Clinical Course and Molecular Viral Shedding Among Asymptomatic and Symptomatic Patients With SARS-CoV-2 Infection in a Community Treatment Center in the Republic of Korea

Seroprevalence of Anti-SARS-CoV-2 Antibodies in Blood Donors from Nuevo Leon State, Mexico, during 2020: A Retrospective Cross-Sectional Evaluation

The progression and distribution of the SARS-CoV-2 pandemic are continuously changing over time and can be traced by blood donors' serological survey. Here, we investigated the seroprevalence of anti-SARS-CoV-2 antibodies in blood donors in Nuevo Leon, Mexico during 2020 as a strategy for the rapid evaluation of the spread of SARS-CoV-2 and asymptomatic case detection. We collected residual plasma samples from blood donors who attended two regional donation centers from January to December of 2020 to identify changes in anti-SARS-CoV-2 IgG prevalence. Plasma samples were analyzed on the Abbott Architect instrument using the commercial Abbott SARS-CoV-2 IgG chemiluminescent assay. We found a total of 99 reactive samples from 2068 analyzed plasma samples, resulting in a raw prevalence of 4.87%. Donors aged 18-49 years were more likely to be seropositive compared to those aged >50 years (p < 0.001). Weekly seroprevalence increased from 1.8% during the early pandemic stage to 27.59% by the end of the year. Prevalence was 1.46-fold higher in females compared to males. Case geographical mapping showed that Monterrey city recorded the majority of SARS-CoV-2 cases. These results show that there is a growing trend of seroprevalence over time associated with asymptomatic infection that is unnoticed under the current epidemiological surveillance protocols.

SARS-CoV-2 quantitative real time PCR and viral loads analysis among asymptomatic and symptomatic patients: an observational study on an outbreak in two nursing facilities in Campania Region (Southern Italy)

BACKGROUND

In December 2019 an outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 was first observed in Wuhan, China. The virus has spread rapidly throughout the world creating a pandemic scenario. Several risk factors have been identified, such as age, sex, concomitant diseases as well as viral load. A key point is the role of asymptomatic people in spreading SARS-CoV-2. An observational study in Southern Italy was conducted in order to elucidate the possible role of asymptomatic individuals related to their viral loads in the transmission of the virus within two nursing facilities.

METHODS

Oro-nasopharyngeal swabs from 179 nursing health care workers and patients were collected. SARS-CoV-2 RT-qPCR was performed and viral loads were calculated by using standard curve. A statistical correlation between viral loads, the presence/absence of symptoms, age and sex variables was investigated.

RESULTS

SARS-CoV-2 was confirmed in the 50.8 % (n = 91) of the cases. Median age of positive individuals resulted higher than negative ones. Over 65 year as well as female individuals showed higher susceptibility to SARS-CoV-2 infection, OR = 3.93 and 2.86, respectively. Among 91 tested positive, the 70.3 % was symptomatic while the 29.7 % was asymptomatic. Median viral loads of asymptomatic individuals were found statistically significant higher than symptomatic ones (p = 0.001), while no influence was observed in age and sex variables. The presence of comorbidities was 8.9 folds higher in patients who showed and developed symptoms compared to non-symptomatic ones. Moreover, higher viral loads were found in patients who remained asymptomatic than pre-symptomatic (p = 0.022).

CONCLUSIONS

A range from 9.2 to 69 % of confirmed SARS-CoV-2 cases remains asymptomatic, moreover, sporadic transmissions from asymptomatic people are reported, that makes their involvement an important issue to take into account in the spreading control of the virus. An asymptomatic clinical course was observed in the 29.7 % of positive individuals, moreover, median viral loads resulted to be statistically significant when compared to symptomatic ones. Surely, such a relevant frequency should not be ignored in relation to the spread of the disease in an environment which has not only important intrinsic (age, sex, concomitant diseases) but also extrinsic factors such as high population density and close contacts.

SARS-CoV-2 quantitative real time PCR and viral loads analysis among asymptomatic and symptomatic patients: an observational study on an outbreak in two nursing facilities in Campania Region (Southern Italy)

BACKGROUND

In December 2019 an outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 was first observed in Wuhan, China. The virus has spread rapidly throughout the world creating a pandemic scenario. Several risk factors have been identified, such as age, sex, concomitant diseases as well as viral load. A key point is the role of asymptomatic people in spreading SARS-CoV-2. An observational study in Southern Italy was conducted in order to elucidate the possible role of asymptomatic individuals related to their viral loads in the transmission of the virus within two nursing facilities.

METHODS

Oro-nasopharyngeal swabs from 179 nursing health care workers and patients were collected. SARS-CoV-2 RT-qPCR was performed and viral loads were calculated by using standard curve. A statistical correlation between viral loads, the presence/absence of symptoms, age and sex variables was investigated.

RESULTS

SARS-CoV-2 was confirmed in the 50.8 % (n = 91) of the cases. Median age of positive individuals resulted higher than negative ones. Over 65 year as well as female individuals showed higher susceptibility to SARS-CoV-2 infection, OR = 3.93 and 2.86, respectively. Among 91 tested positive, the 70.3 % was symptomatic while the 29.7 % was asymptomatic. Median viral loads of asymptomatic individuals were found statistically significant higher than symptomatic ones (p = 0.001), while no influence was observed in age and sex variables. The presence of comorbidities was 8.9 folds higher in patients who showed and developed symptoms compared to non-symptomatic ones. Moreover, higher viral loads were found in patients who remained asymptomatic than pre-symptomatic (p = 0.022).

CONCLUSIONS

A range from 9.2 to 69 % of confirmed SARS-CoV-2 cases remains asymptomatic, moreover, sporadic transmissions from asymptomatic people are reported, that makes their involvement an important issue to take into account in the spreading control of the virus. An asymptomatic clinical course was observed in the 29.7 % of positive individuals, moreover, median viral loads resulted to be statistically significant when compared to symptomatic ones. Surely, such a relevant frequency should not be ignored in relation to the spread of the disease in an environment which has not only important intrinsic (age, sex, concomitant diseases) but also extrinsic factors such as high population density and close contacts.

Association Between Vaccination With BNT162b2 and Incidence of Symptomatic and Asymptomatic SARS-CoV-2 Infections Among Health Care Workers

IMPORTANCE

Randomized clinical trials have provided estimates of the effectiveness of the BNT162b2 vaccine against symptomatic SARS-CoV-2 infection, but its effect on asymptomatic infections remains unclear.

OBJECTIVE

To estimate the association of vaccination with the Pfizer-BioNTech BNT162b2 vaccine with symptomatic and asymptomatic SARS-CoV-2 infections among health care workers.

DESIGN, SETTING, AND PARTICIPANTS

This was a single-center, retrospective cohort study conducted at a tertiary medical center in Tel Aviv, Israel. Data were collected on symptomatic and asymptomatic SARS-CoV-2 infections confirmed via polymerase chain reaction (PCR) tests in health care workers undergoing regular screening with nasopharyngeal swabs between December 20, 2020, and February 25, 2021. Logistic regression was used to calculate incidence rate ratios (IRRs) comparing the incidence of infection between fully vaccinated and unvaccinated participants, controlling for demographics and the number of PCR tests performed.

EXPOSURES

Vaccination with the BNT162b2 vaccine vs unvaccinated status was ascertained from the employee health database. Full vaccination was defined as more than 7 days after receipt of the second vaccine dose.

MAIN OUTCOMES AND MEASURES

The primary outcome was the regression-adjusted IRR for symptomatic and asymptomatic SARS-CoV-2 infection of fully vaccinated vs unvaccinated health care workers. The secondary outcomes included IRRs for partially vaccinated health care workers (days 7-28 after first dose) and for those considered as late fully vaccinated (>21 days after second dose).

RESULTS

A total of 6710 health care workers (mean [SD] age, 44.3 [12.5] years; 4465 [66.5%] women) were followed up for a median period of 63 days; 5953 health care workers (88.7%) received at least 1 dose of the BNT162b2 vaccine, 5517 (82.2%) received 2 doses, and 757 (11.3%) were not vaccinated. Vaccination was associated with older age compared with those who were not vaccinated (mean age, 44.8 vs 40.7 years, respectively) and male sex (31.4% vs 17.7%). Symptomatic SARS-CoV-2 infection occurred in 8 fully vaccinated health care workers and 38 unvaccinated health care workers (incidence rate, 4.7 vs 149.8 per 100 000 person-days, respectively, adjusted IRR, 0.03 [95% CI, 0.01-0.06]). Asymptomatic SARS-CoV-2 infection occurred in 19 fully vaccinated health care workers and 17 unvaccinated health care workers (incidence rate, 11.3 vs 67.0 per 100 000 person-days, respectively, adjusted IRR, 0.14 [95% CI, 0.07-0.31]). The results were qualitatively unchanged by the propensity score sensitivity analysis.

CONCLUSIONS AND RELEVANCE

Among health care workers at a single center in Tel Aviv, Israel, receipt of the BNT162b2 vaccine compared with no vaccine was associated with a significantly lower incidence of symptomatic and asymptomatic SARS-CoV-2 infection more than 7 days after the second dose. Findings are limited by the observational design.

SARS-CoV-2 viral load in nasopharyngeal swabs is not an independent predictor of unfavorable outcome

The aim was to assess the ability of nasopharyngeal SARS-CoV-2 viral load at first patient's hospital evaluation to predict unfavorable outcomes. We conducted a prospective cohort study including 321 adult patients with confirmed COVID-19 through RT-PCR in nasopharyngeal swabs. Quantitative Synthetic SARS-CoV-2 RNA cycle threshold values were used to calculate the viral load in log₁₀ copies/mL. Disease severity at the end of follow up was categorized into mild, moderate, and severe. Primary endpoint was a composite of intensive care unit (ICU) admission and/or death (n = 85, 26.4%). Univariable and multivariable logistic regression analyses were performed. Nasopharyngeal SARS-CoV-2 viral load over the second quartile (≥ 7.35 log₁₀ copies/mL, p = 0.003) and second tertile (≥ 8.27 log₁₀ copies/mL, p = 0.01) were associated to unfavorable outcome in the unadjusted logistic regression analysis. However, in the final multivariable analysis, viral load was not independently associated with an unfavorable outcome. Five predictors were independently associated with increased odds of ICU admission and/or death: age ≥ 70 years, SpO₂, neutrophils > 7.5 × 10³/µL, lactate dehydrogenase ≥ 300 U/L, and C-reactive protein ≥ 100 mg/L. In summary, nasopharyngeal SARS-CoV-2 viral load on admission is generally high in patients with COVID-19, regardless of illness severity, but it cannot be used as an independent predictor of unfavorable clinical outcome.

Comparison of the Quantitative DiaSorin Liaison Antigen Test to Reverse Transcription-PCR for the Diagnosis of COVID-19 in Symptomatic and Asymptomatic Outpatients

We evaluated the quantitative DiaSorin Liaison severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen test in symptomatic and asymptomatic individuals consulting their general practitioners (GPs) during a period of stable intense virus circulation (213/100,000 habitants per day). Leftover reverse transcription-PCR (RT-PCR) positive (n = 204) and negative (n = 210) nasopharyngeal samples were randomly selected among fresh routine samples collected from patients consulting their GPs. Samples were tested on Liaison XL according to the manufacturer's instructions. Equivocal results were considered negative. The overall sensitivity and specificity of the Liaison antigen test compared to RT-PCR were 65.7% (95% confidence interval [CI], 58.9% to 71.9%) and 100% (CI, 97.8% to 100%). Sensitivity in samples with viral loads of ≥10⁵, ≥10⁴, and ≥10³ copies/ml were 100% (CI, 96.3% to 100.0%), 96.5% (CI, 91.8% to 98.7%), and 87.4% (CI, 81.3% to 91.5%), respectively. All samples with ≤10³ copies/ml were antigen negative. The ratio of antigen concentration to viral load in samples with ≥10³ copies/ml was comparable in symptomatic and asymptomatic individuals (P = 0.58). The proportion of RT-PCR-positive participants with a high viral load (≥10⁵ copies/ml) was not significantly higher in symptomatic than in asymptomatic participants (63.9% [CI, 54.9% to 72.0%] versus 51.9% [CI, 41.1% to 62.6%]; P = 0.11), but the proportion of participants with a low viral load (<10³ copies/ml) was significantly higher in asymptomatic than in symptomatic RT-PCR-positive participants (35.4% [CI, 25.8% to 46.4%] versus 14.3% [CI, 9.0% to 21.8%]; P < 0.01). Sensitivity and specificity in samples with a viral load of ≥10⁴ copies/ml were 96.5% and 100%. The correlation of antigen concentration with viral load was comparable in symptomatic and asymptomatic individuals.

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.

Clinical Performance of the Standard Q COVID-19 Rapid Antigen Test and Simulation of its Real-World Application in Korea

The rapid antigen test (RAT) for coronavirus disease (COVID-19) represents a potent diagnostic method in situations of limited molecular testing resources. However, considerable performance variance has been reported with the RAT. We evaluated the clinical performance of Standard Q COVID-19 RAT (SQ-RAT; SD Biosensor, Suwon, Korea), the first RAT approved by the Korean Ministry of Food and Drug Safety. In total, 680 nasopharyngeal swabs previously tested using real-time reverse-transcription PCR (rRT-PCR) were retested using SQ-RAT. The clinical sensitivity of SQ-RAT relative to that of rRT-PCR was 28.7% for all specimens and was 81.4% for specimens with RNA-dependent RNA polymerase gene (RdRp) threshold cycle (Ct) values ≤23.37, which is the limit of detection of SQ-RAT. The specificity was 100%. The clinical sensitivity of SQ-RAT for COVID-19 diagnosis was assessed based on the Ct distribution at diagnosis of 33,294 COVID-19 cases in Korea extracted from the laboratory surveillance system of Korean Society for Laboratory Medicine. The clinical sensitivity of SQ-RAT for COVID-19 diagnosis in the Korean population was 41.8%. Considering the molecular testing capacity in Korea, use of the RAT for COVID-19 diagnosis appears to be limited.

Valorisation of medical waste through pyrolysis for a cleaner environment: Progress and challenges

The COVID-19 pandemic has exerted great shocks and challenges to the environment, society and economy. Simultaneously, an intractable issue appeared: a considerable number of hazardous medical wastes have been generated from the hospitals, clinics, and other health care facilities, constituting a serious threat to public health and environmental sustainability without proper management. Traditional disposal methods like incineration, landfill and autoclaving are unable to reduce environmental burden due to the issues such as toxic gas release, large land occupation, and unsustainability. While the application of clean and safe pyrolysis technology on the medical wastes treatment to produce high-grade bioproducts has the potential to alleviate the situation. Besides, medical wastes are excellent and ideal raw materials, which possess high hydrogen, carbon content and heating value. Consequently, pyrolysis of medical wastes can deal with wastes and generate valuable products like bio-oil and biochar. Consequently, this paper presents a critical and comprehensive review of the pyrolysis of medical wastes. It demonstrates the feasibility of pyrolysis, which mainly includes pyrolysis characteristics, product properties, related problems, the prospects and future challenges of pyrolysis of medical wastes.

Potent SARS-CoV-2-Specific T Cell Immunity and Low Anaphylatoxin Levels Correlate With Mild Disease Progression in COVID-19 Patients

T cells play a fundamental role in the early control and clearance of many viral infections of the respiratory system. In SARS-CoV-2-infected individuals, lymphopenia with drastically reduced CD4⁺ and CD8⁺ T cells correlates with Coronavirus disease 2019 (COVID-19)-associated disease severity and mortality. In this study, we characterized cellular and humoral immune responses induced in patients with mild, severe and critical COVID-19. Peripheral blood mononuclear cells of 37 patients with mild, severe and critical COVID-19 and 10 healthy individuals were analyzed by IFNγ ELISpot and multi-color flow cytometry upon stimulation with peptide pools covering complete immunodominant SARS-CoV-2 matrix, nucleocapsid and spike proteins. In addition SARS-CoV-2 antibody levels, neutralization abilities and anaphylatoxin levels were evaluated by various commercially available ELISA platforms. Our data clearly demonstrates a significantly stronger induction of SARS-CoV-2 specific CD8⁺ T lymphocytes and higher IFNγ production in patients with mild compared to patients with severe or critical COVID-19. In all patients SARS-CoV-2-specific antibodies with similar neutralizing activity were detected, but highest titers of total IgGs were observed in critical patients. Finally, elevated anaphylatoxin C3a and C5a levels were identified in severe and critical COVID-19 patients probably caused by aberrant immune complex formation due to elevated antibody titers in these patients. Crucially, we provide a full picture of cellular and humoral immune responses of COVID-19 patients and prove that robust polyfunctional CD8⁺ T cell responses concomitant with low anaphylatoxin levels correlate with mild infections. In addition, our data indicates that high SARS-CoV-2 antibody titers are associated with severe disease progression.

ENE-COVID nationwide serosurvey served to characterize asymptomatic infections and to develop a symptom-based risk score to predict COVID-19

Objectives

To characterize asymptomatic SARS-CoV-2 infections and develop a symptom-based risk score useful in primary healthcare.

Study design and setting

Sixty-one thousand ninty-two community-dwelling participants in a nationwide population-based serosurvey completed a questionnaire on COVID-19 symptoms and received an immunoassay for SARS-CoV-2 IgG antibodies between April 27 and June 22, 2020. Standardized prevalence ratios for asymptomatic infection were estimated across participant characteristics. We constructed a symptom-based risk score and evaluated its ability to predict SARS-CoV-2 infection.

Results

Of all, 28.7% of infections were asymptomatic (95% CI 26.1–31.4%). Standardized asymptomatic prevalence ratios were 1.19 (1.02–1.40) for men vs. women, 1.82 (1.33–2.50) and 1.45 (0.96–2.18) for individuals <20 and ≥80 years vs. those aged 40–59, 1.27 (1.03–1.55) for smokers vs. nonsmokers, and 1.91 (1.59–2.29) for individuals without vs. with case contact. In symptomatic population, a symptom-based score (weights: severe tiredness = 1; absence of sore throat = 1; fever = 2; anosmia/ageusia = 5) reached standardized seroprevalence ratio of 8.71 (7.37–10.3), discrimination index of 0.79 (0.77–0.81), and sensitivity and specificity of 71.4% (68.1–74.4%) and 74.2% (73.1–75.2%) for a score ≥3.

Conclusion

The presence of anosmia/ageusia, fever with severe tiredness, or fever without sore throat should serve to suspect COVID-19 in areas with active viral circulation. The proportion of asymptomatics in children and adolescents challenges infection control.

Disposable face masks and reusable face coverings as non-pharmaceutical interventions (NPIs) to prevent transmission of SARS-CoV-2 variants that cause coronavirus disease (COVID-19): Role of new sustainable NPI design innovations and predictive mathematical modelling

Best-published evidence supports the combined use of vaccines with non-pharmaceutical interventions (NPIs), to reduce the relative risk of contracting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19; this will enable a safe transition to achieving herd immunity. Albeit complex, the strategic public health goal is to bundle NPIs to keep the basic reproduction number R₀ below one. However, validation of these NPIs is conducted using random clinical trials, which is challenging in a swiftly moving pandemic given the need for recruiting large participant cohort over a longitudinal analysis period. This review highlights emerging innovations for potentially improving the design, functionality and improved waste management of disposable face masks such as filtering facepiece (FFPs) respirators, medical masks, and reusable face coverings to help prevent COVID-19. It describes use of different mathematical models under varying scenarios to inform efficacy of single and combined use of NPIs as important counter-measures to break the cycle of COVID-19 infection including new SARS-CoV-2 variants. Demand for face masks during COVID-19 pandemic keeps increasing, especially for FFPs worn by medical workers. Collaborative and well-conducted randomised controlled trials across borders are required to generate robust data to inform common and consistent policies for COVID-19 and future pandemic planning and management; however, current use of systematic reviews of best available evidence can be considered to guide interim policies.

Patients' treatment limitations as predictive factor for mortality in COVID-19: results from hospitalized patients of a hotspot region for SARS-CoV-2 infections

Background

In hospitalized patients with SARS-CoV-2 infection, outcomes markedly differ between locations, regions and countries. One possible cause for these variations in outcomes could be differences in patient treatment limitations (PTL) in different locations. We thus studied their role as predictor for mortality in a population of hospitalized patients with COVID-19.

Methods

In a region with high incidence of SARS-CoV-2 infection, adult hospitalized patients with PCR-confirmed SARS-CoV-2 infection were prospectively registered and characterized regarding sex, age, vital signs, symptoms, comorbidities (including Charlson comorbidity index (CCI)), transcutaneous pulse oximetry (SpO₂) and laboratory values upon admission, as well as ICU-stay including respiratory support, discharge, transfer to another hospital and death. PTL assessed by routine clinical procedures comprised the acceptance of ICU-therapy, orotracheal intubation and/or cardiopulmonary resuscitation.

Results

Among 526 patients included (median [quartiles] age 73 [57; 82] years, 47% female), 226 (43%) had at least one treatment limitation. Each limitation was associated with age, dementia and eGFR (p < 0.05 each), that regarding resuscitation additionally with Charlson comorbidity index (CCI) and cardiac disease. Overall mortality was 27% and lower (p < 0.001) in patients without treatment limitation (12%) compared to those with any limitation (47%). In univariate analyses, age and comorbidities (diabetes, cardiac, cerebrovascular, renal, hepatic, malignant disease, dementia), SpO₂, hemoglobin, leucocyte numbers, estimated glomerular filtration rate (eGFR), C-reactive protein (CRP), Interleukin-6 and LDH were predictive for death (p < 0.05 each). In multivariate analyses, the presence of any treatment limitation was an independent predictor of death (OR 4.34, 95%-CI 2.10–12.30; p = 0.001), in addition to CCI, eGFR < 55 ml/min, neutrophil number > 5 G/l, CRP > 7 mg/l and SpO₂ < 93% (p < 0.05 each).

Conclusion

In hospitalized patients with SARS-CoV-2, the percentage of patients with treatment limitations was high. PTL were linked to age, comorbidities and eGFR assessed upon admission and strong, independent risk factors for mortality. These findings might be useful for further understanding of COVID-19 mortality and its regional variations.

Clinical trial registration ClinicalTrials.gov Identifier: NCT04344171

Supplementary Information

The online version contains supplementary material available at 10.1186/s12931-021-01756-2.

Knowledge, Attitude, and Self-Reported Practice Towards Measures for Prevention of the Spread of COVID-19 Among Australians: A Nationwide Online Longitudinal Representative Survey

Objective: To assess and share learnings on the motivators and behavioural adherence across sex and age to evolving strategies in public policy to prevent the spread of SARS-CoV-2 at the end of a first COVID-19 wave and the beginning of a second COVID-19 wave in Australia.

Design and Setting: A national longitudinal survey using a framework based on evidence-based behaviour change models. The survey was administered to a national sample representative across sex, age and location was undertaken at two time points: May 1st to 5th, 2020, and July 1st to 7th, 2020.

Results: Overall 2,056 surveys were completed across the first and second rounds, with 63% (1,296/2,056) completing both. Age range was 18–99 years (median 53, IQR: 34–64). Suboptimal physical distancing and self-quarantining if unwell/diagnosed was reported in one in four respondents and not getting a test at onset of symptoms reported in one in three. Those non-adherent to all three behaviours (19%, 60/323), were mainly male, younger, lived in major cities and reported fewer concerns or motivators to change behaviour. Overall, government lockdown measures were considered very important by 81% (835/1,032) and appropriate by 75% (772/1,029).

Conclusions: Prior to the suppression of a second COVID-19 wave, a significant minority of Australians reported suboptimal behavioural adherence to vital policy strategies to limit SARS-CoV-2 spread, mostly young adults and men. Successful wave 2 suppression required consistent communication from political and health leaders and supportive public health and economic strategies. Additional lockdown and punitive strategies were needed in Victoria and were generally well-supported and adhered to. To limit subsequent lockdown, this work reinforces the need for a mix of communication around saving lives of the vulnerable, and other strategies targeting high risk groups, facilitation of easy testing and minimisation of financial impacts.

Epidemiological profiles and associated risk factors of SARS-CoV-2 positive patients based on a high-throughput testing facility in India

We describe the epidemiological characteristics and associated risk factors of those presenting at a large testing centre for SARS-CoV-2 infection. This is a retrospective record review of individuals who underwent SARS-CoV-2 testing by reverse transcription–polymerase chain reaction (RT-PCR) at a high-throughput national-level government facility located in the north of India. Samples collected from 6 April to 31 December 2020 are included in this work and represent four highly populous regions. Additionally, there was a prospective follow-up of 1729 cases through telephone interviews from 25 May 2020 to 20 June 2020. Descriptive analysis has been performed for profiling clinic-epidemiological aspects of suspect cases. Multivariable logistic regression analysis was undertaken to determine risk factors that are associated with SARS-CoV-2 test positivity and symptom status. A total of 125 600 participants' details have been included in this report. The mean (s.d.) age of the participants was 33.1 (±15.3) years and 66% were male. Among these tested, 9515 (7.6%) were positive for COVID-19. A large proportion of positive cases were asymptomatic. In symptomatic positive cases, the commonest symptoms were cough and fever. Increasing age (groups 20–59 and ≥60 years compared to age group less than 5 years), male sex, history of international travel, symptoms for SARS-CoV-2, and participants from Delhi and Madhya Pradesh were positively associated with SARS-CoV-2 test positivity. Having co-morbidity, risk behaviours and intra-familial positivity were associated with a positive odds ratio for exhibiting SARS-CoV-2 symptoms. Intensified testing and isolation of cases, identification of both asymptomatic and symptomatic individuals and additional care of those with co-morbidities and risk behaviours will all be collectively important for disease containment in India. Reasons for differentials in testing between men and women remain an important area for in-depth study. The increased deployment of vaccines is likely to impact the trajectory of COVID-19 in the coming time, and therefore our data will serve as a comparative resource as India experiences the second wave of infection in light of newer variants that are likely to accelerate disease spread.

Antibody and viral RNA kinetics in SARS-CoV2 infected patients admitted to a Romanian University Hospital of Infectious Diseases

OBJECTIVES

To assess the antibody and viral kinetics in asymptomatic/mild confirmed SARS-CoV-2 infections compared to more severe patients.

MATERIAL AND METHODS

Retrospective analysis of data obtained from adult patients with a confirmed SARS-CoV2 infection having at least one SARS-CoV-2 pair of specific IgM/IgG tests, admitted in The University Hospital of Infectious Diseases Cluj-Napoca, Romania (28 February to 31 August 2020). The database also included: demographic, clinical, chest X-ray and/or CT scan results, RT-PCR SARS-CoV-2, and dexamethasone treatment. A total of 469 patients were evaluated as "asymptomatic/mild" and "moderate/severe/critical" cases.

RESULTS

The median time since confirmation to SARS-CoV-2 PCR negativity was 15 days [95% CI: 13-18] in asymptomatic/mild cases and 17 days [95% CI: 16-21] in moderate/severe ones. The median time to seroconversion for both IgM and IgG was 13 days [95% CI: 13-14] in asymptomatic/mild cases and 11 days [95% CI: 10-13] in moderate/severe ones. For both antibody types, the highest reactivity was significantly associated with more severe presentation (IgM: OR = 10.30, IgG: OR = 7.97).

CONCLUSION

Asymptomatic/mild COVID-19 cases had a faster RT-PCR negativity rate compared to moderate/severe/critical patients. IgG and IgM dynamics were almost simultaneous, more robust for IgG in more severe cases, and at one month after confirmation, almost all patients had detectable antibody titers.

Chronic rhinosinusitis is associated with prolonged SARS-CoV-2 RNA shedding in upper respiratory tract samples: A case-control study

BACKGROUND

SARS-CoV-2, the COVID-19 causative agent, has infected millions of people and killed over 1.6 million worldwide. A small percentage of cases persist with prolonged positive RT-PCR on nasopharyngeal swabs. The aim of this study was to determine risk factors for prolonged viral shedding amongst patient's basal clinical conditions.

METHODS

We have evaluated all 513 patients attended in our hospital between 1 March and 1 July. We have selected all 18 patients with prolonged viral shedding and compared them with 36 sex-matched randomly selected controls. Demographic, treatment and clinical data were systematically collected.

RESULTS

Global median duration of viral clearance was 25.5 days (n = 54; IQR, 22-39.3 days), 48.5 days in cases (IQR 38.7-54.9 days) and 23 days in controls (IQR 20.2-25.7), respectively. There were not observed differences in demographic, symptoms or treatment data between groups. Chronic rhinosinusitis and atopy were more common in patients with prolonged viral shedding (67%) compared with controls (11% and 25% respectively) (P < 0.001 and P = 0.003). The use of inhaled corticosteroids was also more frequent in case group (P = 0.007). Multivariate analysis indicated that CRS (odds ratio [OR], 18.78; 95% confidence interval [95%CI], 3.89-90.59; P < 0.001) was independently associated with prolonged SARS-CoV-2 RNA shedding in URT samples, after adjusting for initial PCR Ct values.

CONCLUSION

We found that chronic rhinosinusitis and atopy might be associated with increased risk of prolonged viral shedding. If confirmed in prospective trials, this finding might have clinical implications for quarantine duration due to increased risk of pandemic spread.

Understanding viral shedding of severe acute respiratory coronavirus virus 2 (SARS-CoV-2): Review of current literature

OBJECTIVE

Transmission of SARS-CoV-2 has significant implications for hospital infection prevention and control, discharge management, and public health. We reviewed available literature to reach an evidenced-based consensus on the expected duration of viral shedding.

DESIGN

We queried 4 scholarly repositories and search engines for studies reporting SARS-CoV-2 viral shedding dynamics by PCR and/or culture available through September 8, 2020. We calculated the pooled median duration of viral RNA shedding from respiratory and fecal sources.

RESULTS

The review included 77 studies on SARS-CoV-2. All studies reported PCR-based testing and 12 also included viral culture data. Among 28 studies, the overall pooled median duration of RNA shedding from respiratory sources was 18.4 days (95% CI, 15.5-21.3; I2 = 98.87%; P < .01). When stratified by disease severity, the pooled median duration of viral RNA shedding from respiratory sources was 19.8 days (95% CI, 16.2-23.5; I2 = 96.42%; P < .01) among severely ill patients and 17.2 days (95% CI, 14.0-20.5; I2 = 95.64%; P < .01) in mild-to-moderate illness. Viral RNA was detected up to 92 days after symptom onset. Viable virus was isolated by culture from -6 to 20 days relative to symptom onset.

CONCLUSIONS

SARS-COV-2 RNA shedding can be prolonged, yet high heterogeneity exists. Detection of viral RNA may not correlate with infectivity since available viral culture data suggests shorter durations of shedding of viable virus. Additional data are needed to determine the duration of shedding of viable virus and the implications for risk of transmission.

Comparative evaluation of Panbio and SD Biosensor antigen rapid diagnostic tests for COVID-19 diagnosis

The aim of our study was to evaluate the diagnostic performance of two antigen rapid diagnostic tests (Ag-RDTs) to diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We evaluated Panbio and SD-Biosensor Ag-RDTs. We employed 186 polymerase chain reaction (PCR) negative samples to evaluate the specificity and 170 PCR positive samples to assess the sensitivity. We evaluated their sensitivity according to Cycle threshold (C _t ) values and days post onset of symptoms (d.p.o.). Tests were compared using the McNemar's test. Agreement was evaluated using the kappa score. Specificity was 100% for Panbio and 97.3% for SD-Biosensor. Sensitivity for samples with C _t ≤ 20 was 100% for both assays and for samples with C _t  = 20-25 was 93.0% (Panbio) and 95.3% (SD-Biosensor) (p =  1.000). Sensitivity decreased for samples wit C _t  = 25-30 (Panbio: 41.3%, SD-Biosensor: 52.2%, p = 0.125) and samples with C _t ≥ 30 (Panbio: 5.0%, SD-Biosensor: 17.5%, p = 0.063). Sensitivity within seven d.p.o. was 87.7% for Panbio and 90.4% for SD-Biosensor and notably decreased after seven d.p.o. Agreement with PCR was excellent for high viral load samples (C _t  ≤ 25): Panbio, 98.9%, kappa = 0.974; SD-Biosensor, 97.4%, kappa = 0.940. Agreement between Ag-RDTs was excellent (94.9%, kappa = 0.882). Panbio and SD-Biosensor Ag-RDTs showed excellent agreement and diagnostic performance results for samples with high viral loads (C _t ≤ 25) or samples within seven d.p.o.

Modeling the early temporal dynamics of viral load in respiratory tract specimens of COVID-19 patients in Incheon, the Republic of Korea

Objective

To investigate the duration and peak of severe acute respiratory syndrome coronavirus 2 shedding as infectivity markers for determining the isolation period.

Methods

A total of 2,558 upper respiratory tract (URT) and lower respiratory tract (LRT) specimens from 138 patients with laboratory-confirmed coronavirus disease were analyzed. Measurements of sequential viral loads were aggregated using the cubic spline smoothing function of a generalized additive model. The time to negative conversion was compared between symptom groups using survival analysis.

Results

In URT samples, viral RNA levels peaked on day 4 after symptom onset and rapidly decreased until day 10 for both E and RdRp genes, whereas those in LRT samples immediately peaked from symptom onset and decreased until days 15.6 and 15.0 for E and RdRp genes, respectively. Median (interquartile range) time to negative conversion was significantly longer in symptomatic (18.0 [13.0–25.0] days) patients than in asymptomatic (13.0 [9.5–17.5] days) patients. The more types of symptoms a patient had, the longer the time to negative conversion.

Conclusions

The viral load rapidly changes depending on the time after symptom onset; the viral shedding period may be longer with more clinical symptoms. Different isolation policies should be applied depending on disease severity.

Misdiagnosis of SARS-CoV-2: A Critical Review of the Influence of Sampling and Clinical Detection Methods

SARS-CoV-2 infection has generated the biggest pandemic since the influenza outbreak of 1918-1919. One clear difference between these pandemics has been the ability to test for the presence of the virus or for evidence of infection. This review examined the performance characteristics of sample types via PCR detection of the virus, of antibody testing, of rapid viral antigen detection kits and computerised tomography (CT) scanning. It was found that combined detection approaches, such as the incorporation of CT scans, may reduce the levels of false negatives obtained by PCR detection in both symptomatic and asymptomatic patients, while sputum and oral throat washing sample types should take precedence over swabbing when available. Rt-PCR assays for detection of the virus remain the gold-standard method for SARS-CoV-2 diagnosis and can be used effectively on pooled samples for widespread screening. The novel Oxford antibody assay was found to have the highest sensitivity and specificity of four currently available commercial antibody kits but should only be used during a specific timeframe post-symptom onset. Further research into transmission modes between symptomatic and asymptomatic patients is needed. Analysis of the performance characteristics of different sampling and detection methods for SARS-CoV-2 showed that timing of sampling and testing methods used can greatly influence the rate of false-positive and false-negative test results, thereby influencing viral spread.

Contrasting SARS-CoV-2 RNA copies and clinical symptoms in a large cohort of Colombian patients during the first wave of the COVID-19 pandemic

BACKGROUND

There is limited and controverting evidence looking at possible associations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA copies and patient variables in large cohorts of symptomatic and asymptomatic patients.

METHODS

We studied 2275 symptomatic and asymptomatic patients from Colombia with coronavirus disease 2019 (COVID-19) and analyzed the associations between RT-PCR cycle threshold (Ct) value with gender, age, comorbidities, symptomatology, and disease severity.

RESULTS

15.4 % of the samples (n = 428) reported at least one comorbidity. There were 2011 symptomatic cases (72.4 %), being the most common reported symptom cough (57.2 %, n = 1586). Respiratory distress was present in 21.4 % of patients (n = 595), and 435 patients (15.6 %) required hospital admission. We observed that patients with no prior medical history harbored higher RNA copies than patients with comorbidities (p = 0.02). No significant differences in RNA copies were observed between symptomatic and asymptomatic patients (p = 0.82). Strong correlations were detected between Ct values and the presence of odynophagia (p = 0.03), diarrhea (p = 0.04), and headache (p = 0.0008). An inverse association was found between RNA copy number and markers of disease severity, namely, respiratory distress (P < 0.0001) and hospitalization requirement (P < 0.0001).

CONCLUSIONS

SARS-CoV-2 RT-PCR cycle thresholds reveal strong associations with a prior medical history, specific symptomatology, and disease severity markers. Further research controlling potential confounding variables needs to be conducted to evaluate the nature and usefulness of these associations in managing COVID-19 patients.

Shedding of Viable Virus in Asymptomatic SARS-CoV-2 Carriers

Information regarding the infectivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in asymptomatic carriers is scarce. In order to determine the duration of infectivity and its correlation with reverse transcription-PCR (RT-PCR) results and time since initial positive PCR test in this population, we evaluated SARS-CoV-2 cell infectivity in nasopharyngeal samples longitudinally obtained from asymptomatic carriers who disembarked from a cruise ship during a COVID-19 outbreak. Of 166 nasopharyngeal samples collected from 39 asymptomatic carriers every 48 h until two consecutive negative PCR test results were obtained, SARS-CoV-2 was successfully isolated from 9 PCR-positive samples which were obtained from 7 persons (18%; 7/39). Viable viruses were isolated predominantly within 7 days after the initial positive PCR test, except for one person who shed viable virus until day 15. The median crossing point (Cp) value of RT-PCR of culture-positive samples was 24.6 (interquartile range [IQR], 20.4 to 25.8; range, 17.9 to 30.3), and Cp values were significantly associated with isolation of viable virus (odds ratio, 0.496; 95% confidence interval [CI], 0.329 to 0.747; P value, 0.001), which was consistent with existing data for symptomatic patients. Genome sequence analysis of SARS-CoV-2 samples consecutively obtained from a person who shed viable virus for 15 days identified the emergence of two novel single nucleotide variants (C8626T transition and C18452T transition) in the sample collected on day 15, with the latter corresponding to an amino acid substitution in nonstructural protein 14. The impact of these mutations on prolonged viable-virus shedding is unclear. These findings underscore the potential role of asymptomatic carriers in transmission.IMPORTANCE A growing number of studies suggest the potential role of asymptomatic SARS-CoV-2 carriers as a major driver of the COVID-19 pandemic; however, virological assessment of asymptomatic infection has largely been limited to reverse transcription-PCR (RT-PCR), which can be persistently positive without necessarily indicating the presence of viable virus (e.g., replication-competent virus). Here, we evaluated the infectivity of asymptomatic SARS-CoV-2 carriers by detecting SARS-CoV-2-induced cytopathic effects on Vero cells using longitudinally obtained nasopharyngeal samples from asymptomatic carriers. We show that asymptomatic carriers can shed viable virus until 7 days after the initial positive PCR test, with one outlier shedding until day 15. The crossing point (Cp) value of RT-PCR was the leading predictive factor for virus viability. These findings provide additional insights into the role of asymptomatic carriers as a source of transmission and highlight the importance of universal source control measures, along with isolation policy for asymptomatic carriers.

Distinct Mucoinflammatory Phenotype and the Immunomodulatory Long Noncoding Transcripts Associated with SARS-CoV-2 Airway Infection

Respiratory epithelial cells are the primary target for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We investigated the 3D human airway tissue model to evaluate innate epithelial cell responses to SARS-CoV-2 infection. A SARS-CoV-2 clinical isolate productively infected the 3D-airway model with a time-dependent increase in viral load (VL) and concurrent upregulation of airway immunomodulatory factors ( IL-6, ICAM-1 , and SCGB1A1 ) and respiratory mucins ( MUC5AC, MUC5B, MUC2 , and MUC4) , and differential modulation of select long noncoding RNAs (lncRNAs i.e., LASI, TOSL, NEAT1 , and MALAT1 ). Next, we examined these immunomodulators in the COVID-19 patient nasopharyngeal swab samples collected from subjects with high- or low-VLs (∼100-fold difference). As compared to low-VL, high-VL patients had prominent mucoinflammatory signature with elevated expression of IL-6, ICAM-1, SCGB1A1, SPDEF, MUC5AC, MUC5B , and MUC4 . Interestingly, LASI, TOSL , and NEAT1 lncRNA expressions were also markedly elevated in high-VL patients with no change in MALAT1 expression. In addition, dual-staining of LASI and SARS-CoV-2 nucleocapsid N1 RNA showed predominantly nuclear/perinuclear localization at 24 hpi in 3D-airway model as well as in high-VL COVID-19 patient nasopharyngeal cells, which exhibited high MUC5AC immunopositivity. Collectively, these findings suggest SARS-CoV-2 induced lncRNAs may play a role in acute mucoinflammatory response observed in symptomatic COVID-19 patients.

Strategies for Vaccine Prioritization and Mass Dispensing

We propose a system that helps decision makers during a pandemic find, in real time, the mass vaccination strategies that best utilize limited medical resources to achieve fast containments and population protection. Our general-purpose framework integrates into a single computational platform a multi-purpose compartmental disease propagation model, a human behavior network, a resource logistics model, and a stochastic queueing model for vaccination operations. We apply the modeling framework to the current COVID-19 pandemic and derive an optimal trigger for switching from a prioritized vaccination strategy to a non-prioritized strategy so as to minimize the overall attack rate and mortality rate. When vaccine supply is limited, such a mixed vaccination strategy is broadly effective. Our analysis suggests that delays in vaccine supply and inefficiencies in vaccination delivery can substantially impede the containment effort. Employing an optimal mixed strategy can significantly reduce the attack and mortality rates. The more infectious the virus, the earlier it helps to open the vaccine to the public. As vaccine efficacy decreases, the attack and mortality rates rapidly increase by multiples; this highlights the importance of early vaccination to reduce spreading as quickly as possible to lower the chances for further mutations to evolve and to reduce the excessive healthcare burden. To maximize the protective effect of available vaccines, of equal importance are determining the optimal mixed strategy and implementing effective on-the-ground dispensing. The optimal mixed strategy is quite robust against variations in model parameters and can be implemented readily in practice. Studies with our holistic modeling framework strongly support the urgent need for early vaccination in combating the COVID-19 pandemic. Our framework permits rapid custom modeling in practice. Additionally, it is generalizable for different types of infectious disease outbreaks, whereby a user may determine for a given type the effects of different interventions including the optimal switch trigger.

Mucosal immunity to severe acute respiratory syndrome coronavirus 2 infection

PURPOSE OF REVIEW

Despite its crucial role in protection against viral infections, mucosal immunity has been largely understudied in the context of coronavirus disease 2019 (COVID-19). This review outlines the current evidence about the role of mucosal immune responses in the clearance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as well as potential mucosal mechanisms of protection against (re-)infection.

RECENT FINDINGS

The angiotensin-converting enzyme 2 cellular entry receptor for SARS-CoV-2 is most highly expressed in the upper respiratory tract and most SARS-CoV-2 shedding occurs from the upper respiratory tract. Viral shedding peaks early during infection around the onset of symptoms, before dropping rapidly in most individuals within 7 days of symptom onset, suggesting mucosal inhibition of viral infection. Serum and mucosal immunoglobulin G and immunoglobulin M responses were found to be strongly correlated in infected patients, whereas correlations were much weaker for immunoglobulin A (IgA). Mucosal IgA responses have been detected in infected cases in the absence of serum antibody responses, with mucosal antibody levels correlating strongly with virus neutralization. Bulk and single-cell RNA sequencing analysis of nasopharyngeal swabs and bronchoalveolar lavage samples of COVID-19 patients revealed the induction of mucosal chemokine and cytokine genes, complement pathways, Janus Kinase/Signal Transducer and Activator of Transcription signaling and cytotoxic T cells.

SUMMARY

Although most clinical studies focus on antibodies and cellular immunity in peripheral blood, mucosal immune responses in the respiratory tract play a key role in the early restriction of viral replication and the clearance of SARS-CoV-2. Identification of mucosal biomarkers associated with viral clearance will allow monitoring of infection-induced immunity. Further studies are needed to understand how the systemic immunological endpoints measured in vaccination studies translate to mucosal protection against SARS-CoV-2 infection.

Detecting in-school transmission of SARS-CoV-2 from case ratios and documented clusters

Claims that in-person schooling has not amplified SARS-CoV-2 transmission are based on similar infection rates in schools and their surrounding communities and limited numbers of documented in-school transmission events. Simulations assuming high in-school transmission suggest that these metrics cannot exclude the possibility that transmission in schools exacerbated overall pandemic risks.

One year of modeling and forecasting COVID-19 transmission to support policymakers in Connecticut

To support public health policymakers in Connecticut, we developed a county-structured compartmental SEIR-type model of SARS-CoV-2 transmission and COVID-19 disease progression. Our goals were to provide projections of infections, hospitalizations, and deaths, as well as estimates of important features of disease transmission, public behavior, healthcare response, and clinical progression of disease. In this paper, we describe a transmission model developed to meet the changing requirements of public health policymakers and officials in Connecticut from March 2020 to February 2021. We outline the model design, implementation and calibration, and describe how projections and estimates were used to support decision-making in Connecticut throughout the first year of the pandemic. We calibrated this model to data on deaths and hospitalizations, developed a novel measure of close interpersonal contact frequency to capture changes in transmission risk over time and used multiple local data sources to infer dynamics of time-varying model inputs. Estimated time-varying epidemiologic features of the COVID-19 epidemic in Connecticut include the effective reproduction number, cumulative incidence of infection, infection hospitalization and fatality ratios, and the case detection ratio. We describe methodology for producing projections of epidemic evolution under uncertain future scenarios, as well as analytical tools for estimating epidemic features that are difficult to measure directly, such as cumulative incidence and the effects of non-pharmaceutical interventions. The approach takes advantage of our unique access to Connecticut public health surveillance and hospital data and our direct connection to state officials and policymakers. We conclude with a discussion of the limitations inherent in predicting uncertain epidemic trajectories and lessons learned from one year of providing COVID-19 projections in Connecticut.

Why is COVID-19 less severe in children? A review of the proposed mechanisms underlying the age-related difference in severity of SARS-CoV-2 infections

In contrast to other respiratory viruses, children have less severe symptoms when infected with the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this review, we discuss proposed hypotheses for the age-related difference in severity of coronavirus disease 2019 (COVID-19).Factors proposed to explain the difference in severity of COVID-19 in children and adults include those that put adults at higher risk and those that protect children. The former include: (1) age-related increase in endothelial damage and changes in clotting function; (2) higher density, increased affinity and different distribution of angiotensin converting enzyme 2 receptors and transmembrane serine protease 2; (3) pre-existing coronavirus antibodies (including antibody-dependent enhancement) and T cells; (4) immunosenescence and inflammaging, including the effects of chronic cytomegalovirus infection; (5) a higher prevalence of comorbidities associated with severe COVID-19 and (6) lower levels of vitamin D. Factors that might protect children include: (1) differences in innate and adaptive immunity; (2) more frequent recurrent and concurrent infections; (3) pre-existing immunity to coronaviruses; (4) differences in microbiota; (5) higher levels of melatonin; (6) protective off-target effects of live vaccines and (7) lower intensity of exposure to SARS-CoV-2.

Time variation in the probability of failing to detect a case of polymerase chain reaction testing for SARS-CoV-2 as estimated from a viral dynamics model

Viral tests including polymerase chain reaction (PCR) tests are recommended to diagnose COVID-19 infection during the acute phase of infection. A test should have high sensitivity; however, the sensitivity of the PCR test is highly influenced by viral load, which changes over time. Because it is difficult to collect data before the onset of symptoms, the current literature on the sensitivity of the PCR test before symptom onset is limited. In this study, we used a viral dynamics model to track the probability of failing to detect a case of PCR testing over time, including the presymptomatic period. The model was parametrized by using longitudinal viral load data collected from 30 hospitalized patients. The probability of failing to detect a case decreased toward symptom onset, and the lowest probability was observed 2 days after symptom onset and increased afterwards. The probability on the day of symptom onset was 1.0% (95% CI: 0.5 to 1.9) and that 2 days before symptom onset was 60.2% (95% CI: 57.1 to 63.2). Our study suggests that the diagnosis of COVID-19 by PCR testing should be done carefully, especially when the test is performed before or way after symptom onset. Further study is needed of patient groups with potentially different viral dynamics, such as asymptomatic cases.

Association Between Upper Respiratory Tract Viral Load, Comorbidities, Disease Severity, and Outcome of Patients With SARS-CoV-2 Infection

Background

There is limited information on the association between upper respiratory tract (URT) viral loads, host factors, and disease severity in SARS-CoV-2 infected patients.

Methods

We studied 1,122 patients (mean age: 46 years) diagnosed by PCR. URT viral load, measured by PCR cycle threshold, was categorized as high, moderate or low.

Results

There were 336 (29.9%) patients with comorbidities; 309 patients (27.5%) had high, 316 (28.2%) moderate, and 497 (44.3%) low viral load. In univariate analyses, compared to patients with moderate or low viral load, patients with high viral load were older, had more often comorbidities, developed symptomatic disease, were intubated and died; in addition, patients with high viral load had longer stay in intensive care unit and longer intubation compared to patients with low viral load (p-values <0.05 for all). Patients with chronic cardiovascular disease, hypertension, chronic pulmonary disease, immunosuppression, obesity and chronic neurological disease had more often high viral load (p-value<0.05 for all). Multivariate analysis found that a high viral load was associated with COVID-19. The level of viral load was not associated with any other outcome.

Conclusions

URT viral load could be used to identify patients at higher risk for morbidity or severe outcome.

Modelling the spread of SARS-CoV-2 pandemic - Impact of lockdowns & interventions

BACKGROUND & OBJECTIVES

To handle the current COVID-19 pandemic in India, multiple strategies have been applied and implemented to slow down the virus transmission. These included clinical management of active cases, rapid development of treatment strategies, vaccines computational modelling and statistical tools to name a few. This article presents a mathematical model for a time series prediction and analyzes the impact of the lockdown.

METHODS

Several existing mathematical models were not able to account for asymptomatic patients, with limited testing capability at onset and no data on serosurveillance. In this study, a new model was used which was developed on lines of susceptible-asymptomatic-infected-recovered (SAIR) to assess the impact of the lockdown and make predictions on its future course. Four parameters were used, namely β, γ, η and ε. β measures the likelihood of the susceptible person getting infected, and γ denotes recovery rate of patients. The ratio β/γ is denoted by R0 (basic reproduction number).

RESULTS

The disease spread was reduced due to initial lockdown. An increase in γ reflects healthcare and hospital services, medications and protocols put in place. In Delhi, the predictions from the model were corroborated with July and September serosurveys, which showed antibodies in 23.5 and 33 per cent population, respectively.

INTERPRETATION & CONCLUSIONS

The SAIR model has helped understand the disease better. If the model is correct, we may have reached herd immunity with about 380 million people already infected. However, personal protective measures remain crucial. If there was no lockdown, the number of active infections would have peaked at close to 14.7 million, resulted in more than 2.6 million deaths, and the peak would have arrived by June 2020. The number of deaths with the current trends may be less than 0.2 million.

COVID-19 - pathogenesis and immunological findings across the clinical manifestation spectrum

PURPOSE OF REVIEW

The wide spectrum of COVID-19 clinical manifestations demonstrates the determinant role played by the individual immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the course of the disease. Thanks to the large number of published data, we are beginning to understand the logic of the human response to a virus adapted to bat immunity.

RECENT FINDINGS

Impairment of types I and III interferon responses may facilitate the occurrence of severe COVID-19 with reduced antiviral activity associated to potent inflammation. The human T and B-cell germline repertoire contain the specificities able to react against SARS-CoV-2 antigens. Although inflammation disrupts the structure of germinal centers, memory T and B cells can be found in the blood of patients after mild and severe COVID 19.

SUMMARY

Further studies are indispensable to better understand the human immune response to SARS-CoV-2. The diversity of the individual reaction may contribute to explain the clinical manifestation spectrum. Immunological memory can be demonstrated in patients, convalescent from mild, moderate, or severe COVID-19, but we do not know whether asymptomatic individuals have memory of the virus. Tailored vaccination protocols may be needed for individuals with previous SAS-CoV-2 infection.

Prolonged Viral Shedding in Patients with Mild to Moderate COVID-19 Disease: A Regional Perspective

BACKGROUND

The risk of transmission of Coronavirus Disease 2019 (COVID-19) is increasingly understood to be greatest early after symptom onset, however, factors associated with prolonged and increased risk of transmission remain unclear. In settings where COVID-19 prevalence is low, there may be a benefit of extending the period that patients are isolated to decrease the risk of transmission. This study explored the duration of viral shedding in such a location, in patients with mild-moderate COVID-19 disease in Ballarat, Australia.

METHODS

Patients diagnosed with COVID-19 disease using a real-time reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assay from oropharyngeal and bilateral deep nasopharyngeal sampling and managed through Ballarat Health Services between March 1 and May 1, 2020 were included. Patients were retested if they were afebrile for >72 hours, asymptomatic and >14 days since symptom onset. If positive on retesting, patients were tested every 3 to 7 days thereafter.

RESULTS

Patients underwent testing a median of 4 days (range 1-12) after initial symptom onset. Duration of symptoms ranged from 1 to 36 days. Positive tests were recorded up to a median of day 21 (range 6-38). Cycle thresholds were inversely correlated with time since symptom onset (P < .0001). Median time to the first negative test was 25 days (range 12-32). Two patients who had remained asymptomatic for >7 days after initial symptom onset had recrudescence of mild symptoms on day 13 and 14; both tested positive on follow-up tests at this time.

CONCLUSIONS

This study demonstrates prolonged shedding of COVID-19 in patients with mild-moderate disease. It suggests that some patients with mild disease may have recrudescence of symptoms a week or more after their initial symptoms resolved.

Early Prognostic Indicators of Subsequent Hospitalization in Patients with Mild COVID-19

Comprehensive data on early prognostic indicators in patients with mild COVID-19 remains sparse. In this single center case series, we characterized the initial clinical presentation in 180 patients with mild COVID-19 and defined the earliest predictors of subsequent deterioration and need for hospitalization. Three broad patient phenotypes and four symptom clusters were characterized, differentiated by varying risk for adverse outcomes. Among 14 symptoms assessed, subjective shortness of breath (SOB) most strongly associated with adverse outcomes (odds ratio (OR) 21.3, 95% confidence interval (CI): 2.7–166.4; p < 0.0001). In combination, SOB and number of comorbidities were highly predictive of subsequent hospitalization (area under the curve (AUC) 92%). Additionally, initial lymphopenia (OR 21.0, 95% CI: 2.1–210.1; p = 0.002) and male sex (OR 3.5, 95% CI: 0.9–13.0; p = 0.05) were associated with increased risk of poor outcomes. Patients with known comorbidities, especially multiple, and those presenting with subjective SOB or lymphopenia should receive close monitoring and consideration for preemptive treatment, even when presenting with mild symptoms.

Asthma in Adult Patients with COVID-19. Prevalence and Risk of Severe Disease

Rationale: Health outcomes of people with coronavirus disease (COVID-19) range from no symptoms to severe illness and death. Asthma, a common chronic lung disease, has been considered likely to increase the severity of COVID-19, although data addressing this hypothesis have been scarce until very recently.Objectives: To review the epidemiologic literature related to asthma's potential role in COVID-19 severity.Methods: Studies were identified through the PubMed (MEDLINE) and medRxiv (preprint) databases using the search terms "asthma," "SARS-CoV-2" (severe acute respiratory syndrome coronavirus 2), and "COVID-19," and by cross-referencing citations in identified studies that were available in print or online before December 22, 2020.Measurements and Main Results: Asthma prevalence data were obtained from studies of people with COVID-19 and regional health statistics. We identified 150 studies worldwide that allowed us to compare the prevalence of asthma in patients with COVID-19 by region, disease severity, and mortality. The results of our analyses do not provide clear evidence of increased risk of COVID-19 diagnosis, hospitalization, severity, or mortality due to asthma.Conclusions: These findings could provide some reassurance to people with asthma regarding its potential to increase their risk of severe morbidity from COVID-19.

Zoonotic coronavirus epidemics: Severe acute respiratory syndrome, Middle East respiratory syndrome, and coronavirus disease 2019

OBJECTIVE

To review the virology, immunology, epidemiology, clinical manifestations, and treatment of the following 3 major zoonotic coronavirus epidemics: severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and coronavirus disease 2019 (COVID-19).

DATA SOURCES

Published literature obtained through PubMed database searches and reports from national and international public health agencies.

STUDY SELECTIONS

Studies relevant to the basic science, epidemiology, clinical characteristics, and treatment of SARS, MERS, and COVID-19, with a focus on patients with asthma, allergy, and primary immunodeficiency.

RESULTS

Although SARS and MERS each caused less than a thousand deaths, COVID-19 has caused a worldwide pandemic with nearly 1 million deaths. Diagnosing COVID-19 relies on nucleic acid amplification tests, and infection has broad clinical manifestations that can affect almost every organ system. Asthma and atopy do not seem to predispose patients to COVID-19 infection, but their effects on COVID-19 clinical outcomes remain mixed and inconclusive. It is recommended that effective therapies, including inhaled corticosteroids and biologic therapy, be continued to maintain disease control. There are no reports of COVID-19 among patients with primary innate and T-cell deficiencies. The presentation of COVID-19 among patients with primary antibody deficiencies is variable, with some experiencing mild clinical courses, whereas others experiencing a fatal disease. The landscape of treatment for COVID-19 is rapidly evolving, with both antivirals and immunomodulators demonstrating efficacy.

CONCLUSION

Further data are needed to better understand the role of asthma, allergy, and primary immunodeficiency on COVID-19 infection and outcomes.

Spectrum and Clinical Characteristics of Symptomatic and Asymptomatic Coronavirus Disease 2019 (COVID-19) With and Without Pneumonia

Background: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, has become a global pandemic. Based on symptoms, COVID-19 cases can be classified as symptomatic or asymptomatic. However, there is limited information about the differences between COVID-19 patients with and without pneumonia. Our study aimed to further discuss the spectrum and clinical characteristics of symptomatic and asymptomatic COVID-19 patients with and without pneumonia. Methods: In China, all COVID-19 cases are hospitalized in designated hospitals until two continuous negative oropharyngeal swabs obtained, which allows the professional monitoring of symptoms and clinical characteristics. We stratified all COVID-19 cases in our database and evaluated clinical characteristics in different COVID-19 subgroups (symptomatic with pneumonia, symptomatic without pneumonia, asymptomatic with pneumonia, and asymptomatic without pneumonia). Results: According to symptoms and laboratory and radiologic findings, COVID-19 cases were defined as symptomatic with pneumonia, symptomatic without pneumonia, asymptomatic with pneumonia, or asymptomatic without pneumonia. There were differences in the clinical characteristics and prognosis among the four groups. Both non-invasive mechanical ventilation (18, 4.2%) and invasive mechanical ventilation (11, 2.6%) were applied in only the symptomatic with pneumonia group. Likewise, extracorporeal membrane oxygenation and continuous renal replacement therapy were applied in only the symptomatic with pneumonia group. There were no differences in viral load, the durations of viral shedding, and hospitalization among the four groups. Conclusion: We have defined a comprehensive spectrum of COVID-19 with and without pneumonia. The symptomatic with pneumonia group consumed more medical resources than the other groups, and extra caution and monitoring should be applied in this group. The asymptomatic COVID-19 group had a similar viral load and viral shedding duration as the symptomatic COVID-19 group.

Vaccines: Underlying Principles of Design and Testing

In this paper, we review the key elements that should be considered to take a novel vaccine from the laboratory through to licensure in the modern era. This paper is divided into four sections. First, we discuss the host immune responses that we engage with vaccines. Second, we discuss how in vivo and in vitro studies can inform vaccine design. Third, we discuss different vaccine modalities that have been licensed or are in testing in humans. Last, we overview the basic principles of vaccine approvals. Throughout we provide real-world examples of vaccine development against infectious diseases, including coronavirus disease 2019 (COVID-19).

Is it enough for COVID-19 screening test? Limitation of swab test and general characteristics of mild symptom patients

The most common method for SARS-CoV-2 testing is throat or nasal swabbing by real-time reverse transcription polymerase chain reaction (RT-PCR) assay. In South Korea, drive-through swab test is used for screening system and community treatment centers (CTCs), which admit and treat confirmed COVID-19 patients with mild symptoms, are being used. This retrospective study was conducted on patients admitted to a CTC on March 6, 2020. A total of 313 patients were admitted. The nasal and throat swabs were collected from the upper respiratory tract, and a sputum test was performed to obtain lower respiratory samples. The positive rate of the first set of test, sputum test was higher than that of the swab test (p = 0.011). In the second set of test, 1 week after the first ones, the rate of positive swab tests was relatively high (p = 0.026). In the first set of test, 66 of 152 (43.4%) patients showed 24-h consecutive negative swab test results, when the sputum test results were considered together, that number fell to 29 patients (19.1%) (p < 0.001). Also, in the second set of test, 63 of 164 (38.4%) patients met the discharge criteria only when the swab test was considered; that number fell to 30 (18.3%) when the sputum test results were also considered (p < 0.001). Using the swab test alone is insufficient for screening test and discharge decision. Patients who may have positive result in the sputum test can be missed.

Assessing asymptomatic, pre-symptomatic and symptomatic transmission risk of SARS-CoV-2

BACKGROUND

The relative contributions of asymptomatic, pre-symptomatic and symptomatic transmission of SARS-CoV-2 have not been clearly measured although control measures may differ in response to the risk of spread posed by different types of cases.

METHODS

We collected detailed information on transmission events and symptom status based on laboratory-confirmed patient data and contact tracing data from four provinces and one municipality in China. We estimated the variation in risk of transmission over time, and the severity of secondary infections, by symptomatic status of the infector.

RESULTS

There were 393 symptomatic index cases with 3136 close contacts and 185 asymptomatic index cases with 1078 close contacts included into the study. The secondary attack rate among close contacts of symptomatic and asymptomatic index cases were 4.1% (128/3136) and 1.1% (12/1078), respectively, corresponding to a higher transmission risk from symptomatic cases than from asymptomatic cases (OR: 3.79, 95% CI: 2.06, 6.95). Approximately 25% (32/128) and 50% (6/12) of the infected close contacts were asymptomatic from symptomatic and asymptomatic index cases, respectively, while more than one third (38%) of the infections in the close contacts of symptomatic cases were attributable to exposure to the index cases before symptom onset. Infected contacts of asymptomatic index cases were more likely to be asymptomatic and less likely to be severe.

CONCLUSIONS

Asymptomatic and pre-symptomatic transmission play an important role in spreading infection, although asymptomatic cases pose a lower risk of transmission than symptomatic cases. Early case detection and effective test-and-trace measures are important to reduce transmission.

Spike vs nucleocapsid SARS-CoV-2 antigen detection: application in nasopharyngeal swab specimens

Public health experts emphasize the need for quick, point-of-care SARS-CoV-2 detection as an effective strategy for controlling virus spread. To this end, many “antigen” detection devices were developed and commercialized. These devices are mostly based on detecting SARS-CoV-2’s nucleocapsid protein. Recently, alerts issued by both the FDA and the CDC raised concerns regarding the devices’ tendency to exhibit false positive results. In this work, we developed a novel alternative spike-based antigen assay, comprising four high-affinity, specific monoclonal antibodies, directed against different epitopes on the spike’s S1 subunit. The assay’s performance was evaluated for COVID-19 detection from nasopharyngeal swabs, compared to an in-house nucleocapsid-based assay, composed of novel antibodies directed against the nucleocapsid. Detection of COVID-19 was carried out in a cohort of 284 qRT-PCR positive and negative nasopharyngeal swab samples. The time resolved fluorescence (TRF) ELISA spike assay displayed very high specificity (99%) accompanied with a somewhat lower sensitivity (66% for Ct < 25), compared to the nucleocapsid ELISA assay which was more sensitive (85% for Ct < 25) while less specific (87% specificity). Despite being outperformed by qRT-PCR, we suggest that there is room for such tests in the clinical setting, as cheap and rapid pre-screening tools. Our results further suggest that when applying antigen detection, one must consider its intended application (sensitivity vs specificity), taking into consideration that the nucleocapsid might not be the optimal target. In this regard, we propose that a combination of both antigens might contribute to the validity of the results.

Continued proportional age shift of confirmed positive COVID-19 incidence over time to children and young adults: Washington State March-August 2020

BACKGROUND

As the coronavirus (COVID-19) epidemic passed initial infection peak in Washington State, phased re-opening lifted stay-at-home orders and restrictions leading to increased non-essential work, social activities and gathering, especially among younger persons.

METHODS

A longitudinal cohort analysis of Washington State Department of Health COVID-19 confirmed case age distribution 1) March-April 2020 (N = 13,934) and 2) March-August 2020 (N = 76,032) for proportional change over time using chi square tests for significance.

RESULTS

From March 1st to April 19, 2020 COVID-19 age distribution shifted with a 10% decline in cases age 60 years and older and a 20% increase in age 0-19/20-39 years (chi-square = 223.10, p < .001). Number of cases over the initial analysis period were 0-19 years n = 515, 20-39 years n = 4078, 40-59 years n = 4788, 60-79 years n = 3221, 80+ years n = 1332. After the peak (March 22, 2020), incidence declined in older age groups and increased among age 0-19 and 20-39 age groups from 20% to 40% of total cases by April 19 and 50% by May 3. During this time testing expanded with more testing among older age groups and less testing among younger age groups while case positivity shifted young. Percent positive cases age 0-19/20-39 years through August 2020 increased to a consistent average of 60% [age 0-19 increased to 19% (N = 10257), age 20-39 increased to 42% (N = 30215)].

CONCLUSIONS

An increased sustained proportion of COVID-19 incidence is present among children (age 0-19) and young adults (age 20-39) indicating an elevated role in disease spread during the epidemic creating a possible reservoir of disease with spillover risk to more vulnerable older persons and those with comorbid conditions. Media savvy age-appropriate messaging to enhance mitigation compliance among less vulnerable, more mobile and lower priority vaccination age groups will be a continued necessity and priority to reduce overall population incidence.

SARS-CoV-2 viral load dynamics and real-time RT-PCR cycle threshold interpretation in symptomatic non-hospitalised individuals in New Zealand: a multicentre cross sectional observational study

We conducted a multicentre cross sectional observational study of laboratory, public health and hospitalisation data for PCR-confirmed COVID-19 cases within the New Zealand Northern Region, between 12 February and 8 June 2020. The aim of this study was to describe population level SARS-CoV-2 upper respiratory tract (URT) viral load dynamics by stratifying positivity rates and polymerase chain reaction (PCR) cycle threshold (Ct) values of URT samples from COVID-19 cases by days since symptom onset, and to explore utility of Ct values in determining length of time post-infection and thus potential infectivity.

Of 123,124 samples tested for SARS-CoV-2 by PCR, 579 samples (407 positive and 172 negative) from 368 symptomatic non-hospitalised individuals with PCR-confirmed infection were included. Sample positivity rate was 61.5% (8/13) for pre-symptomatic samples, rising to 93.2% (317/340) for samples collected during the purported symptomatic infectious period (days 0–10 post-symptom onset), and dropping to 36.3% (82/226) for post-infectious period samples (day 11 onwards). URT viral load peaked shortly after symptom onset, with median Ct values ranging 20.00–29.99 until 15 days post-symptom onset, and >30.00 after this time. Of samples with a Ct value of <20.00, 96.1% were collected during the symptomatic infectious period. However, of samples with a Ct value ≥30.00 and ≥35.00, 46.9% and 18.5%, respectively, were also collected during the symptomatic infectious period.

The findings of this study indicate that at or soon after symptom onset represents the optimum time to test for SARS-CoV-2 in the URT, with median Ct values suggesting the useful testing window extends until around 15 days post-symptom onset. In asymptomatic individuals or those with unknown dates of symptom onset, Ct values <20.00 imply recent onset/potential infectivity, but Ct values ≥30.00 or ≥35.00 do not exclude recent onset/potential infectivity. Individual sample Ct values should not be used as an absolute marker of length of time post-infection or to exclude infectivity where date of symptom onset is unavailable.

Characteristics of Viral Shedding Time in SARS-CoV-2 Infections: A Systematic Review and Meta-Analysis

Background: The viral shedding time (VST) of SARS-CoV-2 mainly determines its transmission and duration of infectiousness. However, it was heterogeneous in the existing studies. Here, we performed a meta-analysis to comprehensively summarize the VST of SARS-CoV-2. Methods: We searched PubMed, Web of Science, MedRxiv, BioRxiv, CNKI, CSTJ, and Wanfang up to October 25, 2020, for studies that reported VSTs of SARS-CoV-2. Pooled estimates and 95% CIs for the VSTs were calculated using log-transformed data. The VSTs in SARS-CoV-2 infections based on different demographic and clinical characteristics, treatments and specimens were stratified by subgroup analysis. Results: A total of 35 studies involving 3,385 participants met the inclusion criteria. The pooled mean VST was 16.8 days (95% CI: 14.8-19.4, I2 = 99.56%) in SARS-CoV-2 infections. The VST was significantly longer in symptomatic infections (19.7 days, 95% CI: 17.2-22.7, I2 = 99.34%) than in asymptomatic infections (10.9 days, 95% CI: 8.3-14.3, I2 = 98.89%) (P < 0.05). The VST was 23.2 days (95% CI: 19.0-28.4, I2 = 99.24%) in adults, which was significantly longer than that in children (9.9 days, 95% CI: 8.1-12.2, I2 = 85.74%) (P < 0.05). The VST was significantly longer in persons with chronic diseases (24.2 days, 95% CI: 19.2-30.2, I2 = 84.07%) than in those without chronic diseases (11.5 days, 95% CI: 5.3-25.0, I2 = 82.11%) (P < 0.05). Persons receiving corticosteroid treatment (28.3 days, 95% CI: 25.6-31.2, I2 = 0.00%) had a longer VST than those without corticosteroid treatment (16.2 days, 95% CI: 11.5-22.5, I2 = 92.27%) (P = 0.06). The VST was significantly longer in stool specimens (30.3 days, 95% CI: 23.1-39.2, I2 = 92.09%) than in respiratory tract specimens (17.5 days, 95% CI: 14.9-20.6, I2 = 99.67%) (P < 0.05). Conclusions: A longer VST was found in symptomatic infections, infected adults, persons with chronic diseases, and stool specimens.