COVID-19-Lessons Learned and Questions Remaining

Study protocol: infectious diseases consortium (I3D) for study on integrated and innovative approaches for management of respiratory infections: respiratory infections research and outcome study (RESPIRO)

BACKGROUND

Community-acquired respiratory infections are a leading cause of illness and death globally. The aetiologies of community-acquired pneumonia remain poorly defined. The RESPIRO study is an ongoing prospective observational cohort study aimed at developing pragmatic logistical and analytic platforms to accurately identify the causes of moderate-to-severe community-acquired pneumonia in adults and understand the factors influencing disease caused by individual pathogens. The study is currently underway in Singapore and has plans for expansion into the broader region.

METHODS

RESPIRO is being conducted at three major tertiary hospitals in Singapore. Adults hospitalised with acute community-acquired pneumonia or lower respiratory tract infections, based on established clinical, laboratory and radiological criteria, will be recruited. Over the course of the illness, clinical data and biological samples will be collected longitudinally and stored in a biorepository for future analysis.

DISCUSSION

The RESPIRO study is designed to be hypothesis generating, complementary to and easily integrated with other research projects and clinical trials. The detailed clinical database and biorepository will yield insights into the epidemiology and outcomes of community-acquired lower respiratory tract infections in Singapore and the surrounding region and offers the opportunity to deeply characterise the microbiology and immunopathology of community-acquired pneumonia.

Non-Pharmacological Strategies and Interventions for Effective COVID-19 Control: A Narrative Review

The COVID-19 pandemic had a devastating impact on the world, causing widespread illness and death. Focusing on prevention strategies to limit the spread of the disease remains essential. Despite the advent of vaccines, maintaining a vigilant approach to prevention remains paramount. We reviewed effective strategies to prevent COVID-19 transmission, including various prevention measures and interventions and both established practices and unresolved issues that have been addressed in meta-analyses, literature reviews, or in the health care context. Standard precautions are the cornerstone of infection control, with hand hygiene and mask use as key components. The use of surgical masks is recommended to prevent droplet transmission, while eye protection is recommended in combination with masks. In terms of room occupancy, ventilation is critical in reducing the risk of transmission in poorly ventilated environments. Chemical disinfection of indoor air with Triethylene glycol-based products can provide safe additional protection. Since viral RNA detection on surfaces does not necessarily indicate infectivity, the risk of transmission by surface contact remains low if surfaces are properly maintained and hand hygiene is practiced regularly. Thus, prevention of SARS-CoV-2 transmission requires a multifaceted approach, including reducing particle emissions from infected persons by wearing masks, eliminating aerosols by ventilation and air treatment, ensuring physical separation, and protecting exposed persons with masks and eye protection.

Dynamics of Gene Expression Profiling and Identification of High-Risk Patients for Severe COVID-19

The clinical manifestations of SARS-CoV-2 infection vary widely, from asymptomatic infection to the development of acute respiratory distress syndrome (ARDS) and death. The host response elicited by SARS-CoV-2 plays a key role in determining the clinical outcome. We hypothesized that determining the dynamic whole blood transcriptomic profile of hospitalized adult COVID-19 patients and characterizing the subgroup that develops severe disease and ARDS would broaden our understanding of the heterogeneity in clinical outcomes. We recruited 60 hospitalized patients with RT-PCR-confirmed SARS-CoV-2 infection, among whom 19 developed ARDS. Peripheral blood was collected using PAXGene RNA tubes within 24 h of admission and on day 7. There were 2572 differently expressed genes in patients with ARDS at baseline and 1149 at day 7. We found a dysregulated inflammatory response in COVID-19 ARDS patients, with an increased expression of genes related to pro-inflammatory molecules and neutrophil and macrophage activation at admission, in addition to an immune regulation loss. This led, in turn, to a higher expression of genes related to reactive oxygen species, protein polyubiquitination, and metalloproteinases in the latter stages. Some of the most significant differences in gene expression found between patients with and without ARDS corresponded to long non-coding RNA involved in epigenetic control.

Association between COVID-19 and consistent mask wearing during contact with others outside the household-A nested case-control analysis, November 2020-October 2021

BACKGROUND

Face masks have been recommended to reduce SARS-CoV-2 transmission. However, evidence of the individual benefit of face masks remains limited, including by vaccination status.

METHODS

As part of the COVID-19 Community Research Partnership cohort study, we performed a nested case-control analysis to assess the association between self-reported consistent mask use during contact with others outside the household and subsequent odds of symptomatic SARS-CoV-2 infection (COVID-19) during November 2020-October 2021. Using conditional logistic regression, we compared 359 case-participants to 3544 control-participants who were matched by date, adjusting for enrollment site, age group, sex, race/ethnicity, urban/rural county classification, and healthcare worker occupation.

RESULTS

COVID-19 was associated with not consistently wearing a mask (adjusted odds ratio [aOR] 1.49; 95% confidence interval [CI] [1.14, 1.95]). Compared with persons ≥14 days after mRNA vaccination who also reported always wearing a mask, COVID-19 was associated with being unvaccinated (aOR 5.94; 95% CI [3.04, 11.62]), not wearing a mask (aOR 1.62; 95% CI [1.07, 2.47]), or both unvaccinated and not wearing a mask (aOR 9.07; 95% CI [4.81, 17.09]).

CONCLUSIONS

Our findings indicate that consistent mask wearing can complement vaccination to reduce the risk of COVID-19.

Living with COVID-19 and preparing for future pandemics: revisiting lessons from the HIV pandemic

In April, 2020, just months into the COVID-19 pandemic, an international group of public health researchers published three lessons learned from the HIV pandemic for the response to COVID-19, which were to: anticipate health inequalities, create an enabling environment to support behavioural change, and engage a multidisciplinary effort. We revisit these lessons in light of more than 2 years' experience with the COVID-19 pandemic. With specific examples, we detail how inequalities have played out within and between countries, highlight factors that support or impede the creation of enabling environments, and note ongoing issues with the scarcity of integrated science and health system approaches. We argue that to better apply lessons learned as the COVID-19 pandemic matures and other infectious disease outbreaks emerge, it will be imperative to create dialogue among polarised perspectives, identify shared priorities, and draw on multidisciplinary evidence.

Hospital-Based Quasi-Experimental Study on Hydroxychloroquine Pre-Exposure Prophylaxis for COVID-19 in Healthcare Providers with Its Potential Side-Effects

Considering that it has been more than 24 months since SARS-CoV-2 emerged, it is crucial to identify measures that prevent and control pathogen transmission in workplace settings. Our aim was to report results of a hospital-based program that delivered hydroxychloroquine (HCQ) tablets as COVID-19 prophylaxis to the frontline healthcare workers (HCW)s who cared for COVID-19 patients and to evaluate the efficacy of HCQ. Setting and participants: Quasi-experimental, controlled, single-center study. The included participants were doctors, nurses, health workers, cleaning staff, and non-healthcare supportive staff. The main outcome was contracting COVID-19 anytime during the period of taking the prophylaxis, confirmed by RT-PCR. A total of 336 participants, without any clinical evidence of COVID-19 and without any known contact with family members, were included in the trial; 230 were assigned to HCQ and 106 declined to take any drug. Results: Among the participants, 43 (18.7%) in the HCQ group and 11 (10.4%) participants in the control group developed COVID-19. For the evaluation of side effects, we evaluated 12-lead ECGs of both groups at the baseline and after 4 weeks to monitor QTc interval. A total of 91% (198 of 217) participants in the prophylaxis group and 92% (11 of 12) in the control group had a QTc < 45o msec, which is within normal limits. Conclusions: Although the number of symptomatic infections in health personnel was lower in the control group, the difference was not statistically significant. However, in the absence of any effective pre-exposure prophylaxis medicine for COVID-19, practicing proper infection prevention and control (IPC) and vaccination is the only way forward.

Building Process-Oriented Data Science Solutions for Real-World Healthcare

The COVID-19 pandemic has highlighted some of the opportunities, problems and barriers facing the application of Artificial Intelligence to the medical domain. It is becoming increasingly important to determine how Artificial Intelligence will help healthcare providers understand and improve the daily practice of medicine. As a part of the Artificial Intelligence research field, the Process-Oriented Data Science community has been active in the analysis of this situation and in identifying current challenges and available solutions. We have identified a need to integrate the best efforts made by the community to ensure that promised improvements to care processes can be achieved in real healthcare. In this paper, we argue that it is necessary to provide appropriate tools to support medical experts and that frequent, interactive communication between medical experts and data miners is needed to co-create solutions. Process-Oriented Data Science, and specifically concrete techniques such as Process Mining, can offer an easy to manage set of tools for developing understandable and explainable Artificial Intelligence solutions. Process Mining offers tools, methods and a data driven approach that can involve medical experts in the process of co-discovering real-world evidence in an interactive way. It is time for Process-Oriented Data scientists to collaborate more closely with healthcare professionals to provide and build useful, understandable solutions that answer practical questions in daily practice. With a shared vision, we should be better prepared to meet the complex challenges that will shape the future of healthcare.

Features of antibody responses after SARS-COV-2 infection in healthcare workers in the first wave of COVID-19 pandemic in Mexico City

Objective

To investigate the antibody response to SARS-CoV-2 and identify associated factors in frontline and second-line healthcare workers (HCWs) at a large hospital in Mexico City during the first wave of COVID-19 pandemic.

Methods

This was a cross-sectional study of HCWs returning to work following mandatory isolation after recovering from COVID-19. Immunoglobulin (Ig) M and IgG antibodies elicited by SARS-CoV-2 were semiquantitatively measured using densitometric analysis of band intensities in lateral flow assay (LFA) devices. The mean pixel intensity (dots-per-inch [dpi]) of each band on the LFA was considered a measure of antibody titre.

Results

Of the 111 HCWs involved in the study, antibody responses were detected in 73/111 (66%) participants. Severe COVID symptoms was associated with old age. No differences in IgM intensity were observed between men and women, but IgG intensity was significantly higher in men than in women. Second-line HCWs produced a higher IgG intensity than firstline HCWs. The IgG intensity was high in severe cases.

Conclusions

For HCWs who may acquire SARS-CoV-2 infection, it is necessary to establish a routine program for detection of the virus to avoid risk of infection and spread of COVID-19.

SARS-CoV-2 Transmission and Prevention in the Era of the Delta Variant

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) delta variant transmits much more rapidly than prior SARS-CoV-2 viruses. The primary mode of transmission is via short range aerosols that are emitted from the respiratory tract of an index case. There is marked heterogeneity in the spread of this virus, with 10% to 20% of index cases contributing to 80% of secondary cases, while most index cases have no subsequent transmissions. Vaccination, ventilation, masking, eye protection, and rapid case identification with contact tracing and isolation can all decrease the transmission of this virus.

COVID-19: the case for aerosol transmission

The COVID-19 pandemic is the most severe pandemic caused by a respiratory virus since the 1918 influenza pandemic. As is the case with other respiratory viruses, three modes of transmission have been invoked: contact (direct and through fomites), large droplets and aerosols. This narrative review makes the case that aerosol transmission is an important mode for COVID-19, through reviewing studies about bioaerosol physiology, detection of infectious SARS-CoV-2 in exhaled bioaerosols, prolonged SARS-CoV-2 infectivity persistence in aerosols created in the laboratory, detection of SARS-CoV-2 in air samples, investigation of outbreaks with manifest involvement of aerosols, and animal model experiments. SARS-CoV-2 joins influenza A virus as a virus with proven pandemic capacity that can be spread by the aerosol route. This has profound implications for the control of the current pandemic and for future pandemic preparedness.

Longitudinal SARS-CoV-2 Testing among the Unvaccinated Is Punctuated by Intermittent Positivity and Variable Rates of Increasing Cycle Threshold Values

The coronavirus disease 2019 (COVID-19) pandemic is complicated by cases of vaccine breakthrough and reinfection and widespread transmission of variants of concern (VOCs). Consequently, the need to interpret longitudinal positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tests is crucial in guiding clinical decisions regarding infection control precautions and treatment. Although diagnostic real-time reverse transcription (RT)-PCR tests yield C_T values that are inversely correlated with RNA quantity, these tests are only approved for qualitative interpretation. In this study, we performed a retrospective review of 72,217 SARS-CoV-2 positive tests and identified 264 patients with longitudinal positivity prior to vaccination and VOC circulation. Patients with longitudinal positivity fell into two categories: short-term (207, 78%) or prolonged (57, 22%) positivity, defined as ≤28 (range, 1 to 28; median, 16) days and >28 (range, 29 to 152; median, 41) days, respectively. In general, C_T values increased over time in both groups; however, 11 short-term-positive patients had greater amounts of RNA detected at their terminal test than at the first positive test, and 6 patients had RNA detected at C_T values of <35 at least 40 days after initial infection. Oscillating positive and negative results occurred in both groups, although oscillation was seen three times more frequently in prolonged-positive patients. Patients with prolonged positivity had diverse clinical characteristics but were often critically ill and were discharged to high-level care or deceased (22%). Overall, this study demonstrates that caution must be emphasized when interpreting C_T values as a proxy for infectivity, a predictor of severity, or a guide for patient care decisions in the absence of additional clinical context, particularly among the unvaccinated population. IMPORTANCE We describe the duration of positivity and the COVID-19 treatment and outcome characteristics of an unvaccinated population of patients with prolonged SARS-CoV-2 positivity. This investigation serves to highlight challenges in using C_T values to guide clinical decisions among unvaccinated individuals.

SARS-CoV-2 and Coronavirus Disease Mitigation: Treatment Options, Vaccinations and Variants

COVID-19 is caused by a novel coronavirus (2019-nCoV), which was declared as a pandemic after it emerged in China 2019. A vast international effort has been conducted to prevent and treat COVID-19 due to its high transmissibility and severe morbidity and mortality rates, particularly in individuals with chronic co-morbidities. In addition, polymorphic variants increased the need for proper vaccination to overcome the infectivity of new variants that are emerging across the globe. Many treatment options have been proposed and more than 25 vaccines are in various stages of development; however, the infection peaks are oscillating periodically, which raises a significant question about the effectiveness of the prevention measures and the persistence of this pandemic disease. In this review, we are exploring the most recent knowledge and advances in the treatment and vaccination options as well as the new emerging variants of 2019-nCoV and the possible mitigation of one of the most aggressive pandemics in the last centuries.

A Personal Respirator to Improve Protection for Healthcare Workers Treating COVID-19 (PeRSo)

Introduction: SARS-CoV-2 infection is a global pandemic. Personal Protective Equipment (PPE) to protect healthcare workers has been a recurrent challenge in terms of global stocks, supply logistics and suitability. In some settings, around 20% of healthcare workers treating COVID-19 cases have become infected, which leads to staff absence at peaks of the pandemic, and in some cases mortality.

Methods: To address shortcomings in PPE, we developed a simple powered air purifying respirator, made from inexpensive and widely available components. The prototype was designed to minimize manufacturing complexity so that derivative versions could be developed in low resource settings with minor modification.

Results: The “Personal Respirator – Southampton” (PeRSo) delivers High-Efficiency Particulate Air (HEPA) filtered air from a battery powered fan-filter assembly into a lightweight hood with a clear visor that can be comfortably worn for several hours. Validation testing demonstrates that the prototype removes microbes, avoids excessive CO₂ build-up in normal use, and passes fit test protocols widely used to evaluate standard N95/FFP2 and N99/FFP3 face masks. Feedback from doctors and nurses indicate the PeRSo prototype was preferred to standard FFP2 and FFP3 masks, being more comfortable and reducing the time and risk of recurrently changing PPE. Patients report better communication and reassurance as the entire face is visible.

Conclusion: Rapid upscale of production of cheaply produced powered air purifying respirators, designed to achieve regulatory approval in the country of production, could protect healthcare workers from infection and improve healthcare delivery during the COVID-19 pandemic.

In-Depth Longitudinal Comparison of Clinical Specimens to Detect SARS-CoV-2

The testing and isolation of patients with coronavirus disease 2019 (COVID-19) are indispensable tools to control the ongoing COVID-19 pandemic. PCR tests are considered the “gold standard” of COVID-19 testing and mostly involve testing nasopharyngeal swab specimens. Our study aimed to compare the sensitivity of tests for various sample specimens. Seventy-five participants with confirmed COVID-19 were included in the study. Nasopharyngeal swabs, oropharyngeal swabs, Oracol-collected saliva, throat washes and rectal specimens were collected along with pooled swabs. Participants were asked to complete a questionnaire to correlate specific clinical symptoms and the symptom duration with the sensitivity of detecting COVID-19 in various sample specimens. Sampling was repeated after 7 to 10 days (T2), then after 14 to 20 days (T3) to perform a longitudinal analysis of sample specimen sensitivity. At the first time point, the highest percentages of SARS-CoV-2-positive samples were observed for nasopharyngeal samples (84.3%), while 74%, 68.2%, 58.8% and 3.5% of throat washing, Oracol-collected saliva, oropharyngeal and rectal samples tested positive, respectively. The sensitivity of all sampling methods except throat wash samples decreased rapidly at later time points compared to the first collection. The throat washing method exhibited better performance than the gold standard nasopharyngeal swab at the second and third time points after the first positive test date. Nasopharyngeal swabs were the most sensitive specimens for early detection after symptom onset. Throat washing is a sensitive alternative method. It was found that SARS-CoV-2 persists longer in the throat and saliva than in the nasopharynx.

Transmission of SARS-CoV-2 After COVID-19 Screening and Mitigation Measures for Primary School Children Attending School in Liège, Belgium

IMPORTANCE

Recent data suggest a relatively low incidence of COVID-19 among children. The possible role that children attending primary school may play in the transmission of SARS-CoV-2 remains poorly understood.

OBJECTIVE

To gain a better understanding of the possible role of children in the transmission of SARS-CoV-2.

DESIGN, SETTING, AND PARTICIPANTS

This prospective cohort study was conducted from September 21 to December 31, 2020, in a primary school in Liège, Belgium, among a volunteer sample of 181 children, parents, and school employees.

EXPOSURES

Participants were tested for SARS-CoV-2 infection once a week for 15 weeks through throat washing, performed with 5 mL of saline and collected in a sterile tube after approximately 30 seconds of gargling. Quantitative reverse transcription-polymerase chain reaction was performed to detect SARS-CoV-2 infection.

MAIN OUTCOMES AND MEASURES

In case of test positivity, participants were asked to complete a questionnaire aimed at determining the timing of symptom onset and symptom duration. SARS-CoV-2 genetic sequencing was also performed. Confirmed cases were linked based on available information on known contacts and viral sequences.

RESULTS

A total of 181 individuals participated in this study, including 63 children (34 girls [54.0%]; mean [SD] age, 8.6 [1.9] years [range, 5-13 years]) and 118 adults (75 women [63.6%]; mean [SD] age, 42.5 [5.7] years [range, 30-59 years]). Forty-five individuals (24.9%) tested positive: 13 children (20.6%; 95% CI, 10.6%-30.6%) and 32 adults (27.1%; 95% CI, 19.1%-35.7%) (P = .34). Children were more often asymptomatic compared with adults (6 [46.2%; 95% CI, 19.1%-73.3%] vs 4 of 31 [12.9%; 95% CI, 1.3%-24.5%]; P = .04). The median duration of symptoms was shorter in children than in adults (0.00 days [IQR, 0.00-1.00 days] vs 15.00 days [IQR, 7.00-22.00 days]). A reconstruction of the outbreak revealed that most transmission events occurred between teachers and between children within the school. Of the observed household transmission events, most seemed to have originated from a child or teacher who acquired the infection at school.

CONCLUSIONS AND RELEVANCE

Despite the implementation of several mitigation measures, the incidence of COVID-19 among children attending primary school in this study was comparable to that observed among teachers and parents. Transmission tree reconstruction suggests that most transmission events originated from within the school. Additional measures should be considered to reduce the transmission of SARS-CoV-2 at school, including intensified testing.

SARS-CoV-2 vaccination in solid-organ transplant recipients: What the clinician needs to know

In response to the COVID-19 pandemic, SARS-CoV-2 vaccines have been developed at an unparalleled speed, with 14 SARS-CoV-2 vaccines currently authorized. Solid-organ transplant (SOT) recipients are at risk for developing a higher rate of COVID-19-related complications and therefore they are at priority for immunization against SARS-CoV-2. Preliminary data suggest that although SARS-CoV-2 vaccines are safe in SOT recipients (with similar rate of adverse events than in the general population), the antibody responses are decreased in this population. Risk factors for poor vaccine immunogenicity include older age, shorter time from transplantation, use of mycophenolate and belatacept, and worse allograft function. SOT recipients should continue to be advised to maintain hand hygiene, use of facemasks, and social distancing after SARS-CoV-2 vaccine. Vaccination of household contacts should be also prioritized. Although highly encouraged for research purposes, systematic assessment in clinical practice of humoral and cellular immune responses after SARS-CoV-2 vaccination is controversial, since correlation between immunological findings and clinical protection from severe COVID-19, and cutoffs for protection are currently unknown in SOT recipients. Alternative immunization schemes, including a booster dose, higher doses, and modulation of immunosuppression during vaccination, need to be assessed in the context of well-designed clinical trials.

Aerosol SARS-CoV-2 in hospitals and long-term care homes during the COVID-19 pandemic

BACKGROUND

Few studies have quantified aerosol concentrations of SARS-CoV-2 in hospitals and long-term care homes, and fewer still have examined samples for viability. This information is needed to clarify transmission risks beyond close contact.

METHODS

We deployed particulate air samplers in rooms with COVID-19 positive patients in hospital ward and ICU rooms, rooms in long-term care homes experiencing outbreaks, and a correctional facility experiencing an outbreak. Samplers were placed between 2 and 3 meters from the patient. Aerosol (small liquid particles suspended in air) samples were collected onto gelatin filters by Ultrasonic Personal Air Samplers (UPAS) fitted with <2.5μm (micrometer) and <10 μm size-selective inlets operated for 16 hours (total 1.92m3), and with a Coriolis Biosampler over 10 minutes (total 1.5m3). Samples were assayed for viable SARS-CoV-2 virus and for the viral genome by multiplex PCR using the E and N protein target sequences. We validated the sampling methods by inoculating gelatin filters with viable vesicular stomatitis virus (VSV), and with three concentrations of viable SARS-CoV-2, operating personal samplers for 16hrs, and quantifying viable virus recovery by TCID50 assay.

RESULTS

In total, 138 samples were collected from 99 rooms. RNA samples were positive in 9.1% (6/66) of samples obtained with the UPAS 2.5μm samplers, 13.5% (7/52) with the UPAS 10μm samplers, and 10.0% (2/20) samples obtained with the Coriolis samplers. Culturable virus was not recovered in any samples. Viral RNA was detected in 15.1% of the rooms sampled. There was no significant difference in viral RNA recovery between the different room locations or samplers. Method development experiments indicated minimal loss of SARS-CoV-2 viability via the personal air sampler operation.

Critical Capability Needs for Reduction of Transmission of SARS-CoV-2 Indoors

Coordination of efforts to assess the challenges and pain points felt by industries from around the globe working to reduce COVID-19 transmission in the indoor environment as well as innovative solutions applied to meet these challenges is mandatory. Indoor infectious viral disease transmission (such as coronavirus, norovirus, influenza) is a complex problem that needs better integration of our current knowledge and intervention strategies. Critical to providing a reduction in transmission is to map the four core technical areas of environmental microbiology, transmission science, building science, and social science. To that end a three-stage science and innovation Summit was held to gather information on current standards, policies and procedures applied to reduce transmission in built spaces, as well as the technical challenges, science needs, and research priorities. The Summit elucidated steps than can be taken to reduce transmission of SARS-CoV-2 indoors and calls for significant investments in research to enhance our knowledge of viral pathogen persistence and transport in the built environment, risk assessment and mitigation strategy such as processes and procedures to reduce the risk of exposure and infection through building systems operations, biosurveillance capacity, communication form leadership, and stakeholder engagement for optimal response. These findings reflect the effective application of existing knowledge and standards, emerging science, and lessons-learned from current efforts to confront SARS-CoV-2.

Comparison of SARS-CoV-2 PCR-Based Detection Using Saliva or Nasopharyngeal Swab Specimens in Asymptomatic Populations

The coronavirus disease 2019 (COVID-19) pandemic has challenged clinical diagnostic operations due to supply shortages and high staffing needs to collect nasopharyngeal (NP) swab samples. Saliva is an easily accessible alternative specimen type to overcome some of these challenges. In this study, we first used paired saliva and NP swab specimens (n = 128) to compare test performance characteristics with three RNA extraction platforms, i.e., Maxwell RSC (Promega), MagNA Pure 96 (Roche), and KingFisher Flex (Thermo Fisher Scientific), together with two PCR chemistries, i.e., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (2019-nCoV) Centers for Disease Control and Prevention (CDC) quantitative PCR (qPCR) probe assay (Integrated DNA Technologies) and TagPath COVID-19 combination kit (Thermo Fisher Scientific). This study demonstrated that both saliva and NP swab specimens performed well, with 97% agreement when tested by the CDC qPCR chemistry using Maxwell and MagNA Pure RNA extraction platforms. We then compared 12 weeks of saliva and NP swab testing results using two independent asymptomatic populations, including a community surveillance program using saliva samples only (n = 466) and preoperative screening using NP swab samples only (n = 8,461). The positive detection rates among participants with either saliva or NP swab samples were 1.07% and 1.12%, respectively, which confirms the low pretest probabilities for COVID-19 infections in asymptomatic populations. Notably, there was no increased proportion of low-titer cases (inconclusive results) reported in the asymptomatic groups, compared with the all-comers groups (0.21% and 0.66%, respectively, in the community population and 0.25% and 0.49%, respectively, in the preoperative population); this suggests that low-viral-titer carriers can be found similarly in both groups with saliva or NP swab specimens. In summary, saliva can be considered a good alternative for noninvasive but well-instructed self-collection.

IMPORTANCE Our study shows that saliva is a noninvasive respiratory secretion sample type that contains equal or more host materials (RNase P), compared with those contained in the corresponding NP swab specimens, in 103 paired samples. SARS-CoV-2 detection with two RNA extraction platforms, Maxwell and MagNA Pure, with CDC qPCR chemistry showed similar test sensitivities for paired specimens. We then analyzed SARS-CoV-2 detections rates in two independent groups of asymptomatic participants, i.e., a group at a community screening station with supervised saliva collection only (n = 466) and a preoperative screening group (n = 8,461) with NP swabbing only. Similar detection rates of 1.07% for the community group and 1.12% for the preoperative group supported the similar test performances in these groups predicted to have low pretest probabilities of infection. With mindful preparation, saliva can be considered for schools and clinical participants when adequate collection education can be provided and compliance can be established.

A review of mathematical model-based scenario analysis and interventions for COVID-19

Mathematical model-based analysis has proven its potential as a critical tool in the battle against COVID-19 by enabling better understanding of the disease transmission dynamics, deeper analysis of the cost-effectiveness of various scenarios, and more accurate forecast of the trends with and without interventions. However, due to the outpouring of information and disparity between reported mathematical models, there exists a need for a more concise and unified discussion pertaining to the mathematical modeling of COVID-19 to overcome related skepticism. Towards this goal, this paper presents a review of mathematical model-based scenario analysis and interventions for COVID-19 with the main objectives of (1) including a brief overview of the existing reviews on mathematical models, (2) providing an integrated framework to unify models, (3) investigating various mitigation strategies and model parameters that reflect the effect of interventions, (4) discussing different mathematical models used to conduct scenario-based analysis, and (5) surveying active control methods used to combat COVID-19.

An outbreak caused by the SARS-CoV-2 Delta variant (B.1.617.2) in a secondary care hospital in Finland, May 2021

An outbreak caused by the SARS-CoV-2 Delta variant (B.1.617.2) spread from one inpatient in a secondary care hospital to three primary care facilities, resulting in 58 infections including 18 deaths in patients and 45 infections in healthcare workers (HCW). Only one of the deceased cases was fully vaccinated. Transmission occurred despite the use of personal protective equipment by the HCW, as advised in national guidelines, and a high two-dose COVID-19 vaccination coverage among permanent staff members in the COVID-19 cohort ward.

Safety and Reverence: How Roman Catholic Liturgy Can Respond to the COVID-19 Pandemic

The current COVID-19 pandemic is a major challenge for many religious denominations. The Roman Catholic Church strongly depends on physical communal worship and sacraments. Disagreements grow concerning the best balance between safety and piety. To address this issue, I review the major transmission risks for the SARS-CoV-2 virus and list certain measures to enhance the safety of the Roman Catholic Liturgy without compromising its intrinsic beauty and reverent spiritual attitude. This can be achieved through assimilation of several traditional elements into the modern liturgy. I emphasize that religious leadership and decision-making should be transparent and based on inclusiveness, pluralism, best scientific evidence and voluntary cooperation.

Long-term clinical follow-up of patients suffering from moderate-to-severe COVID-19 infection: a monocentric prospective observational cohort study

Objectives

Various symptoms and considerable organ dysfunction persist following infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Uncertainty remains about the potential mid- and long-term health sequelae. This prospective study of patients hospitalized with coronavirus disease 2019 (COVID-19) in Liège University Hospital, Belgium aimed to determine the persistent consequences of COVID-19.

Methods

Patients admitted to the University Hospital of Liège with moderate-to-severe confirmed COVID-19, discharged between 2 March and 1 October 2020, were recruited prospectively. Follow-up at 3 and 6 months after hospital discharge included demographic and clinical data, biological data, pulmonary function tests (PFTs) and high-resolution computed tomography (CT) scans of the chest.

Results

In total, 199 individuals were included in the analysis. Most patients received oxygen supplementation (80.4%). Six months after discharge, 47% and 32% of patients still had exertional dyspnoea and fatigue. PFTs at 3-month follow-up revealed a reduced diffusion capacity of carbon monoxide (mean 71.6 ± 18.6%), and this increased significantly at 6-month follow-up (P<0.0001). Chest CT scans showed a high prevalence (68.9% of the cohort) of persistent abnormalities, mainly ground glass opacities. Duration of hospitalization, intensive care unit admission and mechanical ventilation were not associated with the persistence of symptoms 3 months after discharge.

Conclusion

The prevalence of persistent symptoms following hospitalization with COVID-19 is high and stable for up to 6 months after discharge. However, biological, functional and iconographic abnormalities improved significantly over time.

COVID-19 Antibody Detecting Rapid Diagnostic Tests Show High Cross-Reactivity When Challenged with Pre-Pandemic Malaria, Schistosomiasis and Dengue Samples

COVID-19 Antibody Detecting Rapid Diagnostic Tests (COVID-19 Ab RDTs) are the preferred tool for SARS-CoV-2 seroprevalence studies, particularly in low- and middle-income countries. The present study challenged COVID-19 Ab RDTs with pre-pandemic samples of patients exposed to tropical pathogens. A retrospective study was performed on archived serum (n = 94) and EDTA whole blood (n = 126) samples obtained during 2010–2018 from 196 travelers with malaria (n = 170), schistosomiasis (n = 25) and dengue (n = 25). COVID-19 Ab RDTs were selected based on regulatory approval status, independent evaluation results and detecting antigens. Among 13 COVID-19 Ab RDT products, overall cross-reactivity was 18.5%; cross-reactivity for malaria, schistosomiasis and dengue was 20.3%, 18.1% and 7.5%, respectively. Cross-reactivity for current and recent malaria, malaria antibodies, Plasmodium species and parasite densities was similar. Cross-reactivity among the different RDT products ranged from 2.7% to 48.9% (median value 14.5%). IgM represented 67.9% of cross-reactive test lines. Cross-reactivity was not associated with detecting antigens, patient categories or disease (sub)groups, except for schistosomiasis (two products with ≥60% cross-reactivity). The high cross-reactivity for malaria, schistosomiasis and—to a lesser extent—dengue calls for risk mitigation when using COVID-19 Ab RDTs in co-endemic regions.

Role of laboratory biomarkers in assessing the severity of COVID-19 disease. A cross-sectional study

BACKGROUND

Corona virus disease 2019 (Covid-19) has high infectivity and mortality rate. Covid-19 patients can suddenly deteriorate and develop life threatening complications. Hence, there is a need to identify laboratory biomarkers in order to categorize high risk patients. The main purpose of the study is to investigate the role and correlation of laboratory parameters such as total leucocyte count (TLC), absolute lymphocyte count, platelet count, C-Reactive Proteins (CRP), serum ferritin, serum lactate dehydrogenase (LDH), serum procalcitonin and D-dimer in severe and non-severe Covid-19 patients.

METHODOLOGY

This retrospective cross-sectional study was conducted at Latifa Women and Child Hospital in the UAE after obtaining ethical committee clearance. Based on the symptoms and the criteria by National Institute of Health, USA, 109 patients were divided into three groups: Non-severe with 75, severe with 18 and critical with 16 patients. Laboratory data of these patients were assessed through the electronic medical records (SALAMA). Statistical analysis was done using Statistical Packages for Social Sciences (SPSS) version 25.0 (SPSS/PC; SPSS-25.0, Chicago, USA). Laboratory test profiles were expressed as mean (SD). Independent 't' test and ANOVA were used to study the significance of means. P value less than 0.05 was considered significant.

RESULT

Males were more severely affected than females. Severe and critically ill Covid-19 patients had a significantly higher TLC, serum LDH, ferritin and CRP and lower absolute lymphocyte count. PCT and D-dimer were significantly elevated in critical group.

CONCLUSION

Along with clinical presentation and radiological findings, biochemical parameter may also be considered as important predictors for assessing severity in covid-19 patients.

Non-invasive adapted N-95 mask sampling captures variation in viral particles expelled by COVID-19 patients: Implications in understanding SARS-CoV2 transmission

Infectious respiratory particles expelled by SARS-CoV-2 positive patients are attributed to be the key driver of COVID-19 transmission. Understanding how and by whom the virus is transmitted can help implement better disease control strategies. Here we have described the use of a noninvasive mask sampling method to detect and quantify SARS-CoV-2 RNA in respiratory particles expelled by COVID-19 patients and discussed its relationship to transmission risk. Respiratory particles of 31 symptomatic SARS-CoV-2 positive patients and 31 asymptomatic healthy volunteers were captured on N-95 masks layered with a gelatin membrane in a 30-minute process that involved talking/reading, coughing, and tidal breathing. SARS-CoV-2 viral RNA was detected and quantified using rRT-PCR in the mask and in concomitantly collected nasopharyngeal swab (NPS) samples. The data were analyzed with respect to patient demographics and clinical presentation. Thirteen of 31(41.9%) patients showed SARS-COV-2 positivity in both the mask and NPS samples, while 16 patients were mask negative but NPS positive. Two patients were both mask and NPS negative. All healthy volunteers except one were mask and NPS negative. The mask positive patients had significantly lower NPS Ct value (26) compared to mask negative patients (30.5) and were more likely to be rapid antigen test positive. The mask positive patients could be further grouped into low emitters (expelling <100 viral copies) and high emitters (expelling >1000 viral copies). The study presents evidence for variation in emission of SARS-CoV-2 virus particles by COVID-19 patients reflecting differences in infectivity and transmission risk among individuals. The results conform to reported secondary infection rates and transmission and also suggest that mask sampling could be explored as an effective tool to assess individual transmission risks, at different time points and during different activities.

Back to normal; serological testing for COVID-19 diagnosis unveils missed infections

Background

The gold standard for coronavirus disease (COVID‐19) diagnosis has been the detection of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) RNA by nucleic acid amplification testing (NAAT). On the other hand, serological testing for COVID‐19 may offer advantages in detecting possibly overlooked infections by NAAT.

Methods

To evaluate seroconversion of NAAT‐negative pneumonia patients, immunoglobulin M (IgM) and IgG targeting the spike protein of SARS‐CoV‐2 were semiquantified by an immunofluorescence assay. Seroconversion was confirmed by another serological method, targeting the nucleocapsid protein.

Results

Eight suspected but unconfirmed COVID‐19 pneumonia patients (median age, 39 years; range, 21–55) were included. The median period between symptom onset and NAAT sample collection was 6 days (2–27 days). None of them had tested positive for SARS‐CoV‐2 by NAAT. In contrast, all eight patients revealed seropositivity with the two serological methods, indicating actual seroconversion against SARS‐CoV‐2. The median period between onset and blood sampling was 26.5 days (7–51 days).

Conclusion

Eight patients with COVID‐19 pneumonia, initially tested negative for SARS‐CoV‐2 by NAAT, were finally confirmed of the diagnosis by serological testing. To cover the whole spectrum of this heterogenous infectious disease, serology testing should be implemented to the multitiered diagnostic algorithm for COVID‐19.

French Public Familiarity and Attitudes toward Clinical Research during the COVID-19 Pandemic

The COVID-19 pandemic put clinical research in the media spotlight globally. This article proposes a first measure of familiarity with and attitude toward clinical research in France. Drawing from the “Health Literacy Survey 2019” (HLS19) conducted online between 27 May and 5 June 2020 on a sample of the French adult population (N = 1003), we show that a significant proportion of the French population claimed some familiarity with clinical trials (64.8%) and had positive attitudes (72%) toward them. One of the important findings of this study is that positive attitudes toward clinical research exist side by side with a strong distancing from the pharmaceutical industry. While respondents acknowledged that the pharmaceutical industry plays an important role in clinical research (68.3%), only one-quarter indicated that they trust the industry (25.7%). Positive attitudes toward clinical trials were associated with familiarity with clinical trials (Odds Ratio, OR 2.97 [1.90–4.63]), financial difficulties (OR 0.63 [0.46–0.85]), as well as mistrust of doctors (0.48 [0.27–0.85]) and of scientists (OR 0.62 [0.38–0.99]). Although the French media provided a great deal of information on how clinical research works during the first months of the pandemic, there remains profound mistrust of the pharmaceutical industry in France. This suspicion can undermine crisis management, especially in the areas of vaccine development and preparation for future pandemics.

Mechanistic transmission modeling of COVID-19 on the Diamond Princess cruise ship demonstrates the importance of aerosol transmission

Several lines of existing evidence support the possibility of airborne transmission of coronavirus disease 2019 (COVID-19). However, quantitative information on the relative importance of transmission pathways of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains limited. To evaluate the relative importance of multiple transmission routes for SARS-CoV-2, we developed a modeling framework and leveraged detailed information available from the Diamond Princess cruise ship outbreak that occurred in early 2020. We modeled 21,600 scenarios to generate a matrix of solutions across a full range of assumptions for eight unknown or uncertain epidemic and mechanistic transmission factors. A total of 132 model iterations met acceptability criteria (R2 > 0.95 for modeled vs. reported cumulative daily cases and R2 > 0 for daily cases). Analyzing only these successful model iterations quantifies the likely contributions of each defined mode of transmission. Mean estimates of the contributions of short-range, long-range, and fomite transmission modes to infected cases across the entire simulation period were 35%, 35%, and 30%, respectively. Mean estimates of the contributions of larger respiratory droplets and smaller respiratory aerosols were 41% and 59%, respectively. Our results demonstrate that aerosol inhalation was likely the dominant contributor to COVID-19 transmission among the passengers, even considering a conservative assumption of high ventilation rates and no air recirculation conditions for the cruise ship. Moreover, close-range and long-range transmission likely contributed similarly to disease progression aboard the ship, with fomite transmission playing a smaller role. The passenger quarantine also affected the importance of each mode, demonstrating the impacts of the interventions.

Mechanistic transmission modeling of COVID-19 on the Diamond Princess cruise ship demonstrates the importance of aerosol transmission

Several lines of existing evidence support the possibility of airborne transmission of coronavirus disease 2019 (COVID-19). However, quantitative information on the relative importance of transmission pathways of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains limited. To evaluate the relative importance of multiple transmission routes for SARS-CoV-2, we developed a modeling framework and leveraged detailed information available from the Diamond Princess cruise ship outbreak that occurred in early 2020. We modeled 21,600 scenarios to generate a matrix of solutions across a full range of assumptions for eight unknown or uncertain epidemic and mechanistic transmission factors. A total of 132 model iterations met acceptability criteria (R² > 0.95 for modeled vs. reported cumulative daily cases and R² > 0 for daily cases). Analyzing only these successful model iterations quantifies the likely contributions of each defined mode of transmission. Mean estimates of the contributions of short-range, long-range, and fomite transmission modes to infected cases across the entire simulation period were 35%, 35%, and 30%, respectively. Mean estimates of the contributions of larger respiratory droplets and smaller respiratory aerosols were 41% and 59%, respectively. Our results demonstrate that aerosol inhalation was likely the dominant contributor to COVID-19 transmission among the passengers, even considering a conservative assumption of high ventilation rates and no air recirculation conditions for the cruise ship. Moreover, close-range and long-range transmission likely contributed similarly to disease progression aboard the ship, with fomite transmission playing a smaller role. The passenger quarantine also affected the importance of each mode, demonstrating the impacts of the interventions.

COVID-19-Related Fatalities and Intensive-Care-Unit Admissions by Age Groups in Europe: A Meta-Analysis

Objectives: Precise international estimates of the age breakdown of COVID-19–related deaths and intensive-care-unit (ICU) admissions are lacking. We evaluated the distribution of COVID-19–related fatalities and ICU admissions by age groups in Europe.

Materials and methods: On April 6, 2020, we systematically reviewed official COVID-19–related data from 32 European countries. We included countries that provided data regarding more than 10 COVID-19–related deaths stratified by age according to pre-specified age groups (i.e., <40, 40–69, ≥70 years). We used random-effects meta-analysis to summarize the data.

Results: Thirteen European countries were included in the review, for a total of 31,864 COVID-19–related deaths (range: 27–14,381 per country). In the main meta-analysis (including data from Germany, Hungary, Italy, The Netherlands, Portugal, Spain, Switzerland; 21,522 COVID-19–related fatalities), the summary proportions of individuals <40, 40–69, and ≥70 years old among all COVID-19–related deaths were 0.1% (0.0–0.2; I² 28.6%), 13.0% (10.8–15.4; I² 91.5%), and 86.6% (84.2–88.9; I² 91.5%), respectively. ICU data were available for four countries (France, Greece, Spain, Sweden). The summary proportions of individuals around <40–50, around 40–69, and around ≥60–70 years old among all COVID-19–related ICU admissions were 5.4% (3.4–7.8; I² 89.0%), 52.6% (41.8–63.3; I² 98.1%), and 41.8% (32.0–51.9; I² 99%), respectively.

Conclusions: People under 40 years old represent a small fraction of most severe COVID-19 cases in Europe. These results may help health authorities respond to public concerns and guide future physical distancing and mitigation strategies. Specific measures to protect older people should be considered.

Filling the Gap Until Full Vaccine Deployment in the War on Coronavirus Disease-19

The authorization for emergency use of a vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been issued in diverse countries in December 2020, and additional vaccine candidates soon may be cleared for a similar emergency use. If it is reasonable to believe that in some Western countries most people may be vaccinated by the end of 2021, insufficient supplies, access inequities across countries, and deficiencies in enforcing the participatory engagement of communities will present important challenges for the achievement of sufficient vaccination coverage worldwide in less than 2–3 years. A possible strategy for bridging the gap until full vaccine deployment is based on the integration of improved non-pharmaceutical measures and recently authorized pharmaceutical interventions to reduce as much as possible hospitalizations and deaths in the coming months, when recurring infection peaks are expected.

COVID-19 and Corticosteroids: Unfamiliar but Potentially Fatal Infections That Can Arise following Short-Course Steroid Treatment

Corticosteroid use is increasing worldwide as recent studies confer survival benefit of corticosteroids in the management of patients with severe COVID-19. Strongyloides and amebic infections are neglected diseases that can progress to catastrophic complications in patients exposed to corticosteroids, even with short treatment courses. To prevent lethal outcomes, clinicians should be aware of the threat these two parasitic infections pose to at-risk patients receiving corticosteroids, especially in the era of COVID-19.

Statewide evaluation of infection control measures for preventing coronavirus disease 2019 in hemodialysis facilities

OBJECTIVE

This study aimed to evaluate the occurrence of coronavirus disease 2019 (COVID-19) in hemodialysis facilities and the occurrence of and risk factors for clustering of COVID-19 cases.

METHODS

We conducted a cross-sectional online survey between March and July 2020, in all dialysis facilities in São Paulo state, using Google Forms. The online questionnaire contained questions addressing specific components of infection prevention and control practices and the number of cases during the COVID-19 pandemic.

RESULTS

A total of 1,093 (5%) COVID-19 cases were reported among 20,984 patients; approximately 56% of the facilities had ≥1 cluster. Most facilities implemented various measures (such as allocation of dedicated COVID-19 areas/shifts, symptom screening, environmental disinfection, and maintenance of adequate ventilation) to prevent the transmission of severe acute respiratory syndrome coronavirus 2. Clustering of COVID-19 cases was suspected in only 7% of dialysis facilities. The only variable associated with this event was the performance of aerosol-generating procedures (odds ratio: 4.74; 95% confidence interval: 1.75-12.86).

CONCLUSION

Attention should be paid to avoiding the performance of aerosol-generating procedures in dialysis facilities and monitoring the clustering of cases.

Low-dose and oral exposure to SARS-CoV-2 may help us understand and prevent severe COVID-19

Background

The effectiveness and sustainability of current public health interventions designed to prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission remain of great concern in many settings, especially in the absence of a transmission-preventing vaccine.

Hypothesis

It was hypothesized that a more targeted set of interventions focusing on preventing severe coronavirus disease 2019 (COVID-19), rather than SARS-CoV-2 transmission, would be less disruptive to society. To identify these, it would be helpful to better understand how the infecting dose of SARS-CoV-2 and its route of infection influence the clinical outcome, immunological protection, and likelihood of onward transmission.

Proposal

It is suggested that carefully controlled human infection model (CHIM) studies involving intranasal and oral administration of progressively increasing doses of SARS-CoV-2, starting with low levels, to healthy young adult volunteers may be the most expeditious and definitive way to answer these questions. Such studies would differ in objective from CHIM proposals designed to expedite vaccine development, although the latter might be adapted to address some of the questions raised here.

Implications

Results from the studies proposed here could help elucidate the relationship of infection to COVID-19 and thereby provide a scientific basis for more targeted and sustainable application of public health control measures, and inform the design of improved immunotherapeutics and more targeted vaccine development.