Differences of Severe Acute Respiratory Syndrome Coronavirus 2 Shedding Duration in Sputum and Nasopharyngeal Swab Specimens Among Adult Inpatients With Coronavirus Disease 2019

Comprehensive Review of COVID-19: Epidemiology, Pathogenesis, Advancement in Diagnostic and Detection Techniques, and Post-Pandemic Treatment Strategies

At present, COVID-19 remains a public health concern due to the ongoing evolution of SARS-CoV-2 and its prevalence in particular countries. This paper provides an updated overview of the epidemiology and pathogenesis of COVID-19, with a focus on the emergence of SARS-CoV-2 variants and the phenomenon known as 'long COVID'. Meanwhile, diagnostic and detection advances will be mentioned. Though many inventions have been made to combat the COVID-19 pandemic, some outstanding ones include multiplex RT-PCR, which can be used for accurate diagnosis of SARS-CoV-2 infection. ELISA-based antigen tests also appear to be potential diagnostic tools to be available in the future. This paper also discusses current treatments, vaccination strategies, as well as emerging cell-based therapies for SARS-CoV-2 infection. The ongoing evolution of SARS-CoV-2 underscores the necessity for us to continuously update scientific understanding and treatments for it.

A robust web-based tool to predict viral shedding in patients with Omicron SARS-CoV-2 variants

Background

Data on viral kinetics and variants affecting the duration of viral shedding were limited. Our objective was to determine viral shedding in distinct severe acute respiratory syndrome coronavirus 2 variants, including Omicron BA.4/5 and BF.7, and to identify the relevant influencing factors.

Methods

We carried out a longitudinal cohort study at Beijing Xiaotangshan Fangcang shelter hospital from May to June 2022 (Omicron BA.4/5) and from November to December 2022 (Omicron BF.7). Nucleocapsid protein (N) and open reading frame (ORF) genes were considered as the target genes of the reverse transcription PCR. The daily results of cycle threshold (CT), including lowest ORF1ab-CT values for days 1-3 post-hospitalisation and lowest N-CT values for days 1-3 post-hospitalisation (CT3minN) and demographic and clinical characteristics were collected.

Results

1433 patients with coronavirus disease 2019 (COVID-19) were recruited from the Fangcang shelter hospital, in which 278 patients were diagnosed with Omicron BA.4/5 and 1155 patients with Omicron BF.7. Patients with BF.7 infection showed a longer duration of viral shedding. The duration of viral shedding was associated with the variants age, alcohol use, the severity of COVID-19 and CT3minN. Moreover, the nomogram had excellent accuracy in predicting viral shedding.

Conclusions

Our results indicated that patients with Omicron BF.7 had a longer period of contagiousness than those with BA.4/5. The duration of viral shedding was affected by a variety of factors and the nomogram may become an applicable clinical instrument to predict viral shedding. Furthermore, we developed a new COVID-19 viral shedding predicting model that can accurately predict the duration of viral shedding for COVID-19, and created a user-friendly website to apply this prediction model (https://puh3.shinyapps.io/CVSP_Model/).

Guidance for prevention and management of COVID-19 in children and adolescents: A consensus statement from the Pediatric Infectious Diseases Society Pediatric COVID-19 Therapies Taskforce

BACKGROUND

Since November 2019, the SARS-CoV-2 pandemic has created challenges for preventing and managing COVID-19 in children and adolescents. Most research to develop new therapeutic interventions or to repurpose existing ones has been undertaken in adults, and although most cases of infection in pediatric populations are mild, there have been many cases of critical and fatal infection. Understanding the risk factors for severe illness and the evidence for safety, efficacy, and effectiveness of therapies for COVID-19 in children is necessary to optimize therapy.

METHODS

A panel of experts in pediatric infectious diseases, pediatric infectious diseases pharmacology, and pediatric intensive care medicine from 21 geographically diverse North American institutions was re-convened. Through a series of teleconferences and web-based surveys and a systematic review with meta-analysis of data for risk factors, a guidance statement comprising a series of recommendations for risk stratification, treatment, and prevention of COVID-19 was developed and refined based on expert consensus.

RESULTS

There are identifiable clinical characteristics that enable risk stratification for patients at risk for severe COVID-19. These risk factors can be used to guide the treatment of hospitalized and non-hospitalized children and adolescents with COVID-19 and to guide preventative therapy where options remain available.

Impact of Tuberculosis on Disease Severity and Viral Shedding Duration in COVID-19 Patients

Accumulating evidence show a potential association between tuberculosis and COVID-19 disease severity. To further clarify the impact of tuberculosis on COVID-19 disease severity and viral shedding duration, a retrospective study was conducted on 223 COVID-19 patients, including 34 with tuberculosis and 189 without tuberculosis. Clinical information and viral load shedding time were collected. A higher percentage of severe/critical COVID-19 diagnosis and deaths was observed in patients with tuberculosis than in those without tuberculosis (8.8% vs. 3.2%, p = 0.142; 2.9% vs. 1.1%, p = 0.393), and COVID-19 patients with tuberculosis had longer viral shedding than those without tuberculosis (median: 15.0 days vs. 11.0 days; p = 0.0001). Having tuberculosis (HR = 2.21, 95% CI 1.37-3.00; p = 0.000), being of elderly age (HR = 1.02, 95% CI 1.01-1.03; p = 0.001) and being diagnosed with severe or critical COVID-19 (HR = 5.63, 95% CI 2.10-15.05; p = 0.001) were independent factors associated with prolonged virus time of SARS-CoV-2. COVID-19 patients with tuberculosis receiving anti-tuberculosis therapy time (ATT) for <2 months had a significantly longer virus shedding duration than those receiving ATT for ≥ 4 months (17.5 vs. 11.5 days, p = 0.012). Our results demonstrated that COVID-19 patients with tuberculosis tend to have more severe disease and a worse prognosis, and tuberculosis prolonged viral shedding, highlighting special attention and/or care required for COVID-19 patients with tuberculosis receiving ATT for <2 months.

Clinical characteristics and outcomes of patients with COVID-19 and tuberculosis coinfection

BACKGROUND

Data on the coincidence of Tuberculosis (TB) and Coronavirus disease 2019 (COVID-19) are limited. We sought to investigate the clinical characteristics and outcomes of coinfected patients in Henan and identify whether TB disease is associated with an increased risk of intensive care unit (ICU) admission and mortality.

METHOD

We conducted a retrospective matched cohort study of COVID-19 inpatients involving 41 TB-positive patients with 82 patients without TB. Leveraging data was collected from electronic medical records.

RESULTS

There were no significant differences in clinical manifestations, the need for mechanical ventilation and vasopressors, ICU admission, or in-hospital mortality between 2 groups. TB-positive patients had a lower lymphocyte counts (1.24 ± 0.54 vs. 1.59 ± 0.58, p = 0.01), B cells (99/µl vs. 201/µl, p < 0.01), CD4+ T cells (382/µl vs. 667/µl, p < 0.01), CD8+ T cells (243/µl vs. 423/µl, p < 0.01), NK cells (145/µl vs. 216/µl, p = 0.01), IL-2 (14.18 ± 11.23 vs. 31.86 ± 34.55, p < 0.01) and TNF-α (3.42 ± 2.93 vs. 5.62 ± 3.69, p < 0.01). Notably, the TB-positive group had a longer duration of SARS-CoV-2 shedding (67 days vs. 22 days, p < 0.01).

CONCLUSIONS

Concomitant TB does not significantly impact clinical outcomes of hospitalised patients with acute COVID-19. However, TB-positive patients had longer duration of SARS-COV-2-RNA positivity.

A retrospective study of Reyanning mixture in elderly patients infected with SARS-CoV-2 Omicron variant

Objective: Reyanning mixture has been demonstrated to be effective in treating infected patients during the outbreak pandemic of SARS-CoV-2 Omicron variant of Coronavirus disease 2019 (COVID-19) in Shanghai 2022. The aim of this study is to further investigate the role of Reyanning mixture specifically in the treatment of elderly patients. Methods: This study enrolled 1,102 elderly patients who were infected with SARS-CoV-2 Omicron variant. Of these, 291 patients received Reyanning mixture in conjunction with conventional Western medicine treatment were assigned to the treatment group, while 811 patients only received conventional Western medicine treatment were assigned to the control group. Clinical parameters including hospitalization duration, viral shedding time, and Cycle Threshold (Ct) values of novel coronavirus nucleic acid tests, as well as adverse events were recorded and analyzed in both groups. Results: There was no significant difference in baseline characteristics between two groups. In comparison to the control group, the treatment group demonstrated a substantial difference in hospitalization duration (median: 8 days vs. 10 days, HR: 0.638, 95% CI: 0.558-0.731, p < 0.001). The treatment group also showed a significantly shorter viral shedding time compared to the control group (median: 7 days vs. 8 days, HR: 0.754, 95% CI: 0.659-0.863, p < 0.001). Multivariate Cox proportional-hazards model analysis indicated that the use of Reyanning mixture was closely associated with a reduction in hospitalization duration (HR: 1.562, 95% CI: 1.364-1.789, p < 0.001) and viral shedding time (HR: 1.335, 95% CI: 1.166-1.528, p < 0.001). In addition, during the treatment process, no serious adverse event occurred in either group. Conclusion: The improvement of clinical parameters in the treatment group indicate a promising therapeutic benefit of Reyanning mixture for elderly patients infected with SARS-CoV-2 Omicron variant in the present study. Further investigations are required to validate this finding by examining the underlying mechanism and function of Reyanning mixture.

Effects of dexamethasone use on viral clearance among patients with COVID-19: a multicenter cohort study

OBJECTIVES

This study explored the outcomes and predictors of early viral clearance among patients with COVID-19.

METHODS

This study recruited consecutive patients from March 1, 2020 to July 31, 2021. Early viral clearance was defined as having a duration from symptom onset to successive detection of SARS-CoV-2 polymerase chain reaction cycle threshold (Ct) value of ≥30 within 10 days.

RESULTS

Among the 239 enrolled patients, 54.4% (130 patients) had early viral clearance. A multivariate logistic regression analysis identified that dexamethasone use and day 1 Ct values were independent factors associated with late viral clearance. Patients with mild-moderate severity and who received dexamethasone therapy had a longer time to viral clearance than those who did not receive dexamethasone (17.2 ± 1.8 days vs 12.3 ± 1.1 days, P = 0.018). Patients with severe-critical severity had a similar duration from symptom onset to Ct value ≥30, regardless of dexamethasone therapy (18.3 ± 0.9 days vs 16.7 ± 4.7 days, P = 0.626).

CONCLUSION

The study revealed that dexamethasone therapy and Ct values are independent predictors of late viral clearance. Patients with severe disease course due to older age, increased number of comorbidities, and worse clinical outcomes experienced delayed viral clearance.

Duration of Replication-Competent Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Shedding Among Patients With Severe or Critical Coronavirus Disease 2019 (COVID-19)

BACKGROUND

Patterns of shedding replication-competent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in severe or critical COVID-19 are not well characterized. We investigated the duration of replication-competent SARS-CoV-2 shedding in upper and lower airway specimens from patients with severe or critical coronavirus disease 2019 (COVID-19).

METHODS

We enrolled patients with active or recent severe or critical COVID-19 who were admitted to a tertiary care hospital intensive care unit (ICU) or long-term acute care hospital (LTACH) because of COVID-19. Respiratory specimens were collected at predefined intervals and tested for SARS-CoV-2 using viral culture and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Clinical and epidemiologic metadata were reviewed.

RESULTS

We collected 529 respiratory specimens from 78 patients. Replication-competent virus was detected in 4 of 11 (36.3%) immunocompromised patients up to 45 days after symptom onset and in 1 of 67 (1.5%) immunocompetent patients 10 days after symptom onset (P = .001). All culture-positive patients were in the ICU cohort and had persistent or recurrent symptoms of COVID-19. Median time from symptom onset to first specimen collection was 15 days (range, 6-45) for ICU patients and 58.5 days (range, 34-139) for LTACH patients. SARS-CoV-2 RNA was detected in 40 of 50 (80%) ICU patients and 7 of 28 (25%) LTACH patients.

CONCLUSIONS

Immunocompromise and persistent or recurrent symptoms were associated with shedding of replication-competent SARS-CoV-2, supporting the need for improving respiratory symptoms in addition to time as criteria for discontinuation of transmission-based precautions. Our results suggest that the period of potential infectiousness among immunocompetent patients with severe or critical COVID-19 may be similar to that reported for patients with milder disease.

Clinical characteristics and risk factors for a prolonged length of stay of patients with asymptomatic and mild COVID-19 during the wave of Omicron from Shanghai, China

BACKGROUND

This study aims to investigate the clinical characteristics and the length of hospital stay (LOS), as well as risk factors for prolonged LOS in a cohort of asymptomatic and mild COVID-19 patients infected with the Omicron variant.

METHODS

A total of 1166 COVID-19 patients discharged from the inpatient ward of the largest makeshift hospital (May 8-10, 2022) in Shanghai, China, were included. The demographics, medical history, and the lowest and admission cycle threshold (Ct) values of the RT-PCR tests for SARS-CoV-2 genes of the open reading frame 1ab (Ct-ORF) and the nucleocapsid protein (Ct-N) during hospitalization were recorded. Patients with LOS > 7 days, or LOS ≤ 7 days were included in the Prolonged group or the Control group, separately. The clinical characteristics and LOS of the participants in the two groups were described and compared. Multivariate Logistic and linear regression analyses were applied to explore the risk factors for prolonged LOS. The diagnostic efficacy of the lowest and admission Ct values for the Prolonged group was tested via the receiver operating characteristic (ROC) curve analysis.

RESULTS

The median LOS was 6 days in the total study population. The age was older (45.52 ± 14.78 vs. 42.54 ± 15.30, P = 0.001), while both the lowest and admission Ct-ORF (27.68 ± 3.88 vs. 37.00 ± 4.62, P < 0.001; 30.48 ± 5.03 vs. 37.79 ± 3.81, P < 0.001) and Ct-N (25.79 ± 3.60 vs. 36.06 ± 5.39, P < 0.001; 28.71 ± 4.95 vs. 36.95 ± 4.59, P < 0.001) values were significantly lower in the Prolonged group. There were more mild cases in the Prolonged group (23.8% vs. 11.5%, P < 0.001). The symptom spectrum differed between the two groups. In multivariate analyses, age, disease category, and the lowest Ct-N values were shown to be associated with prolonged LOS. Besides, both the lowest and admission Ct-ORF (AUC = 0.911 and 0.873) and Ct-N (AUC = 0.912 and 0.874) showed robust diagnostic efficacy for prolonged LOS.

CONCLUSIONS

Our study firstly reports the clinical characteristics and risk factors for prolonged LOS during the wave of the Omicron epidemic in Shanghai, China. These findings provide evidence for the early identification of asymptomatic and mild COVID-19 patients at a high risk of prolonged hospitalization who may require early intervention, and long-term monitoring and management.

COVID-19 patient characteristics and time to viral clearance: A retrospective observational study in a multiethnic population (United Arab Emirates)

BACKGROUND

SARS-CoV-2 virus is the causing agent of COVID-19. The factors contributing to delayed viral clearance are still unclear.

METHODS

We investigated the factors influencing the time to viral clearance in COVID-19 patients using medical records from 1785 adult patients of various ethnicities treated at NMC Royal Hospital in Abu Dhabi, UAE. The Cox-proportional Hazard Model was utilized to identify risk variables for delayed viral clearance, and the Kaplan-Meier plot was used to measure the time to viral clearance among different groups.

RESULTS

several factors have been associated with an increased risk of delayed viral clearance, including advanced age (p = 0.006), presence of cardiovascular diseases (p = 0.016), presentation with upper respiratory tract infection (URTI) (p = 0.043), and combined gastrointestinal (GIT) and symptoms (URTI) (p = 0.012). ICU admission and severity of COVID-19 also increased the risk for delayed viral clearance (p = 0.006, p < 0.001, respectively). 'The overall median viral clearance time was 24 days. It was 32 days among patients over 60, 21 among those with URTI, GIT symptoms, and asymptomatic, 24 among diabetics, and 46.5 days among cardiovascular patients. The median time till viral clearance was 30 days among severe COVID-19 patients and 39 days among ICU-admitted patients.

CONCLUSIONS

We concluded that advanced age, cardiovascular comorbidities, disease presentation, and severe COVID-19 outcomes increased the risk of delayed viral clearance. Identifying these factors allow decision makers to implement an early and comprehensive management strategy to improve the outcome.

Household Transmission of SARS-CoV-2 in Bhutan

Introduction

The transmission trend of SARS-CoV-2 is continuously evolving. Understanding the dynamics in different settings is crucial for any effective containment measures. We aimed to study the characteristics of household transmission of SARS-CoV-2 in Bhutanese households by determining the transmissibility within household contacts of confirmed COVID-19 index cases and their factors of infectivity.

Methods

We conducted a retrospective observational study on household transmission in 306 household contacts of 93 COVID-19 positive index cases diagnosed from April 16, 2021, to June 30, 2021. A pro forma was used to collect data on the epidemiological, demographic, and clinical profile of all recruited individuals. Secondary attack rates (SAR) were calculated, and risk factors for transmission were estimated.

Results

180 of 306 household contacts developed secondary household transmission (SAR 58.8%; 95% CI: 53.2-64.2). The median age of household contacts was 22 years. The median household size was 4 (mean 4.3 ± 2.199) members. Contacts exposed to adult index cases (aPR 1; 95% CI 1, 1.02, p = 0.01) and vaccinated index cases (uPR 0.41, 95% CI 0.25, 0.66, p < 0.001) had a higher SAR and prevalence of secondary infections.

Conclusions

Our findings suggest substantial evidence of secondary infections among household contacts, especially in the context of public health mandated lockdowns. Aggressive early contact tracing and case identification with subsequent case isolation from other household members remains a crucial step in preventing secondary transmission.

Intravenous delivery of GS-441524 is efficacious in the African green monkey model of SARS-CoV-2 infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 pandemic, has infected over 260 million people over the past 2 years. Remdesivir (RDV, VEKLURY®) is currently the only antiviral therapy fully approved by the FDA for the treatment of COVID-19. The parent nucleoside of RDV, GS-441524, exhibits antiviral activity against numerous respiratory viruses including SARS-CoV-2, although at reduced in vitro potency compared to RDV in most assays. Here we find in both human alveolar and bronchial primary cells, GS-441524 is metabolized to the pharmacologically active GS-441524 triphosphate (TP) less efficiently than RDV, which correlates with a lower in vitro SARS-CoV-2 antiviral activity. In vivo, African green monkeys (AGM) orally dosed with GS-441524 yielded low plasma levels due to limited oral bioavailability of <10%. When GS-441524 was delivered via intravenous (IV) administration, although plasma concentrations of GS-441524 were significantly higher, lung TP levels were lower than observed from IV RDV. To determine the required systemic exposure of GS-441524 associated with in vivo antiviral efficacy, SARS-CoV-2 infected AGMs were treated with a once-daily IV dose of either 7.5 or 20 mg/kg GS-441524 or IV RDV for 5 days and compared to vehicle control. Despite the reduced lung TP formation compared to IV dosing of RDV, daily treatment with IV GS-441524 resulted in dose-dependent efficacy, with the 20 mg/kg GS-441524 treatment resulting in significant reductions of SARS-CoV-2 replication in the lower respiratory tract of infected animals. These findings demonstrate the in vivo SARS-CoV-2 antiviral efficacy of GS-441524 and support evaluation of its orally bioavailable prodrugs as potential therapies for COVID-19.

A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities

The COVID-19 pandemic has stimulated wastewater-based surveillance, allowing public health to track the epidemic by monitoring the concentration of the genetic fingerprints of SARS-CoV-2 shed in wastewater by infected individuals. Wastewater-based surveillance for COVID-19 is still in its infancy. In particular, the quantitative link between clinical cases observed through traditional surveillance and the signals from viral concentrations in wastewater is still developing and hampers interpretation of the data and actionable public-health decisions. We present a modelling framework that includes both SARS-CoV-2 transmission at the population level and the fate of SARS-CoV-2 RNA particles in the sewage system after faecal shedding by infected persons in the population. Using our mechanistic representation of the combined clinical/wastewater system, we perform exploratory simulations to quantify the effect of surveillance effectiveness, public-health interventions and vaccination on the discordance between clinical and wastewater signals. We also apply our model to surveillance data from three Canadian cities to provide wastewater-informed estimates for the actual prevalence, the effective reproduction number and incidence forecasts. We find that wastewater-based surveillance, paired with this model, can complement clinical surveillance by supporting the estimation of key epidemiological metrics and hence better triangulate the state of an epidemic using this alternative data source.

Predictors and time to recovery from COVID-19 among patients attended at the treatment centers in Ekiti State, South West, Nigeria

Introduction

time to clinical recovery from COVID-19 infection and associated factors has not been explored in Nigeria. This study was conducted to assess the predictors and time to recovery from COVID-19 among patients attended to at the treatment centers in Ekiti State, South West.

Methods

a facility-based retrospective cohort study was conducted between March 2020 to October 2021. Laboratory confirmed COVID-19 positive test result of 586 patients receiving treatment at the treatment centres in Ekiti were included. Data were extracted from COVID-19 intake forms and medical records of patients. Data were analysed using descriptive statistics and survival analysis methods including Cox proportional hazards regression model. Level of significance was set at 5%.

Results

the mean age of the patients was 43.46 (SD 0.74) years. Forty-seven percent (47%) of the patients were aged 25-44 years, fifty-one percent (51%) were males. The median recovery time of COVID-19 patients was 21 days (IQR: 14-23). Being a male-patient (95% CI 20.46-21.54), older age (95% CI 20.14-21.86), not admitted in the hospital (95% CI 22.74-23.26), and associated multiple co-morbidities (95% CI 17.65-28.35) were associated with delayed recovery time. Predictors of recovery time of patients from COVID-19 infection were admission status (aHR: 0.71, 95%CI 0.56-0.88; p=0.002) and symptoms on admission (aHR: 0.81, 95%CI 0.66-0.99; p=0.020).

Conclusion

patients with comorbidities, older and those not admitted were more likely to have a delayed clinical recovery from COVID-19. Knowledge of the predictors might help health professionals in risk stratification and better management of patients with COVID-19.

Predictors for adult COVID-19 hospitalized inpatient mortality rate in North West Ethiopia

Objectives:

The spread of severe acute respiratory syndrome coronavirus 2 in Ethiopia is below par understood and to date has been poorly characterized by a lower number of confirmed cases and deaths to other regions of the sub-Sahara African including Ethiopia. Timely and effective predictors for inpatient mortality rate were crucial for improving the management of hospitalized cases. This study aimed to assessed predictors for inpatient mortality of COVID-19 hospitalized adult patients in two diagnosed and treatment centers, North West Ethiopia.

Methods:

A facility-based retrospective cohort study was conducted among COVID-19 adult admitted cases in two treatment centers, Northwest Ethiopia, from 1 October 2020 to 30 December 2020. Data from the records of children were extracted using a standardized checklist. Epi-Data version 3.2 was used for data entry, and Stata version 14 was used for analysis. Bi-variable and multivariable Cox regression analyses were conducted to identify predictors of mortality. Finally, variables with P < 0.05 were a significant predictor of inpatient mortality.

Result:

The mean (±standard deviation) age of participant cases was 48.6 (±18.8) years. The median (±interquartile range) time for death reported after was 13 (±6) days. The overall incidence rate inpatient mortality rate was determined as 1.8 (95% confidence interval: 1.72, 2.15) per100 person per days of observation. Cases at baseline age ⩾ 61 years (adjusted hazard ratio = 1.56; 95% confidence interval: 1.3, 2.4), being male gender (adjusted hazard ratio = 1.9; 95% CI: 2.1, 8.6), admission with comorbidity (adjusted hazard ratio: 4.4, 95% confidence interval: 2.3, 8.4), and decreased neutrophil count ⩽ 65 10³/uL at (P < 0.03) were independent predictors for inpatient mortality.

Conclusion:

In general, 72.4% of COVID-19 inpatient deaths were occurred within 2 weeks after admission. The mortality risk factors for severe patients identified in this study using a multivariate Cox regression model included elderly age (⩾60 years), being male, baseline comorbidity, and neutrophil count ⩽65 10³/uL were associated with inpatient mortality.

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.

Epidemiologic characteristics of cases with reinfection, recurrence, and hospital readmission due to COVID-19: A systematic review and meta-analysis

Recent studies reported that some recovered COVID-19 patients have tested positive for virus nucleic acid again. A systematic search was performed in Web of Science, PubMed, Scopus, and Google Scholar up to March 6, 2021. The pooled estimation of reinfection, recurrence, and hospital readmission among recovered COVID-19 patients was 3, 133, and 75 per 1000 patients, respectively. The overall estimation of reinfection among males compared to females was greater. The prevalence of recurrence in females compared to males was more common. Also, hospital readmission between sex groups was the same. There is uncertainty about long-term immunity after SARS-Cov-2 infection. Thus, the possibility of reinfection and recurrence after recovery is not unexpected. In addition, there is a probability of hospital readmission due to adverse events of COVID-19 after discharge. However, with mass vaccination of people and using the principles of prevention and appropriate management of the disease, frequent occurrence of the disease can be controlled.

The SARS-CoV-2 pandemic: remaining uncertainties in our understanding of the epidemiology and transmission dynamics of the virus, and challenges to be overcome

Great progress has been made over the past 18 months in scientific understanding of the biology, epidemiology and pathogenesis of SARS-CoV-2. Extraordinary advances have been made in vaccine development and the execution of clinical trials of possible therapies. However, uncertainties remain, and this review assesses these in the context of virus transmission, epidemiology, control by social distancing measures and mass vaccination and the effect on all of these on emerging variants. We briefly review the current state of the global pandemic, focussing on what is, and what is not, well understood about the parameters that control viral transmission and make up the constituent parts of the basic reproductive number R 0. Major areas of uncertainty include factors predisposing to asymptomatic infection, the population fraction that is asymptomatic, the infectiousness of asymptomatic compared to symptomatic individuals, the contribution of viral transmission of such individuals and what variables influence this. The duration of immunity post infection and post vaccination is also currently unknown, as is the phenotypic consequences of continual viral evolution and the emergence of many viral variants not just in one location, but globally, given the high connectivity between populations in the modern world. The pattern of spread of new variants is also examined. We review what can be learnt from contact tracing, household studies and whole-genome sequencing, regarding where people acquire infection, and how households are seeded with infection since they constitute a major location for viral transmission. We conclude by discussing the challenges to attaining herd immunity, given the uncertainty in the duration of vaccine-mediated immunity, the threat of continued evolution of the virus as demonstrated by the emergence and rapid spread of the Delta variant, and the logistics of vaccine manufacturing and delivery to achieve universal coverage worldwide. Significantly more support from higher income countries (HIC) is required in low- and middle-income countries over the coming year to ensure the creation of community-wide protection by mass vaccination is a global target, not one just for HIC. Unvaccinated populations create opportunities for viral evolution since the net rate of evolution is directly proportional to the number of cases occurring per unit of time. The unit for assessing success in achieving herd immunity is not any individual country, but the world.

Prevalence and risk factors associated with repeat positive SARS-CoV-2 nucleic acid test results among discharged COVID-19 patients: A protocol for systematic review and meta-analysis

BACKGROUND

The COVID-19 (coronavirus disease 2019) pandemic continues to have an immense impact on the world at large. COVID-19 patients who meet the discharge criteria, may subsequently exhibit positive viral RNA test results upon subsequent evaluation. This phenomenon has been a major source of research and public health interest, and poses a major challenge to COVID-19 prevention, treatment, and standardized patient management.

METHODS

We will search the PubMed, MEDLINE, Embase, Cochrane Clinical Trials Database, China National Knowledge Infrastructure, Wanfang Database, Chinese Science Journal Database, and China Biology Medicine databases for all studies published as of November 2021. Data will be extracted independently by two researchers according to the eligibility criteria. Finally, RevMan 5.3.0 will be implemented for statistical analyses.

RESULTS

The results of this study will show the prevalence and risk factors associated with repeat positive SARS-CoV-2 nucleic acid test results among discharged COVID-19 patients.

CONCLUSIONS

This study will provide a reliable evidence-based for the prevalence and risk factors associated with repeat positive SARS-CoV-2 nucleic acid test results among discharged COVID-19 patients.

TRIAL REGISTRATION NUMBER

CRD42021272447.

Point-of-Care Diagnostic Tools for Surveillance of SARS-CoV-2 Infections

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a recently emerged and highly contagious virus that causes coronavirus disease 2019 (COVID-19). As of August 24, 2021, there were more than 212 million confirmed COVID-19 cases and nearly 4.4 million deaths reported globally. Early diagnosis and isolation of infected individuals remains one of the most effective public health interventions to control SARS-CoV-2 spread and for effective clinical management of COVID-19 cases. Currently, SARS-CoV-2 infection is diagnosed presumptively based on clinical symptoms and confirmed by detecting the viral RNA in respiratory samples using reverse transcription polymerase chain reaction (RT-PCR). Standard RT-PCR protocols are time consuming, expensive, and technically demanding, which makes them a poor choice for large scale and point-of-care screening in resource-poor settings. Recently developed isothermal nucleic acid amplification tests (iNAAT), antigen and/or serological tests are cost-effective to scale COVID-19 testing at the point-of-care (PoC) and for surveillance activities. This review discusses the development of rapid PoC molecular tools for the detection and surveillance of SARS-CoV-2 infections.

Results of an early second PCR test performed on SARS-CoV-2 positive patients may support risk assessment for severe COVID-19

Identifying patients at increased risk for severe COVID-19 is of high priority during the pandemic as it could affect clinical management and shape public health guidelines. In this study we assessed whether a second PCR test conducted 2–7 days after a SARS-CoV-2 positive test could identify patients at risk for severe illness. Analysis of a nationwide electronic health records data of 1683 SARS-CoV-2 positive individuals indicated that a second negative PCR test result was associated with lower risk for severe illness compared to a positive result. This association was seen across different age groups and clinical settings. More importantly, it was not limited to recovering patients but also observed in patients who still had evidence of COVID-19 as determined by a subsequent positive PCR test. Our study suggests that an early second PCR test may be used as a supportive risk-assessment tool to improve disease management and patient care.

Deficient DNA mismatch repair and persistence of SARS-CoV-2 RNA shedding: a case report of hereditary nonpolyposis colorectal cancer with COVID-19 infection

BACKGROUND

Several independent risk factors have been reported to influence viral shedding following COVID-19 infection, but the influence of host-related molecular factors has not yet been described. We report a case of a cancer patient with Lynch syndrome (hereditary nonpolyposis colorectal cancer, HNPCC) who manifested SARS-CoV-2 PCR (polymerase chain reaction) positivity for at least 54 days after contracting mild COVID-19 illness. We propose that deficient mismatch repair (MMR) may play a role in the prolonged SARS-CoV-2 RNA shedding.

CASE PRESENTATION

A patient with Lynch syndrome was under surveillance for metastatic adenocarcinoma after completing palliative chemotherapy in October 2019. Between the period of April 2020 to June 2020, he was admitted multiple times to address several clinical needs mainly related to his underlying malignancy. These included progressive disease observed in the aortocaval lymph nodes leading to recurrent episodes of upper gastrointestinal bleeding, dehydration resulting in acute kidney injury and a short-lived episode of pyrexia. A SARS-CoV-2 PCR of the nasopharyngeal swab (NPS) was positive at his initial admission with mild COVID-19 symptoms. He remained positive on subsequent admissions when tested routinely for SARS-CoV-2 without demonstrating any apparent clinical features of COVID-19 infection. The MMR pathway, a component of DNA damage response (DDR), is impaired in Lynch syndrome due to an inherited genetic mutation. This pathway is also required for viral clearance from the host cells following certain RNA viral infections like influenza virus and other coronaviridae. Here we provide a current understanding of the importance of DDR deficiencies in the clearance of RNA virus and suggest how this may play a similar role in the clearance of COVID-19, as evident in our case that demonstrated persistent positivity.

CONCLUSION

The importance of understanding the scientific basis of extended viral shedding during the COVID-19 pandemic is now centre-stage in the establishment of robust track and trace services to allow the recovery and function of societies and economies. This patient with Lynch syndrome recovered from infection but had prolonged viral positivity, which might merit further investigation to better understand the effect of this condition on infection duration and outcome.

Repeat positive SARS-CoV-2 RNA testing in nursing home residents during the initial 9 months of the COVID-19 pandemic: an observational retrospective analysis

BACKGROUND

Nursing homes are high-risk COVID-19 settings with residents who are typically older and have multiple comorbidities. SARS-CoV-2 testing occurs frequently in nursing homes, with public health guidance suggesting that repeat testing is generally not warranted in the 90 days following initial positive test results. Interpretation of repeat positive tests beyond 90 days is challenging and the consequences of decisions following these tests are significant.

METHODS

We utilized a surveillance system for COVID-19 to identify Connecticut nursing home residents who tested positive for SARS-CoV-2 by RNA-based testing ≥ 90 days after initial positive results. We analyzed statewide nursing home testing data over a 9-month period, from the first Connecticut nursing home case identified on March 15 through December 15, 2020, when nursing home COVID-19 vaccinations began in Connecticut.

FINDINGS

We identified 156 residents (median age 75 years) with positive RNA-based PCR tests occurring ≥90 days after an initial positive test. Residents with repeat positives tests represented approximately 2.6% (156/6,079) of nursing home residents surviving beyond 90 days of their initial SARS-CoV-2 diagnosis statewide since the start of the pandemic, with a median time to repeat positivity of 135 days (range 90-245 days). Deaths were reported in 12.8% (20/156) of residents following the repeat positive test, with 80% (16/20) having one or more intervening negative RT-PCR tests prior to the repeat positive test.

INTERPRETATION

Our analysis suggests that repeat positive testing in nursing home populations may exceed those reported in younger age groups. Repeat positive tests beyond 90 days may accompany severe outcomes, and should be prospectively investigated with genomic, virologic and additional data, when feasible. Data shed light on the duration of protective immunity following natural infection in this subset of largely elderly and medically frail individuals.

FUNDING

This work was conducted in the context of the Connecticut DPH COVID-19 response and not supported by specific funding.

Early nasal type I IFN immunity against SARS-CoV-2 is compromised in patients with autoantibodies against type I IFNs

IFN-I and IFN-III immunity in the nasal mucosa is poorly characterized during SARS-CoV-2 infection. We analyze the nasal IFN-I/III signature, namely the expression of ISGF-3-dependent IFN-stimulated genes, in mildly symptomatic COVID-19 patients and show its correlation with serum IFN-α2 levels, which peak at symptom onset and return to baseline from day 10 onward. Moreover, the nasal IFN-I/III signature correlates with the nasopharyngeal viral load and is associated with the presence of infectious viruses. By contrast, we observe low nasal IFN-I/III scores despite high nasal viral loads in a subset of critically ill COVID-19 patients, which correlates with the presence of autoantibodies (auto-Abs) against IFN-I in both blood and nasopharyngeal mucosa. In addition, functional assays in a reconstituted human airway epithelium model of SARS-CoV-2 infection confirm the role of such auto-Abs in abrogating the antiviral effects of IFN-I, but not those of IFN-III. Thus, IFN-I auto-Abs may compromise not only systemic but also local antiviral IFN-I immunity at the early stages of SARS-CoV-2 infection.

Percutaneous tracheostomy in COVID-19 patients: a new apneic approach

Background

Percutaneous dilation tracheostomy is an aerosol-generating procedure carrying a documented infectious risk during respiratory virus pandemics. For this reason, during the COVID-19 outbreak, surgical tracheostomy was preferred to the percutaneous one, despite the technique related complications increased risk.

Methods

We describe a new sequence for percutaneous dilation tracheostomy procedure that could be considered safe both for patients and healthcare personnel. A fiberscope was connected to a video unit to allow bronchoscopy. Guidewire positioning was performed as usual. While the established standard procedure continues with the creation of the stoma without any change in mechanical ventilation, we retracted the bronchoscope until immediately after the access valve in the mount tube, allowing normal ventilation. After 3 minutes of ventilation with 100% oxygen, mechanical ventilation was stopped without disconnecting the circuit. During apnea, the stoma was created by dilating the trachea and the tracheostomy cannula was inserted. Ventilation was then resumed. We evaluated the safeness of the procedure by recording any severe desaturation and by performing serological tests to all personnel.

Results

Thirty-six patients (38%) of 96 underwent tracheostomy; 22 (23%) percutaneous dilation tracheostomies with the new approach were performed without any desaturation. All personnel (150 operators) were evaluated for serological testing: 9 (6%) had positive serology but none of them had participated in tracheostomy procedures.

Conclusion

This newly described percutaneous dilation tracheostomy technique was not related to severe desaturation events and we did not observe any positive serological test in health workers who performed the tracheostomies.

Detection and viral RNA shedding of SARS-CoV-2 in respiratory specimens relative to symptom onset among COVID-19 patients in Bavaria, Germany

We assessed severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) reverse transcriptase-polymerase chain reaction (RT-PCR) diagnostic sensitivity and cycle threshold (Ct) values relative to symptom onset in symptomatic coronavirus disease-2019 (COVID-19) patients from Bavaria, Germany, of whom a subset was repeatedly tested. Locally weighted scatterplot smoothing method was used to assess the relationship between symptom onset and Ct-values. Kaplan−Meier plots were used to visualise the empirical probability of detecting viral ribonucleic acid (RNA) over time and estimate the time until clearance of viral RNA among the repeatedly tested patients. Among 721 reported COVID-19 cases, the viral RNA was detected in specimens taken between three days before and up to 48 days after symptom onset. The mean Ct-value was 28.6 (95% confidence interval (CI) 28.2–29.0) with the lowest mean Ct-value (26.2) observed two days after symptom onset. Up to 7 days after symptom onset, the diagnostic sensitivity of the RT-PCR among repeatedly sampled patients (n = 208) remained above 90% and decreased to 50% at day 12 (95% CI 10.5–21.5). Our data provide valuable estimates to optimise the timing of sampling of individuals for SARS-CoV-2 detection. A considerable proportion of specimens sampled before symptom onset had Ct-values comparable with Ct-values after symptom onset, suggesting the probability of presymptomatic transmission.

SARS-CoV-2 Viral Shedding and Transmission Dynamics: Implications of WHO COVID-19 Discharge Guidelines

The evolving nature of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has necessitated periodic revisions of COVID-19 patient treatment and discharge guidelines. Since the identification of the first COVID-19 cases in November 2019, the World Health Organization (WHO) has played a crucial role in tackling the country-level pandemic preparedness and patient management protocols. Among others, the WHO provided a guideline on the clinical management of COVID-19 patients according to which patients can be released from isolation centers on the 10th day following clinical symptom manifestation, with a minimum of 72 additional hours following the resolution of symptoms. However, emerging direct evidence indicating the possibility of viral shedding 14 days after the onset of symptoms called for evaluation of the current WHO discharge recommendations. In this review article, we carried out comprehensive literature analysis of viral shedding with specific focus on the duration of viral shedding and infectivity in asymptomatic and symptomatic (mild, moderate, and severe forms) COVID-19 patients. Our literature search indicates that even though, there are specific instances where the current protocols may not be applicable ( such as in immune-compromised patients there is no strong evidence to contradict the current WHO discharge criteria.

Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory disease coronavirus 2 (SARS-CoV-2), has led to millions of confirmed cases and deaths worldwide. Efficient diagnostic tools are in high demand, as rapid and large-scale testing plays a pivotal role in patient management and decelerating disease spread. This paper reviews current technologies used to detect SARS-CoV-2 in clinical laboratories as well as advances made for molecular, antigen-based, and immunological point-of-care testing, including recent developments in sensor and biosensor devices. The importance of the timing and type of specimen collection is discussed, along with factors such as disease prevalence, setting, and methods. Details of the mechanisms of action of the various methodologies are presented, along with their application span and known performance characteristics. Diagnostic imaging techniques and biomarkers are also covered, with an emphasis on their use for assessing COVID-19 or monitoring disease severity or complications. While the SARS-CoV-2 literature is rapidly evolving, this review highlights topics of interest that have occurred during the pandemic and the lessons learned throughout. Exploring a broad armamentarium of techniques for detecting SARS-CoV-2 will ensure continued diagnostic support for clinicians, public health, and infection prevention and control for this pandemic and provide advice for future pandemic preparedness.

Diagnosing SARS-CoV-2 with Antigen Testing, Transcription-Mediated Amplification and Real-Time PCR

This study was performed as a head-to-head comparison of the performance characteristics of (1) two SARS-CoV-2-specific rapid antigen assays with real-time PCR as gold standard as well as (2) a fully automated high-throughput transcription-mediated amplification (TMA) assay and real-time PCR in a latent class analysis-based test comparison without a gold standard with several hundred samples in a low prevalence "real world" setting. Recorded sensitivity and specificity of the NADAL and the LumiraDx antigen assays and the Hologic Aptima SARS-CoV-2 TMA assay were 0.1429 (0.0194, 0.5835), 0.7644 (0.7016, 0.8174), and 0.7157 (0, 1) as well as 0.4545 (0.2022, 0.7326), 0.9954 (0.9817, 0.9988), and 0.9997 (not estimable), respectively. Agreement kappa between the positive results of the two antigen-based assays was 0.060 (0.002, 0.167) and 0.659 (0.492, 0.825) for TMA and real-time PCR. Samples with low viral load as indicated by cycle threshold (Ct) values > 30 were generally missed by both antigen assays, while 1:10 pooling suggested higher sensitivity of TMA compared to real-time PCR. In conclusion, both sensitivity and specificity speak in favor of the use of the LumiraDx rather than the NADAL antigen assay, while TMA results are comparably as accurate as PCR, when applied in a low prevalence setting.

Discordant SARS-CoV-2 Detection in the Nasopharynx Versus Trachea for Patients With Tracheostomies

OBJECTIVES/HYPOTHESIS

Patients with tracheostomies have an anatomically altered connection between their upper and lower airways that could impact SARS-CoV-2 testing. Our goal was to evaluate for discordance in SARS-CoV-2 detection in hospitalized patients with COVID-19 and tracheostomies based on the site analyzed.

STUDY DESIGN

Retrospective chart review METHODS: This single-institution study evaluated hospitalized patients with COVID-19 who had tracheostomies placed during their treatment. We analyzed SARS-CoV-2 RNA nucleic acid amplification test (NAAT) results after tracheostomy. All included patients had nasopharyngeal (NP) and tracheal (TR) samples taken within a 48-hour period, allowing us to characterize rate of test concordance.

RESULTS

Forty-five patients met our inclusion criteria. Thirty-two (71.1%) patients had entirely concordant results after tracheostomy. However, 13 (28.9%) patients had at least one set of discordant results, the majority of which were NP negative and TR positive. There were no statistically significant differences in demographic or clinical variables, including time to tracheostomy and time to testing, among patients with concordant versus discordant SARS-CoV-2 results.

CONCLUSION

This represents the first study to examine SARS-CoV-2 RNA NAAT concordance between NP and TR sites in hospitalized patients with COVID-19 and tracheostomies. One-third of patients demonstrated discordant testing when NP and TR specimens were collected within a 48-hour time period. Thus, patients with tracheostomies may have a higher false-negative rate if only one site is assessed for SARS-CoV-2. We recommend analyzing samples from both the nasopharynx and trachea for these patients until more prospective data exist.

LEVEL OF EVIDENCE

IV Laryngoscope, 2021.

Comparison Between a Standard and SalivaDirect RNA Extraction Protocol for Molecular Diagnosis of SARS-CoV-2 Using Nasopharyngeal Swab and Saliva Clinical Samples

During the COVID-19 pandemic, a certified laboratory of Tamaulipas, Mexico has processed over 100,000 samples of COVID-19 suspected patients, working a minimum of 100 tests daily. Thus, it would be beneficial for such certified laboratories nationwide to reduce the time and cost involved in performing the diagnosis of COVID-19, from sample collection, transportation to local lab, processing of samples, and data acquisition. Here, 30 nasopharyngeal swab and saliva samples from the same COVID-19 individuals were assessed by a standard nucleic acid extraction protocol, including protein lysis with proteinase K followed by binding to column, washing, and elution, and by the SalivaDirect protocol based on protein lysis, skipping the other steps to reduce processing time and costs. The genomic RNA was amplified using a SARS-CoV-2 Real-Time PCR kit. A variation (P > 0.05) in the 95% CIs = 72.6%–96.7% was noted by using the SalivaDirect protocol and saliva samples (sensitivity of 88.2%) in comparison to those of standard protocol with oropharyngeal swab samples (95% CIs = 97.5%–100%; sensitivity of 100%) as reported elsewhere. However, when using nasopharyngeal swab samples in the SalivaDirect protocol (sensitivity of 93.6%; 95% CIs = 79.2%–99.2%), it was in concordance (P < 0.05) with those of the standard one. The logical explanation to this was that two samples with Ct values of 38, and 40 cycles for gene E produced two false negatives in the SalivaDirect protocol in relation to the standard one; thus, there was a reduction of the sensitivity of 6.4% in the overall assay performance.

Characteristics of COVID-19 Recurrence: A Systematic Review and Meta-Analysis

Background:

Previous studies reported the recurrence of coronavirus disease 2019 (COVID-19) among discharge patients. This study aimed to examine the characteristic of COVID-19 recurrence cases by performing a systematic review and meta-analysis.

Methods:

A systematic search was performed in PubMed and Embase and gray literature up to September 19, 2020. A random-effects model was applied to obtain the pooled prevalence of disease recurrence among recovered patients and the prevalence of subjects underlying comorbidity among recurrence cases. The other characteristics were calculated based on the summary data of individual studies.

Results:

A total of 41 studies were included in the final analysis, we have described the epidemiological characteristics of COVID-19 recurrence cases. Of 3,644 patients recovering from COVID-19 and being discharged, an estimate of 15% (95% CI, 12% to 19%) patients was re-positive with SARS-CoV-2 during the follow-up. This proportion was 14% (95% CI, 11% to 17%) for China and 31% (95% CI, 26% to 37%) for Korea. Among recurrence cases, it was estimated 39% (95% CI, 31% to 48%) subjects underlying at least one comorbidity. The estimates for times from disease onset to admission, from admission to discharge, and from discharge to RNA positive conversion were 4.8, 16.4, and 10.4 days, respectively.

Conclusion:

This study summarized up-to-date evidence from case reports, case series, and observational studies for the characteristic of COVID-19 recurrence cases after discharge. It is recommended to pay attention to follow-up patients after discharge, even if they have been in discharge quarantine.

A combined oro-nasopharyngeal swab is more sensitive than mouthwash in detecting SARS-CoV-2 by a high-throughput PCR assay

Objectives

The optimal diagnostic specimen to detect SARS-CoV-2 by PCR in the upper respiratory tract is unclear. Mouthwash fluid has been reported as an alternative to nasopharyngeal and oropharyngeal swabs. We compared mouthwash fluid with a combined oro-nasopharyngeal swab regarding test performance.

Methods

In a large refugee facility, we retested individuals with a previous positive test for SARS-CoV-2 and their quarantined close contacts. All individuals were asymptomatic at the time of testing. First, a mouthwash (gargling for at least 5 s) with sterile water was performed. Then, with a single flocked swab the back of the throat and subsequently the nasopharynx were sampled. Samples were inactivated and analysed on a Roche cobas 6800^® system with the Roche SARS-CoV-2 test.

Results

Of 76 individuals, 39 (51%) tested positive for SARS-CoV-2 by oro-nasopharyngeal swab. Mouthwash detected 13 of 76 (17%) infections, but did not detect any additional infection. Samples that were positive in both tests, had lower cycle threshold (Ct)-values for oro-nasopharyngeal samples, indicating a higher virus concentration, compared to samples only positive in oro-nasopharyngeal swabs.

Conclusion

Mouthwash is not as sensitive as combined oro-nasopharyngeal swab in detecting upper respiratory tract infection.

SARS-CoV and SARS-CoV-2 are transmitted through the air between ferrets over more than one meter distance

SARS-CoV-2 emerged in late 2019 and caused a pandemic, whereas the closely related SARS-CoV was contained rapidly in 2003. Here, an experimental set-up is used to study transmission of SARS-CoV and SARS-CoV-2 through the air between ferrets over more than a meter distance. Both viruses cause a robust productive respiratory tract infection resulting in transmission of SARS-CoV-2 to two of four indirect recipient ferrets and SARS-CoV to all four. A control pandemic A/H1N1 influenza virus also transmits efficiently. Serological assays confirm all virus transmission events. Although the experiments do not discriminate between transmission via small aerosols, large droplets and fomites, these results demonstrate that SARS-CoV and SARS-CoV-2 can remain infectious while traveling through the air. Efficient virus transmission between ferrets is in agreement with frequent SARS-CoV-2 outbreaks in mink farms. Although the evidence for virus transmission via the air between humans under natural conditions is absent or weak for SARS-CoV and SARS-CoV-2, ferrets may represent a sensitive model to study interventions aimed at preventing virus transmission.

Risk and predictive factors of prolonged viral RNA shedding in upper respiratory specimens in a large cohort of COVID-19 patients admitted to an Italian reference hospital

Background

Limited data are available about the predictors and outcomes associated with prolonged SARS-CoV-2 RNA shedding (VS).

Methods

A retrospective study including COVID-19 patients admitted to an Italian hospital between March 1 and July 1, 2020. Predictors of viral clearance (VC) and prolonged VS from the upper respiratory tract were assessed by Poisson regression and logistic regression analyses. The causal relation between VS and clinical outcomes was evaluated through an inverse probability weighted Cox model.

Results

The study included 536 subjects. The median duration of VS from symptoms onset was 18 days. The estimated 30-day probability of VC was 70.2%. Patients with comorbidities, lymphopenia at hospital admission, or moderate/severe respiratory disease had a lower chance of VC. The development of moderate/severe respiratory failure, delayed hospital admission after symptoms onset, baseline comorbidities, or D-dimer >1000 ng/mL at admission independently predicted prolonged VS. The achievement of VC doubled the chance of clinical recovery and reduced the probability of death/mechanical ventilation.

Conclusions

Respiratory disease severity, comorbidities, delayed hospital admission and inflammatory markers negatively predicted VC, which resulted to be associated with better clinical outcomes. These findings highlight the importance of prompt hospitalization of symptomatic patients, especially where signs of severity or comorbidities are present.

Factors associated with a prolonged negative conversion of viral RNA in patients with COVID-19

Objectives

The aim of this study was to identify the factors influencing the delay in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA negative conversion.

Methods

A cohort study was conducted that included patients with coronavirus disease 2019 (COVID-19) admitted to the Tunisian national containment center. Follow-up consisted of a weekly RT-PCR test. Multivariate Cox regression analysis was performed to determine independent predictors associated with negative RNA conversion.

Results

Among the 264 patients included, the median duration of viral clearance was 20 days (interquartile range (IQR) 17–32 days). The shortest duration was 9 days and the longest was 58 days. Factors associated with negative conversion of viral RNA were symptoms such as fatigue, fever, and shortness of breath (hazard ratio (HR) 0.600, 95% confidence interval (CI) 0.401–0.897) and face mask use when exposed to COVID-19 cases (HR 2.006, 95% CI 1.247–3.228). The median time to RNA viral conversion was 18 days (IQR 16–21 days) when using masks versus 23 days (IQR 17–36 days) without wearing masks, and 24 days (IQR 18–36 days) for symptomatic patients versus 20 days (IQR 16–30 days) for asymptomatic patients.

Conclusions

The results of this study revealed that during SARS-CoV-2 infection, having symptoms delayed viral clearance, while wearing masks accelerated this conversion. These factors should be taken into consideration for the strategy of isolating infected patients.

Persistence of SARS-CoV-2 RNA in a male with metabolic syndrome for 72 days: A case report

Coronavirus disease-19 (COVID-19) was first identified in Wuhan, China, and spread gradually throughout the world. There are multiple reports of prolonged viral shedding in people infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, such findings have not been documented in Bangladesh. Herein, we present a case of metabolic syndrome that remained positive for SARS-CoV-2 RNA over a prolonged period. On clinical and laboratory examination, the patient was diagnosed with obesity, raised blood pressure, dyslipidemia, and uncontrolled glycemia. However, upon taking appropriate measures and controlling the plasma sugar level, he tested negative for SARS-CoV-2 RNA on the 72nd day since illness onset. We observed that COVID-19 patients with several comorbidities, such as metabolic syndrome, may shed the virus over a prolonged period. Therefore, strict public health measures and isolation rules should be followed by a high-risk population.

Modeling SARS-CoV-2 viral kinetics and association with mortality in hospitalized patients from the French COVID cohort

The characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral kinetics in hospitalized patients and its association with mortality is unknown. We analyzed death and nasopharyngeal viral kinetics in 655 hospitalized patients from the prospective French COVID cohort. The model predicted a median peak viral load that coincided with symptom onset. Patients with age ≥65 y had a smaller loss rate of infected cells, leading to a delayed median time to viral clearance occurring 16 d after symptom onset as compared to 13 d in younger patients (P < 10-4). In multivariate analysis, the risk factors associated with mortality were age ≥65 y, male gender, and presence of chronic pulmonary disease (hazard ratio [HR] > 2.0). Using a joint model, viral dynamics after hospital admission was an independent predictor of mortality (HR = 1.31, P < 10-3). Finally, we used our model to simulate the effects of effective pharmacological interventions on time to viral clearance and mortality. A treatment able to reduce viral production by 90% upon hospital admission would shorten the time to viral clearance by 2.0 and 2.9 d in patients of age <65 y and ≥65 y, respectively. Assuming that the association between viral dynamics and mortality would remain similar to that observed in our population, this could translate into a reduction of mortality from 19 to 14% in patients of age ≥65 y with risk factors. Our results show that viral dynamics is associated with mortality in hospitalized patients. Strategies aiming to reduce viral load could have an effect on mortality rate in this population.

Determinants of prolonged viral RNA shedding in hospitalized patients with SARS-CoV-2 infection

OBJECTIVE

To evaluate determinants of prolonged viral RNA shedding in hospitalized patients with SARS-CoV-2 infection.

MATERIALS AND METHODS

Hospitalized patients with SARS-CoV-2 positive nasopharyngeal RT-PCR were included in a single-center, retrospective study. Patients were divided in 2 groups according to the timing of viral clearance [≤14 days, "early clearance (EC)" and >14 days, "late clearance (LC)"].

RESULTS

179 patients were included in the study (101 EC, 78 LC), with median age 62 years. Median time of viral shedding was 14 days (EC/LC 10 and 19 days, respectively, P < 0.0001). Univariate analyses showed that age, male gender, receiving corticosteroids, receiving tocilizumab, ICU admission, low albumin and NLR ratio were associated with late viral clearance. In the multivariable analysis, older age (P = 0.016), albumin level (P = 0.048), corticosteroids (P = 0.021), and tocilizumab (P = 0.015) were significantly associated with late viral clearance.

CONCLUSIONS

Age, albumin, tocilizumab and corticosteroid treatment were independently associated with a prolonged SARS-CoV-2 RNA shedding.

SARS-CoV-2 Viral RNA Shedding for More Than 87 Days in an Individual With an Impaired CD8+ T Cell Response

Prolonged shedding of viral RNA occurs in some individuals following SARS-CoV-2 infection. We perform comprehensive immunologic evaluation of one individual with prolonged shedding. The case subject recovered from severe COVID-19 and tested positive for SARS-CoV-2 viral RNA repeatedly as many as 87 days after the first positive test, 97 days after symptom onset. The subject did not have any associated rise in anti-Spike protein antibody titers or plasma neutralization activity, arguing against re-infection. This index subject exhibited a profoundly diminished circulating CD8+ T cell population and correspondingly low SARS-CoV-2-specific CD8+ T cell responses when compared with a cohort of other recovering COVID-19 subjects. CD4+ T cell responses and neutralizing antibody responses developed as expected in this individual. Our results demonstrate that detectable viral RNA shedding in the upper airway can occur more than 3 months following infection in some individuals with COVID-19 and suggest that impaired CD8+ T cells may play a role in prolonged viral RNA shedding.

Prolonged adaptive immune activation in COVID-19: implications for maintenance of long-term immunity?

Ongoing observational clinical research has prioritized understanding the human immune response to SARS-CoV-2 during the coronavirus disease 2019 (COVID-19) pandemic. Several recent studies suggest that immune dysregulation with early and prolonged adaptive immune system activation can result in cellular exhaustion. In this issue of the JCI, Files et al. compared cellular immune phenotypes during the first two months of COVID-19 in hospitalized and less severe, non-hospitalized patients. The authors utilized flow cytometry to analyze circulating peripheral blood mononuclear cells. Both patient cohorts maintained B and T cell phenotypes consistent with activation and cellular exhaustion throughout the first two months of infection. Additionally, follow-up samples from the non-hospitalized patient cohort showed that activation markers and cellular exhaustion increased over time. These findings illustrate the persistent nature of the adaptive immune system changes that have been noted in COVID-19 and suggest longer term effects that may shape the maintenance of immunity to SARS-CoV-2.

Time to recovery and its predictors among adults hospitalized with COVID-19: A prospective cohort study in Ethiopia

BACKGROUND

Various factors may determine the duration of viral shedding (the time from infection to viral RNA-negative conversion or recovery) in COVID-19 patients. Understanding the average duration of recovery and its predictors is crucial in formulating preventive measures and optimizing treatment options. Therefore, evidence showing the duration of recovery from COVID-19 in different contexts and settings is necessary for tailoring appropriate treatment and prevention measures. This study aimed to investigate the average duration and the predictors of recovery from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection among COVID-19 patients.

METHOD

A hospital-based prospective cohort study was conducted at Eka Kotebe General Hospital, COVID-19 Isolation and Treatment Center from March 18 to June 27, 2020. The Center was the first hospital designated to manage COVID-19 cases in Ethiopia. The study participants were all COVID-19 adult patients who were admitted to the center during the study period. Follow up was done for the participants from the first date of diagnosis to the date of recovery (negative Real-time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCT) test of throat swab).

RESULT

A total of 306 COVID-19 cases were followed up to observe the duration of viral clearance by rRT-PCR. Participants' mean age was 34 years (18-84 years) and 69% were male. The median duration of viral clearance from each participant's body was 19 days, but the range was wide: 2 to 71 days. Cough followed by headache was the leading sign of illness among the 67 symptomatic COVID-19 patients; and nearly half of those with comorbidities were known cancer and HIV/AIDS patients on clinical follow up. The median duration of recovery from COVID-19 was different for those with and without previous medical conditions or comorbidities. The rate of recovery from SARS-CoV-2 infection was 36% higher in males than in females (p = 0.043, CI: 1.01, 1.85). The rate of recovery was 93% higher in those with at least one comorbidity than in those without any comorbidity. The risk of delayed recovery was not influenced by blood type, BMI and presence of signs or symptoms. The findings showed that study participants without comorbidities recovered more quickly than those with at least one comorbidity. Therefore, isolation and treatment centers should be prepared to manage the delayed stay of patients having comorbidity.

Comparison of Tracheal vs Nasopharyngeal Secretions for SARS-CoV-2 RT-PCR Testing in Patients With Tracheostomy

This study compares nasopharyngeal and tracheal samples for COVID-19 viral testing in patients with a tracheostomy. This was a prospective cohort study done at 2 academic hospitals between March and June 2020. Patients admitted through the emergency department who had a COVID-19 test and an existing tracheostomy or underwent a tracheostomy during the admission period were included. Patients with a positive initial nasopharyngeal swab were placed in the experimental group (n = 8), while those with a negative swab were the control group (n = 7). Nasopharyngeal and tracheal samples underwent COVID-19 testing using the Abbott RealTime SARS-CoV-2 RNA assay. Fourteen patients underwent tracheostomy, and 1 had an existing tracheostomy. The average duration of viral shedding in nasopharyngeal samples was 20.9 days. One patient (6.7%) tested positive in tracheal secretions after a negative nasopharyngeal swab. In the remaining patients (93.3%), the nasopharyngeal and tracheal specimens correlated.

Prolonged Positive COVID-19 Test in Recovered Patient

Coronavirus disease 2019 (COVID-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global pandemic that has affected millions worldwide since its initial outbreak in Wuhan, China in December 2019. Discussion of atypical cases of COVID-19 is essential to gaining insight into the clinical presentations of this infection. The authors report a case in which a 74-year-old female who sought medical evaluation via telemedicine for chief complaints of recurrent low-grade fever, dyspnea, dry cough, and myalgias and subsequently tested positive for the SARS-CoV-2 multiple times in over 7 weeks despite prior resolution of symptoms. The patient’s 78-year-old husband who resides in the same household also contracted the SARS-CoV-2.

Association of corticosteroids use and outcomes in COVID-19 patients: A systematic review and meta-analysis

BACKGROUND

To systematically review the literature about the association between systemic corticosteroid therapy (CST) and outcomes of COVID-19 patients.

METHODS

We searched Medline, Embase, EBM Reviews, Scopus, Web of Science, and preprints up to July 20, 2020. We included observational studies and randomized controlled trials (RCT) that assessed COVID-19 patients treated with CST. We pooled adjusted effect estimates of mortality and other outcomes using a random effect model, among studies at low or moderate risk for bias. We assessed the certainty of evidence for each outcome using the GRADE approach.

RESULTS

Out of 1067 citations screened for eligibility, one RCT and 19 cohort studies were included (16,977 hospitalized patients). Ten studies (1 RCT and 9 cohorts) with 10,278 patients examined the effect of CST on short term mortality. The pooled adjusted RR was 0.92 (95% CI 0.69-1.22, I2 = 81.94%). This effect was observed across all stages of disease severity. Four cohort studies examined the effect of CST on composite outcome of death, ICU admission and mechanical ventilation need. The pooled adjusted RR was 0.41(0.23-0.73, I2 = 78.69%). Six cohort studies examined the effect of CST on delayed viral clearance. The pooled adjusted RR was 1.47(95% CI 1.11-1.93, I2 = 43.38%).

CONCLUSION

In this systematic review, as of July 2020, heterogeneous and low certainty cumulative evidence based on observational studies and one RCT suggests that CST was not associated with reduction in short-term mortality but possibly with a delay in viral clearance in patients hospitalized with COVID-19 of different severities. However, the discordant results between the single RCT and observational studies as well as the heterogeneity observed across observational studies, call for caution in using observational data and suggests the need for more RCTs to identify the clinical and biochemical characteristics of patients' population that could benefit from CST.

Analysis of sputum/tracheal aspirate and nasopharyngeal samples for SARS-CoV-2 detection by laboratory-developed test and Panther Fusion system

In this study, 127 sputum/tracheal aspirate specimens were evaluated by a laboratory-developed real-time RT-PCR method and Fusion SARS-CoV-2 assay. These specimens were collected from the patients who have nasopharyngeal swab (NPS) samples being used for SARS-CoV-2 detection previously or simultaneously. The overall agreement was 96% between the lower respiratory tract (LRT) and NPS samples, suggesting that LRT specimens could be an option for patients who develop a productive cough or those receiving invasive mechanical ventilation.

SARS-CoV-2 recurrent RNA positivity after recovering from coronavirus disease 2019 (COVID-19): a meta-analysis

BACKGROUND AND AIM

Isolation of subjects with active severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a pivotal preventive measure in the ongoing coronavirus disease 2019 (COVID-19) pandemic. A growing number of studies reported cases of recurrent SARS-CoV-2 RNA positivity following disease recovery, which were identified with a critical literature search and then meta-analyzed in this article.

MATERIALS AND METHODS

A digital search was performed in Medline and Web of Science, using the keywords "coronavirus disease 2019" OR "COVID-19" OR "severe acute respiratory disease 2" OR "SARS-CoV-2" AND "recurrence" OR "repositivization" OR "retesting", without date or language restrictions. Recovery was defined as resolution of symptoms, with at least two consecutive negative molecular tests.

RESULTS

A total number of 17 studies, with 5,182 COVID-19 patients, were included. SARS-CoV-2 recurrent RNA positivity in recovered COVID-19 patients ranged between 7-23% across the studies, with follow-up testing between 1-60 days. The estimated cumulative rate of SARS-CoV-2 recurrent RNA positivity was 12% (95% confidence interval, 12-13%; I2, 74%).

CONCLUSIONS

Repeated molecular testing on respiratory tracts specimens at 1 and 2 months after recovery from COVID-19 is strongly advisable for early identification, isolation and clinical management of subjects with SARS-CoV-2 recurrent RNA positivity.