Persistent shedding of viable SARS-CoV in urine and stool of SARS patients during the convalescent phase

Identification of shared pathogenetic mechanisms between COVID-19 and IC through bioinformatics and system biology

COVID-19 increased global mortality in 2019. Cystitis became a contributing factor in SARS-CoV-2 and COVID-19 complications. The complex molecular links between cystitis and COVID-19 are unclear. This study investigates COVID-19-associated cystitis (CAC) molecular mechanisms and drug candidates using bioinformatics and systems biology. Obtain the gene expression profiles of IC (GSE11783) and COVID-19 (GSE147507) from the Gene Expression Omnibus (GEO) database. Identified the common differentially expressed genes (DEGs) in both IC and COVID-19, and extracted a number of key genes from this group. Subsequently, conduct Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis on the DEGs. Additionally, design a protein-protein interaction (PPI) network, a transcription factor gene regulatory network, a TF miRNA regulatory network, and a gene disease association network using the DEGs. Identify and extract hub genes from the PPI network. Then construct Nomogram diagnostic prediction models based on the hub genes. The DSigDB database was used to forecast many potential molecular medicines that are associated with common DEGs. Assess the precision of hub genes and Nomogram models in diagnosing IC and COVID-19 by employing Receiver Operating Characteristic (ROC) curves. The IC dataset (GSE57560) and the COVID-19 dataset (GSE171110) were selected to validate the models' diagnostic accuracy. A grand total of 198 DEGs that overlapped were found and chosen for further research. FCER1G, ITGAM, LCP2, LILRB2, MNDA, SPI1, and TYROBP were screened as the hub genes. The Nomogram model, built using the seven hub genes, demonstrates significant utility as a diagnostic prediction model for both IC and COVID-19. Multiple potential molecular medicines associated with common DEGs have been discovered. These pathways, hub genes, and models may provide new perspectives for future research into mechanisms and guide personalised and effective therapeutics for IC patients infected with COVID-19.

Biological mechanisms underpinning the development of long COVID

As COVID-19 evolves from a pandemic to an endemic disease, the already staggering number of people that have been or will be infected with SARS-CoV-2 is only destined to increase, and the majority of humanity will be infected. It is well understood that COVID-19, like many other viral infections, leaves a significant fraction of the infected with prolonged consequences. Continued high number of SARS-CoV-2 infections, viral evolution with escape from post-infection and vaccinal immunity, and reinfections heighten the potential impact of Long COVID. Hence, the impact of COVID-19 on human health will be seen for years to come until more effective vaccines and pharmaceutical treatments become available. To that effect, it is imperative that the mechanisms underlying the clinical manifestations of Long COVID be elucidated. In this article, we provide an in-depth analysis of the evidence on several potential mechanisms of Long COVID and discuss their relevance to its pathogenesis.

SARS-CoV-2 viral load and shedding kinetics

SARS-CoV-2 viral load and detection of infectious virus in the respiratory tract are the two key parameters for estimating infectiousness. As shedding of infectious virus is required for onward transmission, understanding shedding characteristics is relevant for public health interventions. Viral shedding is influenced by biological characteristics of the virus, host factors and pre-existing immunity (previous infection or vaccination) of the infected individual. Although the process of human-to-human transmission is multifactorial, viral load substantially contributed to human-to-human transmission, with higher viral load posing a greater risk for onward transmission. Emerging SARS-CoV-2 variants of concern have further complicated the picture of virus shedding. As underlying immunity in the population through previous infection, vaccination or a combination of both has rapidly increased on a global scale after almost 3 years of the pandemic, viral shedding patterns have become more distinct from those of ancestral SARS-CoV-2. Understanding the factors and mechanisms that influence infectious virus shedding and the period during which individuals infected with SARS-CoV-2 are contagious is crucial to guide public health measures and limit transmission. Furthermore, diagnostic tools to demonstrate the presence of infectious virus from routine diagnostic specimens are needed.

Environmental challenges of COVID-19 pandemic: resilience and sustainability - A review

The emergence of novel respiratory disease (COVID-19) caused by SARS-CoV-2 has become a public health emergency worldwide and perturbed the global economy and ecosystem services. Many studies have reported the presence of SARS-CoV-2 in different environmental compartments, its transmission via environmental routes, and potential environmental challenges posed by the COVID-19 pandemic. None of these studies have comprehensively reviewed the bidirectional relationship between the COVID-19 pandemic and the environment. For the first time, we explored the relationship between the environment and the SARS-CoV-2 virus/COVID-19 and how they affect each other. Supporting evidence presented here clearly demonstrates the presence of SARS-CoV-2 in soil and water, denoting the role of the environment in the COVID-19 transmission process. However, most studies fail to determine if the viral genomes they have discovered are infectious, which could be affected by the environmental factors in which they are found.The potential environmental impact of the pandemic, including water pollution, chemical contamination, increased generation of non-biodegradable waste, and single-use plastics have received the most attention. For the most part, efficient measures have been used to address the current environmental challenges from COVID-19, including using environmentally friendly disinfection technologies and employing measures to reduce the production of plastic wastes, such as the reuse and recycling of plastics. Developing sustainable solutions to counter the environmental challenges posed by the COVID-19 pandemic should be included in national preparedness strategies. In conclusion, combating the pandemic and accomplishing public health goals should be balanced with environmentally sustainable measures, as the two are closely intertwined.

Particle exposure risk to a lavatory user after flushing a squat toilet

Squat toilets are widely used in developing countries due to local customs and low costs. The flushing of a squat toilet can entrain strong airflow and produce aerosols. This investigation constructed a lavatory mock-up with a squat toilet. The flushing-induced airflow was both visualized and quantitatively measured by particle image velocimetry. The maximum height of the impacted airflow was identified by an ultrasonic anemometer. For inference of the particle emission rate, the toilet bowl was covered by an enclosed box for particle concentration measurement. The risks from skin contact of the deposited particles on the flushing button and the door handle and the possible inhalation of the released aerosols were evaluated. The results revealed that flushing a squat toilet can drive toilet plume to rise up to 0.9 m above the toilet bowl. A single flushing process can produce 0.29 million particles with diameters greater than 0.3 μm, among which 90% of the particles are submicron-sized. The flushing may cause particles to deposit on the flushing button and lavatory door handle as well as inhalation exposure even remaining in the lavatory for half a minute after flushing, especially for those lavatory users whose respiratory zones are below 1.0 m.

Distinct Molecular Mechanisms Characterizing Pathogenesis of SARS-CoV-2

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has continued for over 2 years, following the outbreak of coronavirus-19 (COVID-19) in 2019. It has resulted in enormous casualties and severe economic crises. The rapid development of vaccines and therapeutics against SARS-CoV-2 has helped slow the spread. In the meantime, various mutations in the SARS-CoV-2 have emerged to evade current vaccines and therapeutics. A better understanding of SARS-CoV-2 pathogenesis is a prerequisite for developing efficient, advanced vaccines and therapeutics. Since the outbreak of COVID-19, a tremendous amount of research has been conducted to unveil SARSCoV-2 pathogenesis, from clinical observations to biochemical analysis at the molecular level upon viral infection. In this review, we discuss the molecular mechanisms of SARS-CoV-2 propagation and pathogenesis, with an update on recent advances.

A systematic review on the occurrence, fate, and remediation of SARS-CoV-2 in wastewater

The COVID-19 has been declared a pandemic by the World Health Organization. Along with impairing the respiratory system, it also affects the gastrointestinal system. By reviewing experiments on the wastewater analysis for the detection of coronavirus, this study explores the fate, persistence, and various remediation strategies for the virus removal from the wastewater. The results indicated that the virus can be detected in the wastewater samples, feces, and sewage, even before the onset of symptoms. Coronavirus can be a potential panzootic disease, as several mammalian species get infected by the deadly virus. The disinfection strategies used earlier for the treatment of wastewater are not sufficient for the removal of viruses from the wastewater. Therefore, concerted efforts should be made to understand their fate, sources, and occurrence in the environmental matrices. To prevent the spread of the panzootic disease, revised guidelines should be issued for the remediation of the virus. Recent viral remediation methods such as membrane bioreactors and advanced oxidation methods can be used. Therefore, the present review puts a light on the current knowledge on the occurrence of coronaviruses in wastewater, the possible sources, fate, and removal strategies.

Importance of the Precautionary Principle With Regard to the Risk of Exposure to Aerosols Containing Viral Loads of SARS-CoV-2 Present in Feces: In Perspective

In COVID-19 infection, the emissions of droplets and aerosols produced by the respiratory tract of contaminated subjects may represent a high risk of spreading the SARS-COV-2 virus in the environment. Thus, studies have shown that there is, at least, another source of droplets and aerosols in which viral particles of SARS-COV-2 can be found. It happens after flushing of toilet to dispose of the stools of a patient who has contracted COVID-19. The presence of viral particles of SARS-COV-2 in the stool could be linked to the concentration of angiotensin-converting enzyme 2 (ACE2) found on the surface of intestinal cells. Therefore, there is a reason to wonder whether the emission of viral particles by activating a toilet flush could represent an important potential risk of contamination for health care workers. To investigate this hypothesis, we have correlated different studies on the production of droplets and aerosols as well as the presence of viral particles following flush of toilet. This pooling of these studies led to the following conclusion: the precautionary principle should be applied with regard to the potential risk represented by viral particles of SARV-COV-2 in the stool when flushing the toilet.

Potential intestinal infection and faecal-oral transmission of human coronaviruses

Human coronaviruses (HCoVs) were first described in 1960s for patients experiencing common cold. Since then, increasing number of HCoVs have been discovered, including those causing severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the circulating coronavirus disease 2019 (COVID‐19), which can cause fatal respiratory disease in humans on infection. HCoVs are believed to spread mainly through respiratory droplets and close contact. However, studies have shown that a large proportion of patients with HCoV infection develop gastrointestinal (GI) symptoms, and many patients with confirmed HCoV infection have shown detectable viral RNA in their faecal samples. Furthermore, multiple in vitro and in vivo animal studies have provided direct evidence of intestinal HCoV infection. These data highlight the nature of HCoV GI infection and its potential faecal‐oral transmission. Here, we summarise the current findings on GI manifestations of HCoVs. We also discuss how HCoV GI infection might occur and the current evidence to establish the occurrence of faecal‐oral transmission.

Post-COVID-19 syndrome. SARS-CoV-2 RNA detection in plasma, stool, and urine in patients with persistent symptoms after COVID-19

Background

There is a paucity of knowledge on the long-term outcome in patients diagnosed with COVID-19. We describe a cohort of patients with a constellation of symptoms occurring four weeks after diagnosis causing different degrees of reduced functional capacity. Although different hypothesis have been proposed to explain this condition like persistent immune activation or immunological dysfunction, to date, no physiopathological mechanism has been identified. Consequently, there are no therapeutic options besides symptomatic treatment and rehabilitation.

Methods

We evaluated patients with symptoms that persisted for at least 4 weeks after COVID-19. Epidemiological and clinical data were collected. Blood tests, including inflammatory markers, were conducted, and imaging studies made if deemed necessary. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction (RT-PCR) in plasma, stool, and urine were performed. Patients were offered antiviral treatment (compassionate use).

Results

We evaluated 29 patients who reported fatigue, muscle pain, dyspnea, inappropriate tachycardia, and low-grade fever. Median number of days from COVID-19 to positive RT-PCR in extra-respiratory samples was 55 (39–67). Previous COVID-19 was mild in 55% of the cases. Thirteen patients (45%) had positive plasma RT-PCR results and 51% were positive in at least one RT-PCR sample (plasma, urine, or stool). Functional status was severely reduced in 48% of the subjects. Eighteen patients (62%) received antiviral treatment. Improvement was seen in most patients (p = 0.000) and patients in the treatment group achieved better outcomes with significant differences (p = 0.01).

Conclusions

In a cohort of COVID-19 patients with persistent symptoms, 45% of them have detectable plasma SARS-CoV-2 RNA. Our results indicate possible systemic viral persistence in these patients, who may benefit of antiviral treatment strategies.

The Persistence Time of SARS-CoV-2 RNA in hospitalized COVID-19 Patients: A prospective Study

BACKGROUND

In the late December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the causative agent of coronavirus disease 2019 (COVID-19), spreads to almost all countries worldwide. The outbreak of this virus has also been confirmed since 19 February 2020 in Iran.

OBJECTIVE

The aim of this study was to investigate the time of viral RNA clearance in swab and serum samples of COVID-19 patients who received different medications. We also evaluated different factors that may be affected viral RNA persistence in patients infected by SARS-CoV-2.

METHODS

In March 2020, twenty-one hospitalized COVID-19 patients were participated in this prospective study. All patients received antiviral agents in their routine care. Throat swabs and blood samples were obtained from all patients in different intervals including day 3 or 5, day 7, day 10 and finally 14 days after the first positive real time RT-PCR (rRT-PCT) test Results: The median time from the SO to first negative rRT-PCR results for throat swabs and serum samples of COVID-19 patients were 18 and 14 days, respectively. These times were more significant in patients with lymphopenia, oxygen saturation ≤ 90% and comorbidity.

CONCLUSION

This preliminary study highlights that SASR-CoV-2 RNA was not detectable in the upper respiratory tract longer than three weeks. In addition, SARS-CoV may persist for a long period of time in the respiratory than the serum samples. This study support the idea that in the settings of limited resources the patients should cease to be tested earlier than three weeks for discharge management.

The Detection of SARS-CoV-2 in the Environment: Lessons from Wastewater

Wastewater has historically been an important source of enteric pathogens, as well as a source of unconventational or unexpected pathogens, including those present in the respiratory tract, saliva, urine, and blood. This is the case with SARS-CoV-2, the causative agent of the most recent pandemic. SARS-CoV-2 has been identified in wastewater across various geographical regions prior to, and during, the report of cases. The detection of SARS-CoV-2 in wastewater is usually performed using molecular techniques targeting specific genomic regions. High-throughput sequencing techniques, both untargeted and targeted or amplicon-based, are also being applied in combination with molecular techniques for the detection of SARS-CoV-2 variants to determine the genetic diversity and phylogenetic relatedness. The identification of SARS-CoV-2 in wastewater has a number of epidemiological, biological, and ecological applications, which can be incorporated into future outbreaks, epidemics, or pandemics.

Advances in the Rapid Diagnostic of Viral Respiratory Tract Infections

Viral infections are a significant public health problem, primarily due to their high transmission rate, various pathological manifestations, ranging from mild to severe symptoms and subclinical onset. Laboratory diagnostic tests for infectious diseases, with a short enough turnaround time, are promising tools to improve patient care, antiviral therapeutic decisions, and infection prevention. Numerous microbiological molecular and serological diagnostic testing devices have been developed and authorised as benchtop systems, and only a few as rapid miniaturised, fully automated, portable digital platforms. Their successful implementation in virology relies on their performance and impact on patient management. This review describes the current progress and perspectives in developing micro- and nanotechnology-based solutions for rapidly detecting human viral respiratory infectious diseases. It provides a nonexhaustive overview of currently commercially available and under-study diagnostic testing methods and discusses the sampling and viral genetic trends as preanalytical components influencing the results. We describe the clinical performance of tests, focusing on alternatives such as microfluidics-, biosensors-, Internet-of-Things (IoT)-based devices for rapid and accurate viral loads and immunological responses detection. The conclusions highlight the potential impact of the newly developed devices on laboratory diagnostic and clinical outcomes.

Long COVID and COVID-19-associated cystitis (CAC)

Purpose

There is scarce literature regarding genitourinary symptoms in COVID-19, especially post-acute disease otherwise known as Long COVID. We identified recovered COVID-19 patients presenting with new or worsening overactive bladder symptoms, known as COVID-19-associated cystitis (CAC).

Methods

We used the American Urological Association Urology Care Foundation Overactive Bladder (OAB) Assessment Tool to screen COVID-19 recovered patients presenting with urological complaints at our urban-located institution from 5/22/2020 to 12/31/2020. Patients 10–14 weeks post-discharge responded to 5 symptom and 4 quality-of-life (QoL) questions. We reported median symptom scores, as well as QoL scores, based on new or worsening urinary symptoms, and by sex.

Results

We identified 350 patients with de novo or worsening OAB symptoms 10–14 weeks after hospitalization with COVID-19. The median total OAB symptom score in both men and women was 18. The median total QoL score for both men and women was 19. Patients with worsening OAB symptoms had a median pre-COVID-19 symptom score of 8 (4–10) compared to post-COVID-19 median symptom score of 19 (17–21). Median age was 64.5 (range 47–82). Median hospital length-of-stay was 10 days (range 5–30).

Conclusion

We report survey-based results of patients suffering from new or worsening OAB symptoms months after their hospitalization from COVID-19. Future studies with larger sample sizes and more extensive testing will hopefully elucidate the specific pathophysiology of OAB symptoms in the context of long COVID so urologists can timely and appropriately treat their patients.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11255-021-03030-2.

What is the risk of acquiring SARS-CoV-2 from the use of public toilets?

Public toilets and bathrooms may act as a contact hub point where community transmission of SARS-CoV-2 occurs between users. The mechanism of spread would arise through three mechanisms: inhalation of faecal and/or urinary aerosol from an individual shedding SARS-CoV-2; airborne transmission of respiratory aerosols between users face-to-face or during short periods after use; or from fomite transmission via frequent touch sites such as door handles, sink taps, lota or toilet roll dispenser. In this respect toilets could present a risk comparable with other high throughput enclosed spaces such as public transport and food retail outlets. They are often compact, inadequately ventilated, heavily used and subject to maintenance and cleaning issues. Factors such as these would compound the risks generated by toilet users incubating or symptomatic with SARS-CoV-2. Furthermore, toilets are important public infrastructure since they are vital for the maintenance of accessible, sustainable and comfortable urban spaces. Given the lack of studies on transmission through use of public toilets, comprehensive risk assessment relies upon the compilation of evidence gathered from parallel studies, including work performed in hospitals and prior work on related viruses. This narrative review examines the evidence suggestive of transmission risk through use of public toilets and concludes that such a risk cannot be lightly disregarded. A range of mitigating actions are suggested for both users of public toilets and those that are responsible for their design, maintenance and management.

High SARS-CoV-2 Viral Load in Urine Sediment Correlates with Acute Kidney Injury and Poor COVID-19 Outcome

BACKGROUND

AKI is a complication of coronavirus disease 2019 (COVID-19) that is associated with high mortality. Despite documented kidney tropism of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there are no consistent reports of viral detection in urine or correlation with AKI or COVID-19 severity. Here, we hypothesize that quantification of the viral load of SARS-CoV-2 in urine sediment from patients with COVID-19 correlates with occurrence of AKI and mortality.

METHODS

The viral load of SARS-CoV-2 in urine sediments (U-viral load) was quantified by qRT-PCR in 52 patients with PCR-confirmed COVID-19 diagnosis, who were hospitalized between March 15 and June 8, 2020. Immunolabeling of SARS-CoV-2 proteins Spike and Nucleocapsid was performed in two COVID-19 kidney biopsy specimens and urine sediments. Viral infectivity assays were performed from 32 urine sediments.

RESULTS

A total of 20 patients with COVID-19 (39%) had detectable SARS-CoV-2 U-viral load, of which 17 (85%) developed AKI with an average U-viral load four-times higher than patients with COVID-19 who did not have AKI. U-viral load was highest (7.7-fold) within 2 weeks after AKI diagnosis. A higher U-viral load correlated with mortality but not with albuminuria or AKI stage. SARS-CoV-2 proteins partially colocalized with the viral receptor ACE2 in kidney biopsy specimens in tubules and parietal cells, and in urine sediment cells. Infective SARS-CoV-2 was not detected in urine sediments.

CONCLUSION

Our results further support SARS-CoV-2 kidney tropism. A higher SARS-CoV-2 viral load in urine sediments from patients with COVID-19 correlated with increased incidence of AKI and mortality. Urinary viral detection could inform the medical care of patients with COVID-19 and kidney injury to improve prognosis.

Drug repurposing studies targeting SARS-CoV-2: an ensemble docking approach on drug target 3C-like protease (3CLpro)

The COVID-19 pandemic has been responsible for several deaths worldwide. The causative agent behind this disease is the Severe Acute Respiratory Syndrome - novel Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 belongs to the category of RNA viruses. The main protease, responsible for the cleavage of the viral polyprotein is considered as one of the hot targets for treating COVID-19. Earlier reports suggest the use of HIV anti-viral drugs for targeting the main protease of SARS-CoV, which caused SARS in the year 2002-2003. Hence, drug repurposing approach may prove to be useful in targeting the main protease of SARS-CoV-2. The high-resolution crystal structure of the main protease of SARS-CoV-2 (PDB ID: 6LU7) was used as the target. The Food and Drug Administration approved and SWEETLEAD database of drug molecules were screened. The apo form of the main protease was simulated for a cumulative of 150 ns and 10 μs open-source simulation data was used, to obtain conformations for ensemble docking. The representative structures for docking were selected using RMSD-based clustering and Markov State Modeling analysis. This ensemble docking approach for the main protease helped in exploring the conformational variation in the drug-binding site of the main protease leading to the efficient binding of more relevant drug molecules. The drugs obtained as top hits from the ensemble docking possessed anti-bacterial and anti-viral properties. This in silico ensemble docking approach would support the identification of potential candidates for repurposing against COVID-19.Communicated by Ramaswamy H. Sarma.

An Overview of the Pathogenesis, Transmission, Diagnosis, and Management of Endemic Human Coronaviruses: A Reflection on the Past and Present Episodes and Possible Future Outbreaks

The outbreak of the 2019 coronavirus pandemic caught the world by surprise in late 2019 and has held it hostage for months with an increasing number of infections and deaths. Although coronavirus was first discovered in the 1960s and was known to cause respiratory infection in humans, no information was available about the epidemic pattern of the virus until the past two decades. This review addresses the pathogenesis, transmission dynamics, diagnosis, management strategies, the pattern of the past and present events, and the possibility of future outbreaks of the endemic human coronaviruses. Several studies have described bats as presumptive natural reservoirs of coronaviruses. In essence, the identification of a diverse group of similar SARS coronaviruses in bats suggests the possibility of a future epidemic due to severe acute respiratory syndrome (SARS-like) coronaviruses originating from different reservoir hosts. The study also identified a lack of vaccines to prevent human coronavirus infections in humans in the past, however, the recent breakthrough in vaccine discovery and approval for emergency use for the treatment of Severe Acute Respiratory Syndrome Coronavirus 2 is commendable. The high rates of genomic substitution and recombination due to errors in RNA replication and the potential for independent species crossing suggest the chances of an entirely new strain evolving. Therefore, rapid research efforts should be deployed for vaccination to combat the COVID-19 pandemic and prevent a possible future outbreak. More sensitization and enlightenment on the need to adopt good personal hygiene practices, social distancing, and scientific evaluation of existing medications with promising antiviral effects against SARS-CoV-2 is required. In addition, intensive investigations to unravel and validate the possible reservoirs, the intermediate host, as well as insight into the ability of the virus to break the species barrier are needed to prevent future viral spillover and possible outbreaks.

Detection of three pandemic causing coronaviruses from non-respiratory samples: systematic review and meta-analysis

SARS-CoV-2 has posed an unprecedented challenge to the world. Pandemics have been caused previously by viruses of this family like Middle East Respiratory Corona Virus (MERS CoV), Severe Acute Respiratory Syndrome Corona Virus (SARS CoV). Although these viruses are primarily respiratory viruses, but they have been isolated from non-respiratory samples as well. Presently, the detection rate of SARS-CoV-2 RNA from different clinical specimens using Real Time Reverse Transcriptase Polymerized Chain Reaction (qRT-PCR) after onset of symptoms is not yet well established. Therefore, the aim of this systematic review was to establish the profile of detecting SARS-CoV-2, MERS CoV, SARS CoV from different types of clinical specimens other than the respiratory using a standard diagnostic test (qRT-PCR). A total of 3429 non-respiratory specimens were recorded: SARS CoV (total sample-802), MERS CoV (total sample-155), SARS CoV-2 (total sample-2347). Out of all the samples studied high positive rate was seen for saliva with 96.7% (14/14; 95% CI 87.6-100.0%) for SARS CoV and 57.5% (58/250; 95% CI - 1.2 to 116.2%) for SARS CoV-2, while low detection rate in urine samples for SARS CoV-2 with 2.2% (8/318; 95% CI 0.6-3.7%) and 9.6% (12/61; 95% CI - 0.9 to 20.1%) for SARS CoV but there was relatively higher positivity in urine samples for MERS CoV with detection rate of 32.4% (2/38; 95% CI - 37.3 to 102.1%). In Stool sample positivity was 54.9% (396/779; 95% CI 41.0-68.8%), 45.2% (180/430; 95% CI 28.1-62.3%) and 34.7% (4/38; 95% CI - 29.5 to 98.9%) for SARS CoV-2, MERS CoV, and SARS CoV, respectively. In blood sample the positivity was 33.3% (7/21; 95% CI 13.2-53.5%), 23.7% (42/277; 95% CI 10.5-36.9%) and 2.5% (2/81; 95% CI 0.00-5.8%) for MERS CoV, SARS CoV-2 and SARS CoV respectively. SARS-CoV-2 along with previous two pandemic causing viruses from this family, were highly detected stool and saliva. A low positive rate was recorded in blood samples. Viruses were also detected in fluids along with unusual samples like semen and vaginal secretions thus highlighting unique pathogenic potential of SARS-CoV-2.

Evidence of SARS-CoV-2 Infection in Cells, Tissues, and Organs and the Risk of Transmission Through Transplantation

The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus responsible for the coronavirus disease 2019 (COVID-19) pandemic has raised concerns for programs overseeing donation and transplantation of cells, tissues, and organs (CTO) that this virus might be transmissible by transfusion or transplantation. Transplant recipients are considered particularly vulnerable to pathogens because of immunosuppression, and SARS-CoV-2 is likely to generate complications if contracted. Several signs and symptoms observed in COVID-19 positive patients reflect damage to multiple organs and tissues, raising the possibility of extrapulmonary SARS-CoV-2 infections and risk of transmission. At the beginning of the pandemic, a consensus has emerged not to consider COVID-19 positive patients as potential living or deceased donors, resulting in a global decrease in transplantation procedures. Medical decision-making at the time of organ allocation must consider safely alongside the survival advantages offered by transplantation. To address the risk of transmission by transplantation, this review summarizes the published cases of transplantation of cells or organs from donors infected with SARS-CoV-2 until January 2021 and assesses the current state of knowledge for the detection of this virus in different biologic specimens, cells, tissues, and organs. Evidence collected to date raises the possibility of SARS-CoV-2 infection and replication in some CTO, which makes it impossible to exclude transmission through transplantation. However, most studies focused on evaluating transmission under laboratory conditions with inconsistent findings, rendering the comparison of results difficult. Improved standardization of donors and CTO screening practices, along with a systematic follow-up of transplant recipients could facilitate the assessment of SARS-CoV-2 transmission risk by transplantation.

SARS-CoV-2 infection and human semen: possible modes of contamination and transmission

Background

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), has turned into a global pandemic with multitudinous health impacts.

Main body

In light of the higher vulnerability of men to COVID-19 than women, there is rising concerns on the impact of SARS-CoV-2 infection on male fertility and possibilities of seminal contamination and transmission. The pandemic has attributed to the brief suspension of many fertility clinics and pathology laboratories, though many remained functional. Few reports reflect that SARS-CoV-2 can contaminate the semen of COVID-19 patients as well as that of recovering patients. The viral invasion into the testis may be due to the disrupted anatomical barriers of the testis by the inflammatory responses, and the persistence of the virus in the semen may be facilitated by the testicular immune privilege. Since SARS-CoV-2 is an enveloped RNA virus, it is also theoretically possible that this virus can remain viable in the semen samples even after cryopreservation with liquid nitrogen.

Conclusion

The present review emphasizes the possibilities of seminal dissemination of SARS-CoV-2 and thereby the chances of its sexual transmission. These perceptions and predictions are to facilitate immediate necessary actions to improvise the standard precautionary procedures for laboratory practices, including semen analysis or processing the semen sample for fertility treatments.

A critical review on SARS-CoV-2 infectivity in water and wastewater. What do we know?

The COVID-19 outbreak circulating the world is far from being controlled, and possible contamination routes are still being studied. There are no confirmed cases yet, but little is known about the infection possibility via contact with sewage or contaminated water as well as with aerosols generated during the pumping and treatment of these aqueous matrices. Therefore, this article presents a literature review on the detection of SARS-CoV-2 in human excreta and its pathways through the sewer system and wastewater treatment plants until it reaches the water bodies, highlighting their occurrence and infectivity in sewage and natural water. Research lines are still indicated, which we believe are important for improving the detection, quantification, and mainly the infectivity analyzes of SARS-CoV-2 and other enveloped viruses in sewage and natural water. In fact, up till now, no case of transmission via contact with sewage or contaminated water has been reported and the few studies conducted with these aqueous matrices have not detected infectious viruses. On the other hand, studies are showing that SARS-CoV-2 can remain viable, i.e., infectious, for up to 4.3 and 6 days in sewage and water, respectively, and that other species of coronavirus may remain viable in these aqueous matrices for more than one year, depending on the sample conditions. These are strong pieces of evidence that the contamination mediated by contact with sewage or contaminated water cannot be ruled out, even because other more resistant and infectious mutations of SARS-CoV-2 may appear.

Insights into SARS-CoV-2 Persistence and Its Relevance

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), continues to wreak havoc, threatening the public health services and imposing economic collapse worldwide. Tailoring public health responses to the SARS-CoV-2 pandemic depends on understanding the mechanism of viral replication, disease pathogenesis, accurately identifying acute infections, and mapping the spreading risk of hotspots across the globe. However, effective identification and isolation of persons with asymptomatic and mild SARS-CoV-2 infections remain the major obstacles to efforts in controlling the SARS-CoV-2 spread and hence the pandemic. Understanding the mechanism of persistent viral shedding, reinfection, and the post-acute sequalae of SARS-CoV-2 infection (PASC) is crucial in our efforts to combat the pandemic and provide better care and rehabilitation to survivors. Here, we present a living literature review (January 2020 through 15 March 2021) on SARS-CoV-2 viral persistence, reinfection, and PASC. We also highlight potential areas of research to uncover putative links between viral persistence, intra-host evolution, host immune status, and protective immunity to guide and direct future basic science and clinical research priorities.

SARS-CoV-2: sewage surveillance as an early warning system and challenges in developing countries

Transmission of novel coronavirus (SARS-CoV-2) in humans happens either through airway exposure to respiratory droplets from an infected patient or by touching the virus contaminated surface or objects (fomites). Presence of SARS-CoV-2 in human feces and its passage to sewage system is an emerging concern for public health. Pieces of evidence of the occurrence of viral RNA in feces and municipal wastewater (sewage) systems have not only warned reinforcing the treatment facilities but also suggest that these systems can be monitored to get epidemiological data for checking trend of COVID-19 infection in the community. This review summarizes the occurrence and persistence of novel coronavirus in sewage with an emphasis on the possible water environment contamination. Monitoring of novel coronavirus (SARS-CoV-2) via sewage-based epidemiology could deliver promising information regarding rate of infection providing a valid and complementary tool for tracking and diagnosing COVID-19 across communities. Tracking the sewage systems could act as an early warning tool for alerting the public health authorities for necessary actions. Given the impracticality of testing every citizen with limited diagnostic resources, it is imperative that sewage-based epidemiology can be tested as an early warning system. The need for the development of robust sampling strategies and subsequent detection methodologies and challenges for developing countries are also discussed.

Toilet hygiene-review and research needs

The goal of good toilet hygiene is minimizing the potential for pathogen transmission. Control of odours is also socially important and believed to be a societal measure of cleanliness. Understanding the need for good cleaning and disinfecting is even more important today considering the potential spread of emerging pathogens such as SARS‐CoV‐2 virus. While the flush toilet was a major advancement in achieving these objectives, exposure to pathogens can occur from failure to clean and disinfect areas within a restroom, as well as poor hand hygiene. The build‐up of biofilm within a toilet bowl/urinal including sink can result in the persistence of pathogens and odours. During flushing, pathogens can be ejected from the toilet bowl/urinal/sink and be transmitted by inhalation and contaminated fomites. Use of automatic toilet bowl cleaners can reduce the number of microorganisms ejected during a flush. Salmonella bacteria can colonize the underside of the rim of toilets and persist up to 50 days. Pathogenic enteric bacteria appear in greater numbers in the biofilm found in toilets than in the water. Source tracking of bacteria in homes has demonstrated that during cleaning enteric bacteria are transferred from the toilet to the bathroom sinks and that these same bacteria colonize cleaning tools used in the restroom. Quantitative microbial risk assessment has shown that significant risks exist from both aerosols and fomites in restrooms. Cleaning with soaps and detergents without the use of disinfectants in public restrooms may spread bacteria and viruses throughout the restroom. Odours in restrooms are largely controlled by ventilation and flushing volume in toilet/urinals. However, this results in increased energy and water usage. Contamination of both the air and surfaces in restrooms is well documented. Better quantification of the risks of infection are needed as this will help determine what interventions will minimize these risks.

Recent advances and challenges of RT-PCR tests for the diagnosis of COVID-19

Since the outbreak of the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the control of virus spread has remained challenging given the pitfalls of the current diagnostic tests. Nevertheless, RNA amplification techniques have been the gold standard among other diagnostic methods for monitoring clinical samples for the presence of the virus. In the current paper, we review the shortcomings and strengths of RT-PCR (real-time polymerase chain reaction) techniques for diagnosis of coronavirus disease (COVID)-19. We address the repercussions of false-negative and false-positive rates encountered in the test, summarize approaches to improve the overall sensitivity of this method. We discuss the barriers to the widespread use of the RT-PCR test, and some technical advances, such as RT-LAMP (reverse-transcriptase-loop mediated isothermal amplification). We also address how other molecular techniques, such as immunodiagnostic tests can be used to avoid incorrect interpretation of RT-PCR tests.

Prevalence and Persistent Shedding of Fecal SARS-CoV-2 RNA in Patients With COVID-19 Infection: A Systematic Review and Meta-analysis

INTRODUCTION

The prevalence and shedding of fecal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA indicate coronavirus disease 2019 (COVID-19) infection in the gastrointestinal (GI) tract and likely infectivity. We performed a systemic review and meta-analysis to evaluate the prevalence and the duration of shedding of fecal RNA in patients with COVID-19 infection.

METHODS

PubMed, Embase, Web of Science, and Chinese databases Chinese National Knowledge Infrastructure and Wanfang Data up to June 2020 were searched for studies evaluating fecal SARS-CoV-2 RNA, including anal and rectal samples, in patients with confirmed COVID-19 infection. The pooled prevalence of fecal RNA in patients with detectable respiratory RNA was estimated. The days of shedding and days to loss of fecal and respiratory RNA from presentation were compared.

RESULTS

Thirty-five studies (N = 1,636) met criteria. The pooled prevalence of fecal RNA in COVID-19 patients was 43% (95% confidence interval [CI] 34%-52%). Higher proportion of patients with GI symptoms (52.4% vs 25.9%, odds ratio = 2.4, 95% CI 1.2-4.7) compared with no GI symptoms, specifically diarrhea (51.6% vs 24.0%, odds ratio = 3.0, 95% CI 1.9-4.8), had detectable fecal RNA. After loss of respiratory RNA, 27% (95% CI 15%-44%) of the patients had persistent shedding of fecal RNA. Days of RNA shedding in the feces were longer than respiratory samples (21.8 vs 14.7 days, mean difference = 7.1 days, 95% CI 1.2-13.0). Furthermore, days to loss of fecal RNA lagged respiratory RNA by a mean of 4.8 days (95% CI 2.2-7.5).

DISCUSSION

Fecal SARS-CoV-2 RNA is commonly detected in COVID-19 patients with a 3-fold increased risk with diarrhea. Shedding of fecal RNA lasted more than 3 weeks after presentation and a week after last detectable respiratory RNA.

SARS-CoV-2 in hospital wastewater during outbreak of COVID-19: A review on detection, survival and disinfection technologies

Currently, the apparition of new SARS-CoV, known as SARS-CoV-2, affected more than 34 million people and causing high death rates worldwide. Recently, several studies reported SARS-CoV-2 ribonucleic acid (RNA) in hospital wastewater. SARS-CoV-2 can be transmitted between humans via respiratory droplets, close contact and fomites. Fecal-oral transmission is considered also as a potential route of transmission since several scientists confirmed the presence of SARS-CoV-2 RNA in feces of infected patients, therefore its transmission via feces in aquatic environment, particularly hospital wastewater. Hospitals are one of the important classes of polluting sectors around the world. It was identified that hospital wastewater contains hazardous elements and a wide variety of microbial pathogens and viruses. Therefore, this may potentially pose a significant risk of public health and environment infection. This study reported an introduction about the Physical-chemical and microbiological characterization of hospital wastewater, which can be a route to identify potential technology to reduce the impact of hospital contaminants before evacuation. The presence of SARS-CoV-2 in aqueous environment was reviewed. The knowledge of the detection and survival of SARS-CoV-2 in wastewater and hospital wastewater were described to understand the different routes of SARS-CoV-2 transmission, which is also useful to avoid the outbreak of CoV-19. In addition, disinfection technologies used commonly for deactivation of SARS-CoV-2 were highlighted. It was revealed that, chlorine-containing disinfectants are the most commonly used disinfectants in this field of research. Meanwhile, other efficient technologies must be developed and improved to avoid another wave of the pandemic of COVID-19 infections.

Aerosol generation in public restrooms

Aerosolized droplets play a central role in the transmission of various infectious diseases, including Legionnaire's disease, gastroenteritis-causing norovirus, and most recently COVID-19. Respiratory droplets are known to be the most prominent source of transmission for COVID-19; however, alternative routes may exist given the discovery of small numbers of viable viruses in urine and stool samples. Flushing biomatter can lead to the aerosolization of micro-organisms; thus, there is a likelihood that bioaerosols generated in public restrooms may pose a concern for the transmission of COVID-19, especially since these areas are relatively confined, experience heavy foot traffic, and may suffer from inadequate ventilation. To quantify the extent of aerosolization, we measure the size and number of droplets generated by flushing toilets and urinals in a public restroom. The results indicate that the particular designs tested in the study generate a large number of droplets in the size range 0.3   μ m - 3   μ m , which can reach heights of at least 1.52 m. Covering the toilet reduced aerosol levels but did not eliminate them completely, suggesting that aerosolized droplets escaped through small gaps between the cover and the seat. In addition to consistent increases in aerosol levels immediately after flushing, there was a notable rise in ambient aerosol levels due to the accumulation of droplets from multiple flushes conducted during the tests. This highlights the need for incorporating adequate ventilation in the design and operation of public spaces, which can help prevent aerosol accumulation in high occupancy areas and mitigate the risk of airborne disease transmission.

Evaluation of SARS-CoV-2 in Human Semen and Effect on Total Sperm Number: A Prospective Observational Study

PURPOSE

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has created a surge of research to help better understand the breadth of possible sequelae. However, little is known regarding the impact on semen parameters and fertility potential. We sought to investigate for presence of viral RNA in semen of men with SARS-CoV-2 infection and to evaluate its effect on semen parameters in ejaculate.

MATERIALS AND METHODS

We prospectively recruited thirty men diagnosed with acute SARS-CoV-2 infection using real-time reverse transcriptase polymerase chain reaction (RT-PCR) of pharyngeal swab specimens. Semen samples were collected from each individual using mailed kits. Follow-up semen samples were done with mailed kits or in-person in office setting. Semen analysis and PCR was performed after samples were received.

RESULTS

Thirty semen samples from recovered men were obtained 11-64 days after testing positive for SAR-CoV-2 infection. The median duration between positive SAR-CoV-2 test and semen collection was 37 days (interquartile range [IQR]=23). The median total sperm number (TSN) in ejaculate was 12.5 million (IQR=52.1). When compared with age-matched SARS-CoV-2(-) men, TSN was lower among SARS-CoV-2(+) men (p=0.0024). Five men completed a follow-up sperm analysis (median 3 months) and had a median TSN of 18 million (IQR=21.6). No RNA was detected by means of RT-PCR in the semen in 16 samples tested.

CONCLUSIONS

SARS-CoV-2 infection, though not detected in semen of recovered men, can affect TSN in ejaculate in the acute setting. Whether SARS-CoV-2 can affect spermatogenic function long-term remains to be evaluated.

SARS-CoV-2: An Update on Genomics, Risk Assessment, Potential Therapeutics and Vaccine Development

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a great threat to public health, being a causative pathogen of a deadly coronavirus disease (COVID-19). It has spread to more than 200 countries and infected millions of individuals globally. Although SARS-CoV-2 has structural/genomic similarities with the previously reported SARS-CoV and MERS-CoV, the specific mutations in its genome make it a novel virus. Available therapeutic strategies failed to control this virus. Despite strict standard operating procedures (SOPs), SARS-CoV-2 has spread globally and it is mutating gradually as well. Diligent efforts, special care, and awareness are needed to reduce transmission among susceptible masses particularly elder people, children, and health care workers. In this review, we highlighted the basic genome organization and structure of SARS-CoV-2. Its transmission dynamics, symptoms, and associated risk factors are discussed. This review also presents the latest mutations identified in its genome, the potential therapeutic options being used, and a brief explanation of vaccine development efforts against COVID-19. The effort will not only help readers to understand the deadly SARS-CoV-2 virus but also provide updated information to researchers for their research work.

Clinical characteristics and potential factors for recurrence of positive SARS-CoV-2 RNA in convalescent patients: a retrospective cohort study

Background

The recurrence of positive SARS-CoV-2 RT-PCR is frequently found in discharged COVID-19 patients but its clinical significance remains unclear. The potential cause, clinical characteristics and infectiousness of the recurrent positive RT-PCR patients need to be answered.

Methods

A single-centered, retrospective study of 51 discharged COVID-19 patients was carried out at a designated hospital for COVID-19. The demographic data, clinical records and laboratory findings of 25 patients with recurrent positive RT-PCR from hospitalization to follow-up were collected and compared to 26 patients with negative RT-PCR discharged regularly during the same period. Discharged patients’ family members and close contacts were also interviewed by telephone to evaluate patients’ potential infectiousness.

Results

The titer of both IgG and IgM antibodies was significantly lower (p = 0.027, p = 0.011) in patients with recurrent positive RT-PCR. Median duration of viral shedding significantly prolonged in patients with recurrent positive RT-PCR (36.0 days vs 9.0 days, p = 0.000). There was no significant difference in demographic features, clinical features, lymphocyte subsets count and inflammatory cytokines levels between the two groups of patients. No fatal case was noted in two groups. As of the last day of follow-up, none of the discharged patients’ family members or close contact developed any symptoms of COVID-19.

Conclusions

Patients with low levels of IgG and IgM are more likely to have recurrent positive SARS-CoV-2 RT-PCR results and lead to a prolonged viral shedding. The recurrent positive of SARS-CoV-2 RT-PCR may not indicate the recurrence or aggravation of COVID-19. The detection of SARS-CoV-2 by RT-PCR in the patients recovered from COVID-19 is not necessarily correlated with the ability of transmission.

Guidelines and Safety Considerations in the Laboratory Diagnosis of SARS-CoV-2 Infection: A Prerequisite Study for Health Professionals

Coronavirus disease 2019 (COVID-19) is an emerging challenging area for the researchers to buckle up against the spread and control of the virus. Since earlier times, the diagnosis has been an important procedure in estimating the fate of epidemics by indicating the extent to which disease has been spread and to the extent, further disease prognosis would occur. The absence of anti-viral therapies and vaccines for COVID-19 at present suggests early diagnosis and isolation of the patients as the only smart approach available as of now. Presently, the increasing death rates, faster rates of transmission, non-availability of vaccines, and treatment have over-pressurized the researchers, health professionals, and government officials to develop effective clinical strategies in diagnosis and to come up with guidelines to be followed during conduction of each diagnostic procedure for maintaining healthcare systems. Since the incubation period of this virus is 2-14 days, a patient can transmit the infection without showing symptoms. Therefore, early diagnosis and isolation of susceptible individuals are the only way to limit the spread of the virus. Significance of diagnosis and triaging, information on specimen collection, safety considerations while handling, transport, and storage of samples have been highlighted in this paper to make people more aware and develop better clinical strategies in the future.

SARS-CoV-2 in environmental perspective: Occurrence, persistence, surveillance, inactivation and challenges

The unprecedented global spread of the severe acute respiratory syndrome (SARS) caused by SARS-CoV-2 is depicting the distressing pandemic consequence on human health, economy as well as ecosystem services. So far novel coronavirus (CoV) outbreaks were associated with SARS-CoV-2 (2019), middle east respiratory syndrome coronavirus (MERS-CoV, 2012), and SARS-CoV-1 (2003) events. CoV relates to the enveloped family of Betacoronavirus (βCoV) with positive-sense single-stranded RNA (+ssRNA). Knowing well the persistence, transmission, and spread of SARS-CoV-2 through proximity, the faecal-oral route is now emerging as a major environmental concern to community transmission. The replication and persistence of CoV in the gastrointestinal (GI) tract and shedding through stools is indicating a potential transmission route to the environment settings. Despite of the evidence, based on fewer reports on SARS-CoV-2 occurrence and persistence in wastewater/sewage/water, the transmission of the infective virus to the community is yet to be established. In this realm, this communication attempted to review the possible influx route of the enteric enveloped viral transmission in the environmental settings with reference to its occurrence, persistence, detection, and inactivation based on the published literature so far. The possibilities of airborne transmission through enteric virus-laden aerosols, environmental factors that may influence the viral transmission, and disinfection methods (conventional and emerging) as well as the inactivation mechanism with reference to the enveloped virus were reviewed. The need for wastewater epidemiology (WBE) studies for surveillance as well as for early warning signal was elaborated. This communication will provide a basis to understand the SARS-CoV-2 as well as other viruses in the context of the environmental engineering perspective to design effective strategies to counter the enteric virus transmission and also serves as a working paper for researchers, policy makers and regulators.

Occurrence, fate and removal of SARS-CoV-2 in wastewater: Current knowledge and future perspectives

The coronavirus disease 2019 (COVID-19), a pandemic of global concern, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recently, many studies have documented the detection of SARS-CoV-2 in human excreta and wastewater. The presence of SARS-CoV-2 in human excreta and wastewater poses serious implications for wastewater treatment. Thus, this review aims to understand the fate of SARS-CoV-2 in the urban water cycle and its inactivation in different stages of treatment in wastewater treatment plants (WWTPs) for effective control to prevent any recurrence of the outbreak. The viral load of SARS-CoV-2 in feces of individuals tested positive has been reported to be in the range of 10⁴-10⁸ copies/L depending on the infection stages. In the wastewater, dilution of feces results in the decrease of the viral load in the range of 10²-10^6.5 copies/L. Monitoring of SARS-CoV-2 in WWTP samples following the wastewater-based epidemiology (WBE) can complement real epidemiological data from clinical testing to help to monitor disease outbreaks in a community. Though promising, high uncertainty involved with the WBE technique warrants further research for reliable and quantitative information. Inactivation of SARS-CoV-2 in WWTPs depends on the operational parameters and is generally enhanced by the tertiary treatment and disinfection techniques with a higher dosage. However, the risk of SARS-CoV-2 dissemination by the treated effluent intended to be disposed of or reused in the urban water cycle needs to be assessed with respect to the extent of viral infectivity.

SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysis

BACKGROUND

Viral load kinetics and duration of viral shedding are important determinants for disease transmission. We aimed to characterise viral load dynamics, duration of viral RNA shedding, and viable virus shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in various body fluids, and to compare SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV) viral dynamics.

METHODS

In this systematic review and meta-analysis, we searched databases, including MEDLINE, Embase, Europe PubMed Central, medRxiv, and bioRxiv, and the grey literature, for research articles published between Jan 1, 2003, and June 6, 2020. We included case series (with five or more participants), cohort studies, and randomised controlled trials that reported SARS-CoV-2, SARS-CoV, or MERS-CoV infection, and reported viral load kinetics, duration of viral shedding, or viable virus. Two authors independently extracted data from published studies, or contacted authors to request data, and assessed study quality and risk of bias using the Joanna Briggs Institute Critical Appraisal Checklist tools. We calculated the mean duration of viral shedding and 95% CIs for every study included and applied the random-effects model to estimate a pooled effect size. We used a weighted meta-regression with an unrestricted maximum likelihood model to assess the effect of potential moderators on the pooled effect size. This study is registered with PROSPERO, CRD42020181914.

FINDINGS

79 studies (5340 individuals) on SARS-CoV-2, eight studies (1858 individuals) on SARS-CoV, and 11 studies (799 individuals) on MERS-CoV were included. Mean duration of SARS-CoV-2 RNA shedding was 17·0 days (95% CI 15·5-18·6; 43 studies, 3229 individuals) in upper respiratory tract, 14·6 days (9·3-20·0; seven studies, 260 individuals) in lower respiratory tract, 17·2 days (14·4-20·1; 13 studies, 586 individuals) in stool, and 16·6 days (3·6-29·7; two studies, 108 individuals) in serum samples. Maximum shedding duration was 83 days in the upper respiratory tract, 59 days in the lower respiratory tract, 126 days in stools, and 60 days in serum. Pooled mean SARS-CoV-2 shedding duration was positively associated with age (slope 0·304 [95% CI 0·115-0·493]; p=0·0016). No study detected live virus beyond day 9 of illness, despite persistently high viral loads, which were inferred from cycle threshold values. SARS-CoV-2 viral load in the upper respiratory tract appeared to peak in the first week of illness, whereas that of SARS-CoV peaked at days 10-14 and that of MERS-CoV peaked at days 7-10.

INTERPRETATION

Although SARS-CoV-2 RNA shedding in respiratory and stool samples can be prolonged, duration of viable virus is relatively short-lived. SARS-CoV-2 titres in the upper respiratory tract peak in the first week of illness. Early case finding and isolation, and public education on the spectrum of illness and period of infectiousness are key to the effective containment of SARS-CoV-2.

FUNDING

None.

Repositive RT-PCR test in discharged COVID-19 patients during medical isolation observation

Objectives: The epidemiological and clinical characteristics of patients with coronavirus disease 2019 (COVID-19) have been researched. However, the prevalence of repositivity by real-time PCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains unclear. Methods: A retrospective study was conducted involving 599 discharged patients with COVID-19 in a single medical centre. The clinical features of patients during their hospitalization and 14-day post-discharge quarantine were collected. Results: A total of 122 patients (20.4%) out of 599 patients retested positive after discharge. Specifically, 94 (15.7%) retested positive within 24 h of discharge, and another 28 patients (4.7%) were repositive on day 7 after discharge, although none showed any clinical symptomatic recurrence. Both repositives and non‑repositives have similar patterns of IgG and IgM. Notably, the length of hospitalization of non-repositive patients was longer than that of 24-h repositive patients and 7-day repositive patients. In addition, the length of hospitalization of 24-h repositive patients was shorter than that of 7-day repositive patients, indicating that the length of hospitalization was also a determinant of viral shedding. Conclusion: Our study provides further information for improving the management of recovered and discharged patients, and further studies should be performed to elucidate the infectiveness of individuals with prolonged or RNA repositivity.

Early-pandemic wastewater surveillance of SARS-CoV-2 in Southern Nevada: Methodology, occurrence, and incidence/prevalence considerations

The World Health Organization (WHO) classified COVID-19 as a global pandemic, with the situation ultimately requiring unprecedented measures to mitigate the effects on public health and the global economy. Although SARS-CoV-2 (the virus responsible for COVID-19) is primarily respiratory in nature, multiple studies confirmed its genetic material could be detected in the feces of infected individuals, thereby highlighting sewage as a potential indicator of community incidence or prevalence. Numerous wastewater surveillance studies subsequently confirmed detection of SARS-CoV-2 RNA in wastewater and wastewater-associated solids/sludge. However, the methods employed in early studies vary widely so it is unclear whether differences in reported concentrations reflect true differences in epidemiological conditions, or are instead driven by methodological artifacts. The current study aimed to compare the performance of virus recovery and detection methods, detect and quantify SARS-CoV-2 genetic material in two Southern Nevada sewersheds from March-May 2020, and better understand the potential link between COVID-19 incidence/prevalence and wastewater concentrations of SARS-CoV-2 RNA. SARS-CoV-2 surrogate recovery (0.34%-55%) and equivalent sample volume (0.1 mL-1 L) differed between methods and target water matrices, ultimately impacting method sensitivity and reported concentrations. Composite sampling of influent and primary effluent resulted in a ∼10-fold increase in concentration relative to corresponding grab primary effluent samples, presumably highlighting diurnal variability in SARS-CoV-2 signal. Detection and quantification of four SARS-CoV-2 genetic markers (up to ∼106 gene copies per liter), along with ratios of SARS-CoV-2 to pepper mild mottle virus (PMMoV), exhibited comparability with public health data for two sewersheds in an early phase of the pandemic. Finally, a wastewater model informed by fecal shedding rates highlighted the potential significance of new cases (i.e., incidence rather than prevalence) when interpreting wastewater surveillance data.

A neonatal cluster of novel coronavirus disease 2019: clinical management and considerations

BACKGROUND

Lately, one of the major clinical and public health issues has been represented by Coronavirus disease of 2019 (COVID-19) during pregnancy and the risk of transmission of the infection from mother to child. Debate on perinatal management and postnatal care is still ongoing, principally questioning the option of the joint management of mother and child after birth and the safety of breastfeeding. According to the available reports, neonatal COVID-19 appears to have a horizontal transmission and seems to be paucisymptomatic or asymptomatic, compared to older age groups. The aim of this work is to describe a cluster of neonatal COVID-19 and discuss our experience, with reference to current evidence on postnatal care and perinatal management.

METHODS

This is a retrospective observational case series of five mother-child dyads, who attended the Labor and Delivery Unit of a first-level hospital in Italy, in March 2020. Descriptive statistics for continuous variables consisted of number of observations, mean and the range of the minimum and maximum values.

RESULTS

Five women and four neonates tested positive for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). In one case, the mother-child dyad was separated and the neonate remained negative on two consecutive tests. Two positive neonates developed symptoms, with a predominant involvement of the gastrointestinal tract. Blood tests were unremarkable, except for a single patient who developed mild neutropenia. No complications occurred.

CONCLUSIONS

We agree that the decision on whether or not to separate a positive/suspected mother from her child should be made on an individual basis, taking into account the parent's will, clinical condition, hospital logistics and the local epidemiological situation. In conformity with literature, in our study, affected neonates were asymptomatic or paucisymptomatic. Despite these reassuring findings, a few cases of severe presentation in the neonatal population have been reported. Therefore, we agree on encouraging clinicians to monitor the neonates with a suspected or confirmed infection.

Persistent Detection and Infectious Potential of SARS-CoV-2 Virus in Clinical Specimens from COVID-19 Patients

The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) that emerged in December 2019 as the causative agent of Coronavirus 2019 (COVID-19) and was declared a pandemic by the World Health Organization in March 2020 has several distinctive features, including extensive multiorgan involvement with a robust systemic inflammatory response, significant associated morbidity and mortality, and prolonged persistence of viral RNA in the clinical specimens of infected individuals as detected by Reverse Transcription Polymerase Chain Reaction (RT-PCR) amplification. This review begins with an overview of SARS-CoV-2 morphology and replication and summarizes what is known to date about the detection of the virus in nasal, oropharyngeal, and fecal specimens of patients who have recovered from COVID-19, with a focus on the factors thought to contribute to prolonged detection. This review also provides a discussion on the infective potential of this material from asymptomatic, pre-symptomatic, and convalescing individuals, to include a discussion of the relative persistence and infectious potential of virus in clinical specimens recovered from pediatric COVID-19 patients.

Ticking bomb: Prolonged faecal shedding of novel coronavirus (2019-nCoV) and environmental implications

The current global coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a tremendous public health challenge globally. While the respiratory transmission of SARS-CoV-2 has been established, evolving reports on the impact of the gastrointestinal system and the prolonged faecal shedding of SARS-CoV-2 show the likelihood of faecally mediated transmission. The increasing evidential presence of SARS-CoV-2 in wastewater and faecal material poses a significant public health threat which may potentiate global vulnerability to high risk of human exposure through environmental drivers especially in less developed countries. While extensively exploring the likelihood of faecally mediated SARS-CoV-2 transmission, infection control and prevention measures aimed at mitigating this pandemic should holistically include environmental drivers.

Laboratory diagnosis of emerging human coronavirus infections - the state of the art

The three unprecedented outbreaks of emerging human coronavirus (HCoV) infections at the beginning of the twenty-first century have highlighted the necessity for readily available, accurate and fast diagnostic testing methods. The laboratory diagnostic methods for human coronavirus infections have evolved substantially, with the development of novel assays as well as the availability of updated tests for emerging ones. Newer laboratory methods are fast, highly sensitive and specific, and are gradually replacing the conventional gold standards. This presentation reviews the current laboratory methods available for testing coronaviruses by focusing on the coronavirus disease 2019 (COVID-19) outbreak going on in Wuhan. Viral pneumonias typically do not result in the production of purulent sputum. Thus, a nasopharyngeal swab is usually the collection method used to obtain a specimen for testing. Nasopharyngeal specimens may miss some infections; a deeper specimen may need to be obtained by bronchoscopy. Alternatively, repeated testing can be used because over time, the likelihood of the SARS-CoV-2 being present in the nasopharynx increases. Several integrated, random-access, point-of-care molecular devices are currently under development for fast and accurate diagnosis of SARS-CoV-2 infections. These assays are simple, fast and safe and can be used in the local hospitals and clinics bearing the burden of identifying and treating patients.

Gastrointestinal symptoms associated with COVID-19: impact on the gut microbiome

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the greatest worldwide pandemic since the 1918 flu. The consequences of the coronavirus disease 2019 (COVID-19) are devastating and represent the current major public health issue across the globe. At the onset, SARS-CoV-2 primarily attacks the respiratory system as it represents the main point of entry in the host, but it also can affect multiple organs. Although most of the patients do not present symptoms or are mildly symptomatic, some people infected with SARS-CoV-2 that experience more severe multiorgan dysfunction. The severity of COVID-19 is typically combined with a set of comorbidities such as hypertension, diabetes, obesity, and/or advanced age that seriously exacerbates the consequences of the infection. Also, SARS-CoV-2 can cause gastrointestinal symptoms, such as vomiting, diarrhea, or abdominal pain during the early phases of the disease. Intestinal dysfunction induces changes in intestinal microbes, and an increase in inflammatory cytokines. Thus, diagnosing gastrointestinal symptoms that precede respiratory problems during COVID-19 may be necessary for improved early detection and treatment. Uncovering the composition of the microbiota and its metabolic products in the context of COVID-19 can help determine novel biomarkers of the disease and help identify new therapeutic targets. Elucidating changes to the microbiome as reliable biomarkers in the context of COVID-19 represent an overlooked piece of the disease puzzle and requires further investigation.

Positive detection of SARS-CoV-2 combined HSV1 and HHV6B virus nucleic acid in tear and conjunctival secretions of a non-conjunctivitis COVID-19 patient with obstruction of common lacrimal duct

BACKGROUND

The current outbreak of COVID-19 has spread rapidly all over the world. Respiratory droplets and contaction with infected patients are the two major transmission routes. However, the value of tear virus nucleic acid is still not clear. We dynamic detected the SARS-CoV-2 in eye sample of one COVID-19 patient with obstruction of common lacrimal ducts.

METHODS

Besides the routine examination, nasopharyngeal and eye swab were continuously measured by polymerase chain reaction assay and next-generation sequencing (NGS). Gene detection was performed for drug use guidance, and flow cytometry was performed to analyse the lymphocyte subsets.

RESULTS

Nasopharyngeal swabs were positive for 22 days, but eye swabs were still continuously positive for 2 weeks after nasopharyngeal swabs turned negative. The low level of lymphocyte and the high level IL-6 lasted for almost 4 weeks, then became near normal. Next-generation sequencing (NGS) confirmed the existing of SARS-CoV-2, HSV1 and HHV6B virus nucleic acid. The gene detection for drug use guidance showed the genetic locus ABCB1 (3435T>C) rs1045642 belonged to type CC and it mean the efficiency of lopinavir-ritonavir would be significantly decreased. The flow cytometry of lymphocyte subsets showed PD-1⁺  CD95⁺ cells was accounting for 94.8% in CD3⁺  CD8⁺ T subset and for 94.8% in CD3⁺  TCRγδ⁺ T subset.

CONCLUSIONS

As obstruction of common lacrimal duct, positively detection in one eye for 2 weeks more after nasopharyngeal swab became negative. More eye swabs should be collected from COVID-19 patients, especially from those immunocompromised, those with eye symptoms and those had a history of ocular diseases.

New Insight into Laboratory Tests and Imaging Modalities for Fast and Accurate Diagnosis of COVID-19: Alternative Suggestions for Routine RT-PCR and CT-A Literature Review

The globally inimitable and unremitting outbreak of COVID-19 infection confirmed the emergency need for critical detection of human coronavirus infections. Laboratory diagnostic tests and imaging modalities are two test groups used for the detection of COVID-19. Nowadays, real-time polymerase chain reaction (RT-PCR) and computed tomography (CT) have been frequently utilized in the clinic. Some limitations that confront with these tests are false-negative results, tests redone for follow-up procedure, high cost, and unable to do for all patients. To overcome these limitations, modified and alternative tests must be considered. Among these tests, RdRp/Hel RT-PCR assay had the lowest diagnostic limitation and highest sensitivity and specificity for the detection of SARS-CoV-2 RNA in both respiratory tract and nonrespiratory tract clinical specimens. On the other hand, lung ultrasound (LUS) and magnetic resonance imaging (MRI) are CT-alternative imaging modalities for the management, screening, and follow-up of COVID-19 patients.

Laboratory Diagnosis and Monitoring the Viral Shedding of SARS-CoV-2 Infection

The worldwide epidemic of coronavirus disease 2019 (COVID-19) is ongoing. Rapid and accurate detection of the causative virus SARS-CoV-2 is vital for the treatment and control of COVID-19. In this study, the comparative sensitivity of different respiratory specimen types were retrospectively analyzed using 3,552 clinical samples from 410 COVID-19 patients confirmed by Guangdong CDC (Center for Disease Control and Prevention). Except for bronchoalveolar lavage fluid (BALF), the sputum possessed the highest positive rate (73.4%-87.5%), followed by nasal swabs (53.1%-85.3%) for both severe and mild cases during the first 14 days after illness onset (d.a.o.). Viral RNA could be detected in all BALF samples collected from the severe group within 14 d.a.o. and lasted up to 46 d.a.o. Moreover, although viral RNA was negative in the upper respiratory samples, it was also positive in BALF samples in most cases from the severe group during treatment. Notably, no viral RNA was detected in BALF samples from the mild group. Despite typical ground-glass opacity observed via computed tomographic scans, no viral RNA was detected in the first three or all upper respiratory tract specimens from some COVID-19 patients. In conclusion, sputum is most sensitive for routine laboratory diagnosis of COVID-19, followed by nasal swabs. Detection of viral RNA in BALF improves diagnostic accuracy in severe COVID-19 patients.

No detection of SARS-CoV-2 from urine, expressed prostatic secretions, and semen in 74 recovered COVID-19 male patients: A perspective and urogenital evaluation

BACKGROUND

The coronavirus disease 2019 (COVID-19) has been spreading all over the world since December 2019. However, medical information regarding the urogenital involvement in recovered COVID-19 patients is limited or unknown.

OBJECTIVES

To comprehensively evaluate urogenital involvement in recovered COVID-19 patients.

MATERIALS AND METHODS

Men aged between 20 years and 50 years who were diagnosed with SARS-CoV-2 infection and recovered when the study was conducted were enrolled in our study. Demographic and clinical characteristics, and history of hospitalization were collected and analyzed. Urine, expressed prostatic secretions (EPSs), and semen samples were collected for SARS-CoV-2 RNA detection. Semen quality and hormonal profiles were analyzed.

RESULTS

Among 74 male recovered COVID-19 patients, 11 (14.9%) were asymptomatic, classified into mild type, and 31 (41.9%) were classified into moderate type. The remaining patients (32/74, 43.2%) had severe pneumonia. No critically ill recovered COVID-19 patient was recruited in our cohort. The median interval between last positive pharyngeal swab RT-PCR test and semen samples collection was 80 days (IQR, 64-93). The median age was 31 years (IQR, 27-36; range, 21-49), and the median body mass index (BMI) was 24.40 (IQR, 22.55-27.30). Forty-five (61.6%) men were married, and 28 (38.4%) were unmarried. Fifty-three (72.6%) patients denied cigarette smoking, 18 (24.7%) were active smokers, and 2 of them were past smokers. The majority of our participants (53/74, 72.6%) did not consume alcohol. Fever occurred in most of the patients (75.3%), and 63 of them had abnormal chest CT images. Only one patient complained of scrotal discomfort during the course of COVID-19, which was ruled out orchitis by MRI (data not shown). A total of 205 samples were collected for SARS-CoV-2 detection (74 urine samples, 70 semen samples, and 61 EPS samples). However, viral nucleic acid was not detected in body fluids from the urogenital system. In terms of hormonal profiles, the levels of FSH, LH, testosterone, and estradiol were 5.20 [4.23] mIU/mL, 3.95 [1.63] mIU/mL, 3.65 [1.19] ng/mL, and 39.48 [12.51] pg/mL, respectively. And these values were within the normal limits. The overall semen quality of recovered COVID-19 patients was above the lower reference limit released by the WHO. While compared with healthy control, sperm concentration, total sperm count, and total motility were significantly declined. In addition, different clinical types of COVID-19 have no significant difference in semen parameters, but total sperm count showed a descending trend. Interestingly, subjects with a longer recovery time showed worse data for sperm quality. Small sample size and lacking semen parameters before the infection are the major limitations of our study.

DISCUSSION AND CONCLUSIONS

To the best of our knowledge, it is the largest cohort study with longest follow-up for urogenital evaluation comprehensively so far. Direct urogenital involvement was not found in the recovered COVID-19 male patients. SARS-CoV-2 RNA was undetectable in the urogenital secretions, and semen quality declined slightly, while hormonal profiles remained normal. Moreover, patients with a long time (≥90 days) since recovery had lower total sperm count. Great attention and further study should be conducted and follow-up on the reproductive function in the following months.

The impact of new modes of electronic communication in the treatment of severe acute respiratory syndrome coronavirus 2 infection

Background

More than 26,760,000 cases of SARS-CoV-2 infection have been reported globally to date. This study aimed to analyze the impact of new electronic communication tools in the diagnosis and treatment of patients with SARS-CoV-2 infection.

Methods

From January 20 to February 26, 2020, adult patients with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection who were treated in The Fifth Affiliated Hospital, Sun Yat-sen University, in Zhuhai, China, were recruited. Forty-seven eligible patients were enrolled and randomly classified into either the test group or the control group. All of the patients received the standard therapeutic regimen and routine ward rounds. The test group was subdivided into three subgroups: the first subgroup (5-minute group) was given an extra 5-minute ward round by WeChat voice call once daily for basic disease communication; the second subgroup (10-minute group) received an extra 10-minute ward round by WeChat voice call once daily for further detail; and the third subgroup (20-minute group) was given an extra 10-minute ward round via WeChat voice call once daily, as well as an extra 10 minutes every 3 days. The primary outcome was the duration of positive-to-negative conversion of SARS-CoV-2 nucleic acid diagnosed by the NAT (nucleic acid testing).

Results

In the test groups, the median time from diagnosis to the endpoint was 7.0 days [interquartile range (IQR), 3.8–10.8], compared with 10.0 days (IQR, 6.5–14.5) in the control group. It showed significant reduced the duration time of virus from positive to negative by the NAT (nucleic acid testing), (P=0.032) especially between the 10-minute subgroup (3.0 days; IQR, 3.0–7.5) and the control group (P=0.0065).

Conclusions

The use of new modes of electronic communication can benefit patients during the COVID-19 pandemic and could be extremely valuable in addressing the shortage of medical protective equipment and reducing occupational risk of exposure to infection.