism that may facilitate increased COVID-19 disease severity in patients infected with SARS-CoV-2 and HCMV.

A Year of Deaths Due to or With COVID-19 Under Universal Postmortem Testing in San Francisco

ABSTRACT

The Health Officer of the City and County of San Francisco, California, issued the order that all decedents were required to have a documented COVID-19 test effective from June 2020 to June 2021. The justification for the requirement was that complete data on COVID-19 status at the time of death were needed to help protect first responders and funeral home workers, identify missed cases, and characterize the places of death for otherwise unknown COVID-19 cases. To fill the gap in COVID-19 testing for all decedents, particularly among persons dying outside of hospitals, a specialized Decedent Testing Unit was created along with an increased capacity of the Office of the Chief Medical Examiner. From July 1, 2020, to June 30, 2021, the Decedent Testing Unit and Office of the Chief Medical Examiner provided postmortem testing results for 2776 decedents. Of these, 80 tested positive for COVID-19 for a positivity rate of 2.97%. The largest number of COVID-19-positive specimens were collected from persons who died at home (n = 37, 46.3%), followed by those who died in hospice (n = 20, 25.0%), other places outside of homes or facilities (n = 8, 10.0%), and in skilled nursing or long-term care facilities (n = 7, 8.8%). Follow-up of California death records found that 17 of these 80 cases (21.3%) had COVID-19 listed as one of the causes of death, 22 (27.5%) mentioned COVID-19 under "other conditions," and 41 (51.3%) made no mention of COVID-19. In the context of providing the COVID-19 status of decedents not otherwise known to have infection, our data help gauge the likelihood of missing deaths due to or with COVID-19 and inform future public health decisions on whether to require universal postmortem testing with COVID-19 resurgences or with new deadly epidemics.

Exposures to Bleach, Peroxide, Disinfectants, Antimalarials, and Ivermectin Reported to the California Poison Control System Before and During the COVID-19 Pandemic, 2015-2021

OBJECTIVES

The COVID-19 pandemic led to widespread fear of infection, with many people expanding their use of cleaning products and trying unproven prevention and treatment strategies. We described shifts in reported exposures related to COVID-19 home interventions.

METHODS

This study considered suspected toxicity exposures involving household cleaning products (bleach, peroxide, disinfectants), antimalarials (hydroxychloroquine and chloroquine), and ivermectin reported to the California Poison Control System from 2015 through 2021 and assessed trends in exposures by using interrupted time-series analyses.

RESULTS

We found a significant increase in exposures reported to the California Poison Control System related to household cleaning products and ivermectin during the COVID-19 pandemic. As of January 1, 2015, the baseline level of reported exposures to household cleaning products was 707.33 per month and was declining at a rate of 1.71 (95% CI, -2.87 to -0.56) per month through February 29, 2020. In March 2020, an increase of 466.57 (95% CI, 328.08-605.07) reported exposures above baseline occurred, after which exposures to cleaning products decreased at a rate of 23.40 (95% CI, -32.48 to -14.32) per month. The number of reported exposures to antimalarials did not change significantly before or during the pandemic. The number of reported ivermectin exposures before December 2020 was initially stable at 14.50 per month and then increased by 2.05 per month through December 2021.

CONCLUSIONS

Our observations suggest that while some dangerous home prevention and treatment efforts resolve over time, further interventions may be needed to reduce the public health effects related to attempts to self-treat COVID-19 with ivermectin.

Viable SARS-CoV-2 Omicron sub-variants isolated from autopsy tissues

Introduction

Pulmonary and extrapulmonary manifestations have been described after infection with SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). The virus is known to persist in multiple organs due to its tropism for several tissues. However, previous reports were unable to provide definitive information about whether the virus is viable and transmissible. It has been hypothesized that the persisting reservoirs of SARS-CoV-2 in tissues could be one of the multiple potentially overlapping causes of long COVID.

Methods

In the present study, we investigated autopsy materials obtained from 21 cadaveric donors with documented first infection or reinfection at the time of death. The cases studied included recipients of different formulations of COVID-19 vaccines. The aim was to find the presence of SARS-CoV-2 in the lungs, heart, liver, kidneys, and intestines. We used two technical approaches: the detection and quantification of viral genomic RNA using RT-qPCR, and virus infectivity using permissive in vitro Vero E6 culture.

Results

All tissues analyzed showed the presence of SARS-CoV-2 genomic RNA but at dissimilar levels ranging from 1.01 × 10² copies/mL to 1.14 × 10⁸ copies/mL, even among those cases who had been COVID-19 vaccinated. Importantly, different amounts of replication-competent virus were detected in the culture media from the studied tissues. The highest viral load were measured in the lung (≈1.4 × 10⁶ copies/mL) and heart (≈1.9 × 10⁶ copies/mL) samples. Additionally, based on partial Spike gene sequences, SARS-CoV-2 characterization revealed the presence of multiple Omicron sub-variants exhibiting a high level of nucleotide and amino acid identity among them.

Discussion

These findings highlight that SARS-CoV-2 can spread to multiple tissue locations such as the lungs, heart, liver, kidneys, and intestines, both after primary infection and after reinfections with the Omicron variant, contributing to extending knowledge about the pathogenesis of acute infection and understanding the sequelae of clinical manifestations that are observed during post-acute COVID-19.

What can autopsy say about COVID-19? A case series of 60 autopsies

INTRODUCTION

Autopsies in SARS-CoV-2 infected cadavers are mainly performed to distinguish patients who died with SARS-CoV-2 infection from those who died of COVID-19. The aim of the current study is to assess the most frequent autopsy findings in patients who died of COVID-19 and to establish an association with clinical records.

MATERIALS AND METHODS

60 patients died between April 2020 and March 2021 after SARS-CoV-2 infection underwent a full autopsy performed at Fondazione Policlinico Universitario Agostino Gemelli IRCCS (Rome). Ante-mortem diagnosis of SARS-CoV-2 infection was microbiologically confirmed.

RESULTS

55 (92%) of cases had at least a comorbidity. At microscopic examination, 40 (67%) of the patients presented pulmonary intravascular coagulation with an inflammatory pattern. Pulmonary microangiopathy was a rare finding (n = 8; 13%). Myocardiosclerosis was the main heart finding (n = 44; 73%). Liver involvement with congestion and hypotrophy was found in 33 (55%) of cadavers. Renal tubular epithelial exfoliation (n = 12; 20%) and intravascular coagulation (n = 4; 7%) were frequent observations. During hospitalization 31% of patients (n = 19) developed acute kidney injury (AKI).

CONCLUSIONS

Lungs and kidneys have been shown to play a pivotal role in COVID-19. The gradual worsening of renal function and AKI might be the result of the progressive collapse of cardiopulmonary system.

High titers of infectious SARS-CoV-2 in corpses of patients with COVID-19

OBJECTIVES

The prolonged presence of infectious SARS-CoV-2 in deceased patients with COVID-19 has been reported. However, infectious virus titers have not been determined. Such information is important for public health, death investigation, and handling corpses. The aim of this study was to assess the level of SARS-CoV-2 infectivity in the corpses of patients with COVID-19.

METHODS

We collected 11 nasopharyngeal swabs and 19 lung tissue specimens from 11 autopsy cases with COVID-19 in 2021. We then investigated the viral genomic copy number by real-time reverse transcription-polymerase chain reaction and infectious titers by cell culture and virus isolation.

RESULTS

Infectious virus was present in six of 11 (55%) cases, four of 11 (36%) nasopharyngeal swabs, and nine of 19 (47%) lung specimens. The virus titers ranged from 6.00E + 01 plaque-forming units/ml to 2.09E + 06 plaque-forming units/g. In all cases in which an infectious virus was found, the time from death to discovery was within 1 day and the longest postmortem interval was 13 days.

CONCLUSION

The corpses of patients with COVID-19 may have high titers of infectious virus after a long postmortem interval (up to 13 days). Therefore, appropriate infection control measures must be taken when handling corpses.

A Survey on forensic odontologists' activity in Italy during the COVID-19 pandemic

Few information on virus contagion at the beginning of the covid-19 pandemic led to severe restrictions in the dental and forensic activity in Italy, the introduction of procedural guidelines and implementation of preventive measures. A specific survey on Italian forensic odontologists (FOds) activity was conducted to investigate the COVD-19 pandemic impact on daily practices, the preventive measures adopted to manage the risks of contagion procedures performed on living and dead people and the possible peculiar cases that required the intervention of a medical examiner. A total of 122 FOds answered, mostly males over 46 years coming from northern Italy. The results highlight the lack of specific guidelines for the procedures on living people compared to those on the dead but the regulations for the daily clinical practice resulted more than sufficient: in fact, more than 80% of FOds adopted the preventive and safety measures provided for dental practices. The forensic activity significantly decreased during the initial period (more than 75%) and gradually normalized to pre-pandemic numbers in approximately 50% of cases after the implementation of the vaccination campaign. 13 cases of occupational contagion have been reported, most of them (more than 85%) in northern and central Italy. In two cases members of the dental staff sued the employer for responsibility in the contagion. The decrease of the overall ID activity during the pandemic time can be more likely attributed to the of the dental data than the real impact of the pandemic regulations. The use of telematic tools, such as teleconferences, for many procedures proved to be an important resource useful for application even in post-pandemic times.

Postmortem lung and heart examination of COVID-19 patients in a case series from Jordan

BACKGROUND

Coronavirus disease 2019 (COVID-19) has emerged as a pandemic for more than 2 years. Autopsy examination is an invaluable tool to understand the pathogenesis of emerging infections and their consequent mortalities. The aim of the current study was to present the lung and heart pathological findings of COVID-19-positive autopsies performed in Jordan.

METHODS

The study involved medicolegal cases, where the cause of death was unclear and autopsy examination was mandated by law. We included the clinical and pathologic findings of routine gross and microscopic examination of cases that were positive for COVID-19 at time of death. Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed through molecular detection by real-time polymerase chain reaction, serologic testing for IgM and electron microscope examination of lung samples.

RESULTS

Seventeen autopsies were included, with male predominance (76.5%), Jordanians (70.6%), and 50 years as the mean age at time of death. Nine out of 16 cases (56.3%) had co-morbidities, with one case lacking such data. Histologic examination of lung tissue revealed diffuse alveolar damage in 13/17 cases (76.5%), and pulmonary microthrombi in 8/17 cases (47.1%). Microscopic cardiac findings were scarcely detected. Two patients died as a direct result of acute cardiac disease with limited pulmonary findings.

CONCLUSIONS

The detection of SARS-CoV-2 in postmortem examination can be an incidental or contributory finding which highlights the value of autopsy examination to determine the exact cause of death in controversial cases.

SARS-CoV-2 persistence and infectivity in COVID-19 corpses: a systematic review

The persistence and infectivity of SARS-CoV-2 in different postmortem COVID-19 specimens remain unclear despite numerous published studies. This information is essential to improve corpses management related to clinical biosafety and viral transmission in medical staff and the public community. We aim to understand SARS-CoV-2 persistence and infectivity in COVID-19 corpses. We conducted a systematic review according to Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) protocols. A systematic literature search was performed in PubMed, Science Direct Scopus, and Google Scholar databases using specific keywords. We critically reviewed the collected studies and selected the articles that met the criteria. We included 33 scientific papers that involved 491 COVID-19 corpses. The persistence rate and maximum postmortem interval (PMI) range of the SARS-CoV-2 findings were reported in the lungs (138/155, 89.0%; 4 months), followed by the vitreous humor (7/37, 18.9%; 3 months), nasopharynx/oropharynx (156/248, 62.9%; 41 days), abdominal organs (67/110, 60.9%; 17 days), skin (14/24, 58.3%; 17 days), brain (14/31, 45.2%; 17 days), bone marrow (2/2, 100%; 12 days), heart (31/69, 44.9%; 6 days), muscle tissues (9/83, 10.8%; 6 days), trachea (9/20, 45.0%; 5 days), and perioral tissues (21/24, 87.5%; 3.5 days). SARS-CoV-2 infectivity rates in viral culture studies were detected in the lungs (9/15, 60%), trachea (2/4, 50%), oropharynx (1/4, 25%), and perioral (1/4, 25%) at a maximum PMI range of 17 days. The SARS-CoV-2 persists in the human body months after death and should be infectious for weeks. This data should be helpful for postmortem COVID-19 management and viral transmission preventive strategy.

SARS-CoV-2 antigen detection in deceased bodies: implications for infection prevention

Background & objectives

High transmissibility of the SARS-CoV-2 has significant implications on healthcare workers' safety, preservation, handling, transportation and disposal of the deceased bodies. The objective of this study was to detect SARS-CoV-2 antigen in nasopharyngeal samples and its implications in handling and care of COVID-19 deceased bodies.

Methods

A study was conducted at a dedicated COVID-19 centre on deceased individuals from April to December 2020. Rapid antigen test (RAT) and reverse transcription (RT)-PCR was compared on all the SARS-CoV-2 positive cadavers recruited in the study.

Results

A total of 115 deceased individuals were included in the study. Of these, 79 (68.7%) were male and 36 (31.3%) were female and majority were in the age group of 51-60 yr [31 (27%)]. SARS-CoV-2 antigen test was positive in 32 (27.8%) and negative in 83 (72.1%) individuals. The mean time interval between deaths to the sample collection was 13.2 h with interquartile range of eight to 20 h. Reverse transcription (RT)-PCR was used as the reference test and 24 (20.9%) cases were true positive; 93.6 per cent [95% confidence interval (CI) 88.8-98.4%] sensitivity, 45.2 per cent (95% CI 35.5-55%) specificity, 60.2 per cent (95% CI 50.6-69.8%) positive predictive value and 88.8 per cent (95% CI 82.7-95%) negative predictive value of antigen test was computed.

Interpretation & conclusions

SARS-CoV-2 antigen test was positive beyond 19 h in COVID-19 deceased individuals. Antigen test was found to be highly sensitive in the deceased. Patients, suspected of having died due to COVID-19, can be screened by this method. As infectiousness of the virus in the deceased bodies cannot be directly concluded from either the antigen or RT-PCR test, yet possible transmission cannot be completely ruled out. Strict infection control measures need to be followed during the handling and clearance of COVID-19 cadavers.

A systemic review and recommendation for an autopsy approach to death followed the COVID 19 vaccination

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) started in December 2019. An immediate prevention approach for the outbreak is the development of a vaccination program. Despite a growing number of publications showing the effectiveness of vaccination in preventing SARS-CoV-2 outbreak and reducing the mortality rate, substantial fatal adverse effects were reported after vaccination. Confirmation of the causal relationship of death is required to reimburse under the national vaccination program and could provide a reference for the selection of vaccination. However, a lack of guidelines in the laboratory study and autopsy approach hampered the investigation of post-vaccination death. In this paper, we performed a systematic electronic search on scientific articles related to severe Covid-19 vaccination adverse effects and approaches in identifying the severe side effects using PubMed and Cochrane libraries. A summary on the onset, biochemistry changes and histopathological analyzes of major lethally side effects post-vaccination were discussed. Ultimately, a checklist is suggested to improve the quality of investigation.

A Timeframe for SARS-CoV-2 Genomes: A Proof of Concept for Postmortem Interval Estimations

Establishing the timeframe when a particular virus was circulating in a population could be useful in several areas of biomedical research, including microbiology and legal medicine. Using simulations, we demonstrate that the circulation timeframe of an unknown SARS-CoV-2 genome in a population (hereafter, estimated time of a queried genome [QG]; tE-QG) can be easily predicted using a phylogenetic model based on a robust reference genome database of the virus, and information on their sampling dates. We evaluate several phylogeny-based approaches, including modeling evolutionary (substitution) rates of the SARS-CoV-2 genome (~10-3 substitutions/nucleotide/year) and the mutational (substitutions) differences separating the QGs from the reference genomes (RGs) in the database. Owing to the mutational characteristics of the virus, the present Viral Molecular Clock Dating (VMCD) method covers timeframes going backwards from about a month in the past. The method has very low errors associated to the tE-QG estimates and narrow intervals of tE-QG, both ranging from a few days to a few weeks regardless of the mathematical model used. The SARS-CoV-2 model represents a proof of concept that can be extrapolated to any other microorganism, provided that a robust genome sequence database is available. Besides obvious applications in epidemiology and microbiology investigations, there are several contexts in forensic casework where estimating tE-QG could be useful, including estimation of the postmortem intervals (PMI) and the dating of samples stored in hospital settings.

Virtual autopsy in SARS-CoV-2 breakthrough infection: a case report

It is well documented that COVID-19 vaccines are effective tools for limiting the pandemic. Unfortunately, as is true for all vaccines, SARS-CoV-2 infection in vaccinated individuals is still possible.

We present an autopsy case of SARS-CoV-2 infection after vaccination (“breakthrough infection”) in an elderly man with several comorbidities where post-mortem CT scan was performed. The death was histologically attributed to cardio-respiratory arrest due to ischemic heart failure related to superinfected COVID-19 pneumonia and pre-existing comorbidities. For the first time in the literature, PMCT imaging related to a fatal, autopsy case of breakthrough SARS-CoV-2 infection is reported. PMCT of the lungs, in accordance with histopathological results, showed few signs of COVID-19 pneumonia, large area of consolidation in the right lower lobe, interpreted as bronco-pneumonic focus, and hypostasis.

These findings were well-correlated with the previously reported literature about both PMCT and clinical CT imaging of the lungs in non-vaccinated individuals with early COVID-19 pneumonia and about pulmonary clinical CT imaging in COVID-19 pneumonia in breakthrough SARS-COV-2 infections.

Further studies are needed to cover the whole spectrum of PMCT lung imaging in fatal breakthrough SARS-CoV-2 infection, however, this case represent a first step for exploring this difficult challenge during SARS-CoV-2 pandemic using virtual autopsy.

Analysis of the role of PMCT during the COVID-19 pandemic: a systematic review

Objectives

During COVID-19 pandemic PMCT has been proposed as a forensic investigation method. This systematic review is aimed to systematize evidence and peer-reviewed opinions reported during the first two years of pandemic, to evaluate the role of PMCT during the COVID-19 pandemic.

Materials and methods

An online literature search was performed to identify publications on PMCT during the COVID-19 pandemic between December 2019 and March 2022. For each publication included, the following data were collected: title and abstract, year of publication, type of article, number and type of individuals examined. The selected publications were also categorized based on PMCT findings, histopathological results, the comparison between PMCT and histopathological findings, cause of death and proposed role of PMCT during the pandemic.

Results

A total of 20 publications were included, mostly case reports (9/20). All cases examined included adults. The most frequent PMCT pattern in positive cases was diffuse mixed densities with prevalence of consolidations (pattern 1) (54%). In 97% of the cases where a comparison between PMCT and histological results was performed, a correspondence was found. In 82% of the cases the principal cause of death was COVID-19 pneumonia. PMCT has been proposed as a pre-autopsy screening tool in 62%, and as a method for augmenting post-mortem data in 50% of the papers reporting this issue.

Conclusion

This systematic review suggests that PMCT should be regarded as a highly valuable investigative technique for the forensic evaluation of deaths with ascertained or suspected COVID-19 pneumonia.

COVID-19 Medical and Pharmacological Management in the European Countries Compared to Italy: An Overview

(1) Background: Italy accounts for more than 150,000 deaths due to the COVID-19 pandemic, leading the top rank in SARS-CoV-2-caused deceases in Europe. A survey on the different ways by which the COVID-19 pandemic emergency was managed in the foreign European countries compared to Italy is the purpose of this paper. (2) Methods: A literature search and various mathematical algorithms to approach a rank scoring scale were used to describe in detail the different approaches used by European countries to manage the COVID-19 pandemic emergency. (3) Results: The study showed that Italy stands at the bottom ranking for COVID-19 management due to its high mortality rate. Possible causes of the observed huge numbers of hospitalization and deaths were (a) the demographic composition of the European country; (b) its decentralized healthcare system organization; (c) the role of correct pharmacology in the early stages before hospitalization. Post-mortem examinations were of paramount importance to elucidate the etiopathogenesis of COVID-19 and to tailor a suitable and proper therapy in the early symptomatic stages of COVID-19, preventing hospitalization. (4) Conclusions: Factors such as the significant impact on elderly people, the public health organization prevalently state-owned and represented mainly by hospitals, and criticism of the home therapy approach toward SARS-CoV-2-infected people, may have concurred in increasing the number of COVID-19 deaths in Italy.

Microbiological screening tests for SARS-CoV-2 in the first hour since the hospital admission: A reliable tool for enhancing the safety of pediatric care

INTRODUCTION/PURPOSE

Since a significant proportion of SARS-CoV-2 infections occur within healthcare facilities, a multidisciplinary approach is required for careful and timely assessment of the risk of infection in asymptomatic patients or those whose COVID-19 diagnosis has not yet been made. The aim of this study was to investigate whether an adaptative model based on microbiological testing can represent a valid risk management strategy.

MATERIAL AND METHODS

We collected data from the risk management unit database of a 1,550-bed tertiary hospital (Fondazione Policlinico Gemelli IRCCS, Rome, Italy) concerning pediatric admissions to the Emergency Department (ED) from 1 March 2020 to 31 December 2021. The study period was subdivided in period A and period B according to the technique used for the microbiological screening, respectively reverse-transcription polymerase chain reaction (RT-PCR) and antigen-detection test.

RESULTS

In Period A, 426 children (mean age: 6 years) underwent microbiological screening at the ED. The total number of molecular tests performed was 463. 459/463 tested negative at the molecular test. In Period B, 887 children (mean age: 6 years) underwent microbiological screening in the ED. The total number of molecular tests performed was 1,154. 1,117/1,154 tested negative at the molecular test. Neither in Period A nor in Period B hospital-acquired SARS-CoV-2 infections were reported.

DISCUSSION AND CONCLUSION

Despite high volumes, no cases of hospital-acquired SARS-CoV-2 infection have been reported. SARS-CoV-2 antigen-based tests can be used as a first-line option as they provide rapid results compared to RT-PCR, reducing the risk of infection in ED waiting rooms.