The role of asymptomatic and pre-symptomatic infection in SARS-CoV-2 transmission-a living systematic review

Estimating the contribution of setting-specific contacts to SARS-CoV-2 transmission using digital contact tracing data

While many countries employed digital contact tracing to contain the spread of SARS-CoV-2, the contribution of cospace-time interaction (i.e., individuals who shared the same space and time) to transmission and to super-spreading in the real world has seldom been systematically studied due to the lack of systematic sampling and testing of contacts. To address this issue, we utilized data from 2230 cases and 220,878 contacts with detailed epidemiological information during the Omicron outbreak in Beijing in 2022. We observed that contact number per day of tracing for individuals in dwelling, workplace, cospace-time interactions, and community settings could be described by gamma distribution with distinct parameters. Our findings revealed that 38% of traced transmissions occurred through cospace-time interactions whilst control measures were in place. However, using a mathematical model to incorporate contacts in different locations, we found that without control measures, cospace-time interactions contributed to only 11% (95%CI: 10%-12%) of transmissions and the super-spreading risk for this setting was 4% (95%CI: 3%-5%), both the lowest among all settings studied. These results suggest that public health measures should be optimized to achieve a balance between the benefits of digital contact tracing for cospace-time interactions and the challenges posed by contact tracing within the same setting.

Drivers and impact of the early silent invasion of SARS-CoV-2 Alpha

SARS-CoV-2 variants of concern (VOCs) circulated cryptically before being identified as a threat, delaying interventions. Here we studied the drivers of such silent spread and its epidemic impact to inform future response planning. We focused on Alpha spread out of the UK. We integrated spatio-temporal records of international mobility, local epidemic growth and genomic surveillance into a Bayesian framework to reconstruct the first three months after Alpha emergence. We found that silent circulation lasted from days to months and decreased with the logarithm of sequencing coverage. Social restrictions in some countries likely delayed the establishment of local transmission, mitigating the negative consequences of late detection. Revisiting the initial spread of Alpha supports local mitigation at the destination in case of emerging events.

Evaluating Acute Pulmonary Changes in Coronavirus Disease 2019: A Comparative Analysis of Computed Tomography, Chest Radiography, Lung Ultrasound, Magnetic Resonance Imaging, and Positron Emission Tomography with Fluorodeoxyglucose Modalities

This review explores imaging's crucial role in acute Coronavirus Disease 2019 (COVID-19) assessment. High Resolution Computer Tomography is especially effective in detection of lung abnormalities. Chest radiography has limited utility in the initial stages of COVID-19 infection. Lung Ultrasound has emerged as a valuable, radiation-free tool in critical care, and Magnetic Resonance Imaging shows promise as a Computed Tomography alternative. Typical and atypical findings of COVID-19 by each of these modalities are discussed with emphasis on their prognostic value. Considerations for pediatric and immunocompromised cases are outlined. A comprehensive diagnostic approach is recommended, as radiological diagnosis remains challenging in the acute phase.

The seroprevalence of SARS-CoV-2 infection in Malaysia: 7 August to 11 October 2020

Background

From the beginning of the COVID-19 pandemic until mid-October 2020, Malaysia recorded ~15,000 confirmed cases. But there could be undiagnosed cases due mainly to asymptomatic infections. Seroprevalence studies can better quantify underlying infection from SARS-CoV-2 by identifying humoral antibodies against the virus. This study was the first to determine the prevalence of SARS-CoV-2 infection in  Malaysia's general population, as well as the proportion of asymptomatic and undiagnosed infections.

Methods

This cross-sectional seroprevalence study with a two-stage stratified random cluster sampling design included 5,131 representative community dwellers in Malaysia aged ≥1 year. Data collection lasted from 7 August to 11 October 2020 involving venous blood sampling and interviews for history of COVID-19 symptoms and diagnosis. Previous SARS-CoV-2 infection was defined as screened positive using the Wantai SARS-CoV-2 Total Antibody enzyme-linked immunosorbent assay and confirmed positive using the GenScript SARS-CoV-2 surrogate Virus Neutralization Test. We performed a complex sampling design analysis, calculating sample weights considering probabilities of selection, non-response rate and post-stratification weight.

Results

The overall weighted prevalence of SARS-CoV-2 infection was 0.49% (95%CI 0.28-0.85) (N = 150,857). Among the estimated population with past infection, around 84.1% (95%CI 58.84-95.12) (N = 126 826) were asymptomatic, and 90.1% (95%CI 67.06-97.58) (N = 135 866) were undiagnosed.

Conclusions

Our study revealed a low pre-variant and pre-vaccination seroprevalence of SARS-CoV-2 infection in Malaysia up to mid-October 2020, with a considerable proportion of asymptomatic and undiagnosed cases. This led to subsequent adoption of SARS-CoV-2 antigen rapid test kits to increase case detection rate and to reduce time to results and infection control measures.

A novel strategy to avoid sensitivity loss in pooled testing for SARS-CoV-2 surveillance: validation using nasopharyngeal swab and saliva samples

At the peak of the COVID-19 pandemic, pooled surveillance strategies were employed to alleviate the overwhelming demand for clinical testing facilities. A major drawback of most pooled-testing methods is the dilution of positive samples, which leads to a loss of detection sensitivity and the potential for false negatives. We developed a novel pooling strategy that compensates for the initial dilution with an appropriate concentration during nucleic acid extraction and real-time PCR. We demonstrated the proof of principle using laboratory-created 10-sample pools with one positive and corresponding individual positive samples by spiking a known amount of heat-inactivated SARS-CoV-2 into viral transport medium (VTM) or pooled negative saliva. No Ct difference was observed between a 10-sample pool with one positive vs. the corresponding individually analyzed positive sample by this method, suggesting that there is no detectable loss of sensitivity. We further validated this approach by using nasopharyngeal swab (NPS) specimens and showed that there is no loss of sensitivity. Serial dilutions of the virus were spiked into VTM and pooled with negative saliva in simulated 10-sample pools containing one positive to determine the LOD and process efficiency of this pooling methodology. The LOD of this approach was 10 copies/PCR, and the process efficiencies are ~95%-103% for N1 and ~87%-98% for N2 with samples in different matrices and with two different master mixes tested. Relative to TaqPath 1-step master mix, the TaqMan Fast Virus 1-Step master mix showed better sensitivity for the N2 assay, while the N1 assay showed no Ct difference. Our pooled testing strategy can facilitate large-scale, cost-effective SARS-CoV-2 surveillance screening and maintain the same level of sensitivity when analyzed individually or in a pool. This approach is highly relevant for public health surveillance efforts aimed at mitigating SARS-CoV-2 spread.

Impact of variants of concern on SARS-CoV-2 viral dynamics in non-human primates

The impact of variants of concern (VoC) on SARS-CoV-2 viral dynamics remains poorly understood and essentially relies on observational studies subject to various sorts of biases. In contrast, experimental models of infection constitute a powerful model to perform controlled comparisons of the viral dynamics observed with VoC and better quantify how VoC escape from the immune response. Here we used molecular and infectious viral load of 78 cynomolgus macaques to characterize in detail the effects of VoC on viral dynamics. We first developed a mathematical model that recapitulate the observed dynamics, and we found that the best model describing the data assumed a rapid antigen-dependent stimulation of the immune response leading to a rapid reduction of viral infectivity. When compared with the historical variant, all VoC except beta were associated with an escape from this immune response, and this effect was particularly sensitive for delta and omicron variant (p<10-6 for both). Interestingly, delta variant was associated with a 1.8-fold increased viral production rate (p = 0.046), while conversely omicron variant was associated with a 14-fold reduction in viral production rate (p<10-6). During a natural infection, our models predict that delta variant is associated with a higher peak viral RNA than omicron variant (7.6 log10 copies/mL 95% CI 6.8-8 for delta; 5.6 log10 copies/mL 95% CI 4.8-6.3 for omicron) while having similar peak infectious titers (3.7 log10 PFU/mL 95% CI 2.4-4.6 for delta; 2.8 log10 PFU/mL 95% CI 1.9-3.8 for omicron). These results provide a detailed picture of the effects of VoC on total and infectious viral load and may help understand some differences observed in the patterns of viral transmission of these viruses.

Methodological quality and reporting quality of COVID-19 living systematic review: a cross-sectional study

OBJECTIVES

The main objective of this study is to evaluate the methodological quality and reporting quality of living systematic reviews (LSRs) on Coronavirus disease 2019 (COVID-19), while the secondary objective is to investigate potential factors that may influence the overall quality of COVID-19 LSRs.

METHODS

Six representative databases, including Medline, Excerpta Medica Database (Embase), Cochrane Library, China national knowledge infrastructure (CNKI), Wanfang Database, and China Science, Technology Journal Database (VIP) were systematically searched for COVID-19 LSRs. Two authors independently screened articles, extracted data, and then assessed the methodological and reporting quality of COVID-19 LSRs using the "A Measurement Tool to Assess systematic Reviews-2" (AMSTAR-2) tool and "Preferred Reporting Items for Systematic reviews and Meta-Analyses" (PRISMA) 2020 statement, respectively. Univariate linear regression and multivariate linear regression were used to explore eight potential factors that might affect the methodological quality and reporting quality of COVID-19 LSRs.

RESULTS

A total of 64 COVID-19 LSRs were included. The AMSTAR-2 evaluation results revealed that the number of "yes" responses for each COVID-19 LSR was 13 ± 2.68 (mean ± standard deviation). Among them, 21.9% COVID-19 LSRs were rated as "high", 4.7% as "moderate", 23.4% as "low", and 50% as "critically low". The evaluation results of the PRISMA 2020 statement showed that the sections with poor adherence were methods, results and other information. The number of "yes" responses for each COVID-19 LSR was 21 ± 4.18 (mean ± standard deviation). The number of included studies and registration are associated with better methodological quality; the number of included studies and funding are associated with better reporting quality.

CONCLUSIONS

Improvement is needed in the methodological and reporting quality of COVID-19 LSRs. Researchers conducting COVID-19 LSRs should take note of the quality-related factors identified in this study to generate evidence-based evidence of higher quality.

Salivary SARS-CoV-2 RNA for diagnosis of COVID-19 patients: a systematic revisew and meta-analysis of diagnostic accuracy

Accurate, self-collected, and non-invasive diagnostics are critical to perform mass-screening diagnostic tests for COVID-19. This systematic review with meta-analysis evaluated the accuracy, sensitivity, and specificity of salivary diagnostics for COVID-19 based on SARS-CoV-2 RNA compared with the current reference tests using a nasopharyngeal swab (NPS) and/or oropharyngeal swab (OPS). An electronic search was performed in seven databases to find COVID-19 diagnostic studies simultaneously using saliva and NPS/OPS tests to detect SARS-CoV-2 by RT-PCR. The search resulted in 10,902 records, of which 44 studies were considered eligible. The total sample consisted of 14,043 participants from 21 countries. The accuracy, specificity, and sensitivity for saliva compared with the NPS/OPS was 94.3% (95%CI= 92.1;95.9), 96.4% (95%CI= 96.1;96.7), and 89.2% (95%CI= 85.5;92.0), respectively. Besides, the sensitivity of NPS/OPS was 90.3% (95%CI= 86.4;93.2) and saliva was 86.4% (95%CI= 82.1;89.8) compared to the combination of saliva and NPS/OPS as the gold standard. These findings suggest a similarity in SARS-CoV-2 RNA detection between NPS/OPS swabs and saliva, and the association of both testing approaches as a reference standard can increase by 3.6% the SARS-CoV-2 detection compared with NPS/OPS alone. This study supports saliva as an attractive alternative for diagnostic platforms to provide a non-invasive detection of SARS-CoV-2.

Household transmission dynamics of COVID-19 among residents of Delhi, India: a prospective case-ascertained study

Objective

The aim of this study was to observe the secondary infection rate and transmission dynamics of COVID-19 among household contacts, and their associations with various factors across four dimensions of interaction.

Methods

This was a case-ascertained study among unvaccinated household contacts of a laboratory-confirmed COVID-19 case in New Delhi between December 2020 and July 2021. For this study, 99 index cases and their 316 household contacts were interviewed and sampled (blood and oro-nasal swab) on days 1, 7, 14, and 28.

Results

The secondary infection rate among unvaccinated household contacts was 44.6% (95% confidence interval (CI) 39.1-50.1). The predictors of secondary infection among individual contact levels were: being female (odds ratio (OR) 2.13), increasing age (OR 1.01), symptoms at baseline (OR 3.39), and symptoms during follow-up (OR 3.18). Among index cases, age of the primary case (OR 1.03) and symptoms during follow-up (OR 6.29) were significantly associated with secondary infection. Among household-level and contact patterns, having more rooms (OR 4.44) and taking care of the index case (OR 2.02) were significantly associated with secondary infection.

Conclusion

A high secondary infection rate highlights the need to adopt strict measures and advocate COVID-19-appropriate behaviors. A targeted approach for higher-risk household contacts would efficiently limit infections among susceptible contacts.

Parallel dynamics in the yield of universal SARS-CoV-2 admission screening and population incidence

The majority of SARS-CoV-2 transmissions originates from either asymptomatic or presymptomatic individuals. To prevent unnoticed introduction of SARS-CoV-2, many hospitals have implemented universal admission screening during the COVID-19 pandemic. The present study aimed to investigate associations between results of an universal SARS-CoV-2 admission screening and public SARS-CoV-2 incidence. Over a study period of 44 weeks, all patients admitted to a large tertiary care hospital were tested for SARS-CoV-2 by polymerase chain reaction. SARS-CoV-2 positive patients were retrospectively categorized as symptomatic or asymptomatic at admission. Cantonal data were used to calculate weekly incidence rates per 100,000 inhabitants. We used regression models for count data to assess the association of the weekly cantonal incidence rate and the proportion of positive SARS-CoV-2 tests in the canton with (a) the proportion of SARS-CoV-2 positive individuals and (b) the proportion of asymptomatic SARS-CoV-2 infected individuals identified in universal admission screening, respectively. In a 44-week period, a total of 21,508 admission screenings were performed. SARS-CoV-2 PCR was positive in 643 (3.0%) individuals. In 97 (15.0%) individuals, the positive PCR reflected residual viral replication after recent COVID-19, 469 (72.9%) individuals had COVID-19 symptoms and 77 (12.0%) SARS-CoV-2 positive individuals were asymptomatic. Cantonal incidence correlated with the proportion of SARS-CoV-2 positive individuals [rate ratio (RR): 2.03 per 100 point increase of weekly incidence rate, 95%CI 1.92-2.14] and the proportion of asymptomatic SARS-CoV-2 positive individuals (RR: 2.40 per 100 point increase of weekly incidence rate, 95%CI 2.03-2.82). The highest correlation between dynamics in cantonal incidence and results of admission screening was observed at a lag time of one week. Similarly, the proportion of positive SARS-CoV-2 tests in the canton of Zurich correlated with the proportion of SARS-CoV-2 positive individuals (RR: 2.86 per log increase in the proportion of positive SARS-CoV-2 tests in the canton, 95%CI 2.56-3.19) and the proportion of asymptomatic SARS-CoV-2 positive individuals (RR: 6.50 per log increase in the proportion of positive SARS-CoV-2 tests in the canton, 95%CI 3.93-10.75) in admission screening. Around 0.36% of admission screenings were positive in asymptomatic patients. Admission screening results paralleled changes in population incidence with a brief lag.

Duration of viral infectiousness and correlation with symptoms and diagnostic testing in non-hospitalized adults during acute SARS-CoV-2 infection: A longitudinal cohort study

BACKGROUND

Guidelines for SARS-CoV-2 have relied on limited data on duration of viral infectiousness and correlation with COVID-19 symptoms and diagnostic testing.

METHODS

We enrolled ambulatory adults with acute SARS-CoV-2 infection and performed serial measurements of COVID-19 symptoms, nasal swab viral RNA, nucleocapsid (N) and spike (S) antigens, and replication-competent SARS-CoV-2 by viral growth in culture. We determined average time from symptom onset to a first negative test result and estimated risk of infectiousness, as defined by positive viral growth in culture.

RESULTS

Among 95 adults, median [interquartile range] time from symptom onset to first negative test result was 9 [5] days, 13 [6] days, 11 [4] days, and >19 days for S antigen, N antigen, culture growth, and viral RNA by RT-PCR, respectively. Beyond two weeks, virus growth and N antigen titers were rarely positive, while viral RNA remained detectable among half (26/51) of participants tested 21-30 days after symptom onset. Between 6-10 days from symptom onset, N antigen was strongly associated with culture positivity (relative risk=7.61, 95% CI: 3.01-19.22), whereas neither viral RNA nor symptoms were associated with culture positivity. During the 14 days following symptom onset, the presence of N antigen remained strongly associated (adjusted relative risk=7.66, 95% CI: 3.96-14.82) with culture positivity, regardless of COVID-19 symptoms.

CONCLUSIONS

Most adults have replication-competent SARS-CoV-2 for 10-14 after symptom onset. N antigen testing is a strong predictor of viral infectiousness and may be a more suitable biomarker, rather than absence of symptoms or viral RNA, to discontinue isolation within two weeks from symptom onset.

The WE SENSE study protocol: A controlled, longitudinal clinical trial on the use of wearable sensors for early detection and tracking of viral respiratory tract infections

Background

Viral respiratory tract infections (VRTI) are extremely common. Considering the profound social and economic impact of COVID-19, it is imperative to identify novel mechanisms for early detection and prevention of VRTIs, to prevent future pandemics. Wearable biosensor technology may facilitate this. Early asymptomatic detection of VRTIs could reduce stress on the healthcare system by reducing transmission and decreasing the overall number of cases. The aim of the current study is to define a sensitive set of physiological and immunological signature patterns of VRTI through machine learning (ML) to analyze physiological data collected continuously using wearable vital signs sensors.

Methods

A controlled, prospective longitudinal study with an induced low grade viral challenge, coupled with 12 days of continuous wearable biosensors monitoring surrounding viral induction. We aim to recruit and simulate a low grade VRTI in 60 healthy adults aged 18–59 years via administration of live attenuated influenza vaccine (LAIV). Continuous monitoring with wearable biosensors will include 7 days pre (baseline) and 5 days post LAIV administration, during which vital signs and activity-monitoring biosensors (embedded in a shirt, wristwatch and ring) will continuously monitor physiological and activity parameters. Novel infection detection techniques will be developed based on inflammatory biomarker mapping, PCR testing, and app-based VRTI symptom tracking. Subtle patterns of change will be assessed via ML algorithms developed to analyze large datasets and generate a predictive algorithm.

Conclusion

This study presents an infrastructure to test wearables for the detection of asymptomatic VRTI using multimodal biosensors, based on immune host response signature.

CliniclTrials.govregistration:NCT05290792

Effect of COVID-19 vaccination on the SARS-CoV-2 transmission among social and household close contacts: A cohort study

BACKGROUND

COVID-19 vaccination was expected to reduce SARS-CoV-2 transmission, but the relevance of this effect remains unclear. We aimed to estimate the effectiveness of COVID-19 vaccination of the index cases and their close contacts in reducing the probability of SARS-CoV-2 transmission.

METHODS

Transmission of SARS-CoV-2 infection was evaluated in two cohorts of adult close contacts of COVID-19 confirmed cases (social and household settings) by COVID-19 vaccination status of the index case and the close contact, from April to November 2021 in Navarre, Spain. The effects of vaccination of the index case and the close contact were estimated as (1-adjusted relative risk) × 100%.

RESULTS

Among 19,631 social contacts, 3257 (17%) were confirmed with SARS-CoV-2. COVID-19 vaccination of the index case reduced infectiousness by 44% (95% CI, 27-57%), vaccination of the close contact reduced susceptibility by 69% (95% CI, 65-73%), and vaccination of both reduced transmissibility by 74% (95% CI, 70-78%) in social settings, suggesting some synergy of effects. Among 20,708 household contacts, 6269 (30%) were infected, and vaccine effectiveness estimates were 13% (95% CI, -5% to 28%), 61% (95% CI, 58-64%), and 52% (95% CI, 47-56%), respectively. These estimates were lower in older people and had not relevant differences between the Alpha (April-June) and Delta (July-November) variant periods.

CONCLUSIONS

COVID-19 vaccination reduces infectiousness and susceptibility; however, these effects are insufficient for complete control of SARS-CoV-2 transmission, especially in older people and household setting. Relaxation of preventive behaviors after vaccination may counteract part of the vaccine effect on transmission.

What We Know (and Do not Know) Regarding the Pathogenesis of Pulmonary Thrombosis in COVID-19

The clinical course of coronavirus disease 2019 (COVID-19) is often complicated by the onset of venous thrombosis and thromboembolism (VTE), encompassing also pulmonary thrombosis. Recent statistics attests that the cumulative frequency of VTE can be as high as 30% in COVID-19 hospitalized patients, increasing to nearly 40 to 70% (depending on systematic screening) in those with severe illness, mechanical ventilation, or intensive care unit admission. The risk of venous thrombosis seems mostly limited to the active phase of disease, and is directly associated with some genetic (i.e., inherited prothrombotic predisposition) and demographical factors (male sex, overweight/obesity), disease severity (risk increasing progressively from hospitalization to development of severe illness, being the highest in patients needing mechanical ventilation and/or intensive care), presence and extent of pulmonary disease, coexistence of multiple risk factors (immobilization, mechanical ventilation, co- or superinfections), along with increased values of inflammatory and thrombotic biomarkers. At least three different phenotypes of pulmonary thrombosis may develop in COVID-19 patients, one caused by typical embolization from peripheral venous thrombosis (e.g., deep vein thrombosis), a second type triggered by local inflammation of nearby pulmonary tissue, and a third one mostly attributable to the prothrombotic state consequent to the pronounced systemic inflammatory response (i.e., the so-called cytokine storm) that is frequently observed in COVID-19. Although the pathogenesis of these three conditions has different features, their discrimination is essential for diagnostic and therapeutic purposes. The prognosis of COVID-19 patients who develop pulmonary thrombosis is also considerably worse than those who do not, thus probably needing frequent monitoring and more aggressive therapeutic management.

Single-chirality of single-walled carbon nanotubes (SWCNTs) through chromatography and its potential biological applications

Gel chromatography is used to separate single-chirality and selective-diameter SWCNTs. We also explore the use of photothermal therapy and biosensor applications based on single-chirality, selected-diameter, and unique geometric shape.

The next 'pandemic playbook' needs to prioritize the needs of children-and a clear roadmap for opening schools

The national influenza pandemic response plan includes short-term school closures as an infection mitigation measure, based on modeling data regarding the role of pediatric populations and schools as drivers of disease spread. Modeled estimates regarding the role of children and their in-school contacts as drivers of community transmission of endemic respiratory viruses were used in part to justify prolonged school closures throughout the United States. However, disease transmission models extrapolated from endemic pathogens to novel ones may underestimate the degree to which spread is driven by population immunity and overestimate the impact of school closures as a means of reducing child contacts, particularly in the longer-term. These errors, in turn, may have caused incorrect estimations about the potential benefits of closing schools on a society level while simultaneously failing to account for the significant harms of long-term educational disruption. Pandemic response plans need to be updated to include nuances regarding drivers of transmission such as pathogen type, population immunity, and contact patterns, and disease severity in different groups. Expected duration of impact also needs to be considered, recognizing that effectiveness of different interventions, particularly those focused on limiting social interactions, are short-lived. Additionally, future iterations should include risk-benefit assessments. Interventions that are particularly harmful to certain groups, such as school closures are on children, should be de-emphasized and time limited. Finally, pandemic responses should include ongoing and continuous policy re-evaluation and should include a clear plan for de-implementation and de-escalation.

Risk factors for SARS-CoV-2 transmission in close contacts of adults at high risk of infection due to occupation: results from the contact tracing strategy of the CoVIDA epidemiological surveillance study in Bogotá, Colombia, in 2020-2021

OBJECTIVES

To estimate the risk factors for SARS-CoV-2 transmission in close contacts of adults at high risk of infection due to occupation, participants of the CoVIDA study, in Bogotá D.C., Colombia.

SETTING

The CoVIDA study was the largest COVID-19 intensified sentinel epidemiological surveillance study in Colombia thus far, performing over 60 000 RT-PCR tests for SARS-CoV-2 infection. The study implemented a contact tracing strategy (via telephone call) to support traditional surveillance actions performed by the local health authority.

PARTICIPANTS

Close contacts of participants from the CoVIDA study.

PRIMARY AND SECONDARY OUTCOME MEASURES

SARS-CoV-2 testing results were obtained (RT-PCR with CoVIDA or self-reported results). The secondary attack rate (SAR) was calculated using contacts and primary cases features.

RESULTS

The CoVIDA study performed 1257 contact tracing procedures on primary cases. A total of 5551 close contacts were identified and 1050 secondary cases (21.1%) were found. The highest SAR was found in close contacts: (1) who were spouses (SAR=32.7%; 95% CI 29.1% to 36.4%), (2) of informally employed or unemployed primary cases (SAR=29.1%; 95% CI 25.5% to 32.8%), (3) of symptomatic primary cases (SAR of 25.9%; 95% CI 24.0% to 27.9%) and (4) living in households with more than three people (SAR=22.2%; 95% CI 20.7% to 23.8%). The spouses (OR 3.85; 95% CI 2.60 to 5.70), relatives (OR 1.89; 95% CI 1.33 to 2.70) and close contacts of a symptomatic primary case (OR 1.48; 95% CI 1.24 to 1.77) had an increased risk of being secondary cases compared with non-relatives and close contacts of an asymptomatic index case, respectively.

CONCLUSIONS

Contact tracing strategies must focus on households with socioeconomic vulnerabilities to guarantee isolation and testing to stop the spread of the disease.

Structural and Managerial Risk Factors for COVID-19 Occurrence in French Nursing Homes

BACKGROUND

Nursing home (NH) residents accounted for half of the deaths during the 2020 spring wave of the coronavirus disease 2019 (COVID-19) epidemic in France. Our objective was to identify structural and managerial factors associated with COVID-19 outbreaks in NHs.

METHODS

We conducted in July 2020 a retrospective study by questionnaire addressed to NH directors in the Brittany region of France. The questions related to structural characteristics of the establishment, human resources, and crisis management decisions. The primary endpoint was the occurrence of at least one confirmed case of COVID-19 among residents between March 1, 2020 and May 31, 2020. The secondary endpoint was total mortality during this period. We used multivariate regressions to identify factors associated with these outcomes.

RESULTS

Responses were collected from 231 NHs hosting 20,881 residents, representing a participation rate of 47%. In 24 (10%) NHs, at least one resident presented confirmed COVID-19. NHs often implemented stringent protective measures, with 65% of them choosing to confine residents to their rooms. In multivariate analysis, factors associated with a reduced risk of case occurrence were in-room meal service, early ban of family visits, and daily access to an outdoor space. No association was found between mortality and the factors studied. Our results show an early and strict implementation of lockdown measures, with good epidemiological results in a context of shortage of personal protective equipment (PPE) and non-vaccination. Nevertheless, it raises ethical questions concerning respect of residents' wellbeing and rights.

CONCLUSION

Cessation of communal dining seems to be the main measure likely to be effective in preventive terms. It does not seem that room lockdown and cessation of group activities should be recommended, particularly if mask wearing is possible.

Investigating transmission of SARS-CoV-2 using novel face mask sampling: a protocol for an observational prospective study of index cases and their contacts in a congregate setting

INTRODUCTION

This study aims to measure how transmission of SARS-CoV-2 occurs in communities and to identify conditions that lend to increased transmission focusing on congregate situations. We will measure SARS-CoV-2 in exhaled breath of asymptomatic and symptomatic persons using face mask sampling-a non-invasive method for SARS-CoV-2 detection in exhaled air. We aim to detect transmission clusters and identify risk factors for SARS-CoV-2 transmission in presymptomatic, asymptomatic and symptomatic individuals.

METHODS AND ANALYSIS

In this observational prospective study with daily follow-up, index cases and their respective contacts are identified at each participating institution. Contact definitions are based on Centers for Disease Control and Prevention and local health department guidelines. Participants will wear masks with polyvinyl alcohol test strips adhered to the inside for 2 hours daily. The strips are applied to all masks used over at least 7 days. In addition, self-administered nasal swabs and (optional) finger prick blood samples are performed by participants. Samples are tested by standard PCR protocols and by novel antigen tests.

ETHICS AND DISSEMINATION

This study was approved by the Colorado Multiple Institutional Review Board and the WHO Ethics Review Committee. From the data generated, we will analyse transmission clusters and risk factors for transmission of SARS-CoV-2 in congregate settings. The kinetics of asymptomatic transmission and the evaluation of non-invasive tools for detection of transmissibility are of crucial importance for the development of more targeted control interventions-and ultimately to assist with keeping congregate settings open that are essential for our social fabric.

TRIAL REGISTRATION NUMBER

ClinicalTrials.gov (#NCT05145803).

Increasing contributions of airborne route in SARS-CoV-2 omicron variant transmission compared with the ancestral strain

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has become the dominant lineage worldwide. Experimental studies have shown that SARS-CoV-2 Omicron variant is more stable on various environmental surfaces than the ancestral strains of SARS-CoV-2. However, the influences on the role of the contact route in SARS-CoV-2 transmission are still unknown. In this study, we built a Markov chain model to simulate the transmission of the Omicron and ancestral strains of SARS-CoV-2 within a household over a 1-day period from multiple pathways; that is, airborne, droplet, and contact routes. We assumed that there were two adults and one child in the household, and that one of the adults was infected with SARS-CoV-2. We assumed two scenarios. (1) Asymptomatic/presymptomatic infection, and (2) symptomatic infection. During asymptomatic/presymptomatic infection, the contact route contributing the most (37%-45%), followed by the airborne (34%-38%) and droplet routes (21%-28%). During symptomatic infection, the droplet route was the dominant pathway (48%-71%), followed by the contact route (25%-42%), with the airborne route playing a negligible role (<10%). Compared to the ancestral strain, although the contribution of the contact route increased in Omicron variant transmission, the increase was slight, from 25%-41% to 30%-45%. With the growing concern about the increase in the proportion of asymptomatic/presymptomatic infection in Omicron strain transmissions, the airborne route, rather than the fomite route, should be of focus. Our findings suggest the importance of ventilation in the SARS-CoV-2 Omicron variant prevention in building environment.

Characteristics of Living Systematic Review for COVID-19

Purpose

The systematic review aims to analyze and summarize the characteristics of living systematic review (LSR) for coronavirus disease 2019 (COVID-19).

Methods

Six databases including Medline, Excerpta Medica (Embase), Cochrane Library, China National Knowledge Infrastructure (CNKI), Wanfang Database and China Science, and Technology Journal Database (VIP), were searched as the source of basic information and methodology of LSR. Descriptive analytical methods were used to analyze the included COVID-19 LSRs, and the study characteristics of COVID-19 LSRs were further assessed.

Results

Sixty-four COVID-19 LSRs were included. Eighty-nine point one percent of LSRs were published on Science Citation Index (SCI) journals, and 64.1% publication with an impact factor (IF) >5 and 17.2% with an IF >15 among SCI journals. The first unit of the published LSRs for COVID-19 came from 19 countries, with the largest contribution from the UK (17.2%, 11/64). Forty point six percent of LSRs for COVID-19 were related to therapeutics topic which was considered the most concerned perspective for LSRs for COVID-19. Seventy-six point six percent of LSRs focused on the general population, with less attention to children, pregnant women and the elderly. However, the LSR for COVID-19 was reported incomplete on “living” process, including 40.6% of studies without search frequency, 79.7% of studies without screening frequency, 20.3% of studies without update frequency, and 65.6% of studies without the timing or criteria of transitioning LSR out of living mode.

Conclusion

Although researchers in many countries have applied LSRs to COVID-19, most of the LSRs for COVID-19 were incomplete in reporting on the “living” process and less focused on special populations. This could reduce the confidence of health-care providers and policy makers in the results of COVID-19 LSR, thereby hindering the translation of evidence on COVID-19 LSR into clinical practice. It was necessary to explicitly enact preferred reporting items for systematic reviews and meta-analyses (PRISMA) to improve the reporting quality of LSR and support ongoing efforts of therapeutics research for special patients with COVID-19.

Palliative Care Landscape in the COVID-19 Era: Bibliometric Analysis of Global Research

Despite the increasing number of publications globally, the COVID-19 pandemic has underscored significant research gaps that should be resolved, including within PC-related research. This study aimed to map and understand the global trends in palliative care (PC)-related COVID-19 research and provide quantitative evidence to guide future studies. We systematically searched four databases between 1st January 2020 and 25th April 2022. The VOSviewer, Gephi, and R software were utilized for data analysis and results visualization. A total of 673 articles were identified from the databases between 1st January 2020 and 25th April 2022. Canada (6.2%), Australia (5.4%), and the United Kingdom (3.8%) were the most productive countries regarding articles published per million confirmed COVID-19 cases. A lack of international collaborations and an uneven research focus on PC across countries with different pandemic trajectories was observed. The PC research in question focused on cancer, telehealth, death and dying, and bereavement. This study’s conclusions support the recommendation for international collaboration to facilitate knowledge and practice transformation to support countries with unmet PC needs during the pandemic. Further studies are required on the grief and bereavement support of families, healthcare professionals and patients with other life-threatening illnesses.

Misleading Meta-Analyses during COVID-19 Pandemic: Examples of Methodological Biases in Evidence Synthesis

Not all evidence is equal. Evidence-based public health and medicine emanate from the principle that there is a hierarchy of evidence, with systematic reviews and meta-analyses (SRMAs) being at the top, as the highest level of evidence. Despite this, it is common in literature to find SRMAs with methodological issues that can distort the results and can thus have serious public health or clinical implications. During the Coronavirus Disease 2019 (COVID-19) pandemic, the importance of evidence and the way in which evidence was produced was stress tested and revealed a wide array of methodological biases that might have led to misleading conclusions and recommendations. We provide a critical examination of methodological biases in selected SRMAs on COVID-19, which have been widely used to guide or justify some pharmaceutical and nonpharmaceutical interventions with high public health and clinical significance, such as mask wearing, asymptomatic transmission, and ivermectin. Through these selected examples, we highlight the need to address biases related to the methodological quality and relevance of study designs and effect size computations and considerations for critical appraisal of available data in the evidence synthesis process for better quality evidence. Such considerations help researchers and decision makers avoid misleading conclusions, while encouraging the provision of the best policy recommendations for individual and public health.

Proportion of Pre-Symptomatic Transmission Events Associated with COVID-19 in South Korea

Pre-symptomatic transmission potentially reduces the effectiveness of symptom-onset-based containment and control strategies for the coronavirus disease (COVID-19). Despite evidence from multiple settings, the proportion of pre-symptomatic transmission varies among countries. To estimate the extent of pre-symptomatic transmission in South Korea, we used individual-level COVID-19 case records from the Korea Disease Control and Prevention Agency and Central Disease Control Headquarters. We inferred the probability of symptom onset per day since infection based on the density distribution of the incubation period to stratify the serial interval distribution in Period 1 (20 January–10 February 2020) and Period 2 (25 July–4 December 2021), without and with expanded testing or implementation of social distancing strategies, respectively. Assuming both no correlation as well as positive and negative correlations between the incubation period and the serial interval, we estimated the proportion of pre-symptomatic transmission in South Korea as 43.5% (accounting for correlation, range: 9.9–45.4%) and 60.0% (56.2–64.1%) without and with expanded testing, respectively, during the Delta variant’s predominance. This study highlights the importance of considering pre-symptomatic transmission for COVID-19 containment and mitigation strategies because pre-symptomatic transmission may play a key role in the epidemiology of COVID-19.

Screening and vaccination against COVID-19 to minimise school closure: a modelling study

BACKGROUND

Schools were closed extensively in 2020-21 to counter SARS-CoV-2 spread, impacting students' education and wellbeing. With highly contagious variants expanding in Europe, safe options to maintain schools open are urgently needed. By estimating school-specific transmissibility, our study evaluates costs and benefits of different protocols for SARS-CoV-2 control at school.

METHODS

We developed an agent-based model of SARS-CoV-2 transmission in schools. We used empirical contact data in a primary and a secondary school and data from pilot screenings in 683 schools during the alpha variant (B.1.1.7) wave in March-June, 2021, in France. We fitted the model to observed school prevalence to estimate the school-specific effective reproductive number for the alpha (Ralpha) and delta (B.1.617.2; Rdelta) variants and performed a cost-benefit analysis examining different intervention protocols.

FINDINGS

We estimated Ralpha to be 1·40 (95% CI 1·35-1·45) in the primary school and 1·46 (1·41-1·51) in the secondary school during the spring wave, higher than the time-varying reproductive number estimated from community surveillance. Considering the delta variant and vaccination coverage in Europe as of mid-September, 2021, we estimated Rdelta to be 1·66 (1·60-1·71) in primary schools and 1·10 (1·06-1·14) in secondary schools. Under these conditions, weekly testing of 75% of unvaccinated students (PCR tests on saliva samples in primary schools and lateral flow tests in secondary schools), in addition to symptom-based testing, would reduce cases by 34% (95% CI 32-36) in primary schools and 36% (35-39) in secondary schools compared with symptom-based testing alone. Insufficient adherence was recorded in pilot screening (median ≤53%). Regular testing would also reduce student-days lost up to 80% compared with reactive class closures. Moderate vaccination coverage in students would still benefit from regular testing for additional control-ie, weekly testing 75% of unvaccinated students would reduce cases compared with symptom-based testing only, by 23% in primary schools when 50% of children are vaccinated.

INTERPRETATION

The COVID-19 pandemic will probably continue to pose a risk to the safe and normal functioning of schools. Extending vaccination coverage in students, complemented by regular testing with good adherence, are essential steps to keep schools open when highly transmissible variants are circulating.

FUNDING

EU Framework Programme for Research and Innovation Horizon 2020, Horizon Europe Framework Programme, Agence Nationale de la Recherche, ANRS-Maladies Infectieuses Émergentes.

The past, current and future epidemiological dynamic of SARS-CoV-2

SARS-CoV-2, the agent of the COVID-19 pandemic, emerged in late 2019 in China, and rapidly spread throughout the world to reach all continents. As the virus expanded in its novel human host, viral lineages diversified through the accumulation of around two mutations a month on average. Different viral lineages have replaced each other since the start of the pandemic, with the most successful Alpha, Delta and Omicron variants of concern (VoCs) sequentially sweeping through the world to reach high global prevalence. Neither Alpha nor Delta was characterized by strong immune escape, with their success coming mainly from their higher transmissibility. Omicron is far more prone to immune evasion and spread primarily due to its increased ability to (re-)infect hosts with prior immunity. As host immunity reaches high levels globally through vaccination and prior infection, the epidemic is expected to transition from a pandemic regime to an endemic one where seasonality and waning host immunization are anticipated to become the primary forces shaping future SARS-CoV-2 lineage dynamics. In this review, we consider a body of evidence on the origins, host tropism, epidemiology, genomic and immunogenetic evolution of SARS-CoV-2 including an assessment of other coronaviruses infecting humans. Considering what is known so far, we conclude by delineating scenarios for the future dynamic of SARS-CoV-2, ranging from the good-circulation of a fifth endemic 'common cold' coronavirus of potentially low virulence, the bad-a situation roughly comparable with seasonal flu, and the ugly-extensive diversification into serotypes with long-term high-level endemicity.

Modeling the COVID-19 pandemic: a primer and overview of mathematical epidemiology

Since the start of the still ongoing COVID-19 pandemic, there have been many modeling efforts to assess several issues of importance to public health. In this work, we review the theory behind some important mathematical models that have been used to answer questions raised by the development of the pandemic. We start revisiting the basic properties of simple Kermack-McKendrick type models. Then, we discuss extensions of such models and important epidemiological quantities applied to investigate the role of heterogeneity in disease transmission e.g. mixing functions and superspreading events, the impact of non-pharmaceutical interventions in the control of the pandemic, vaccine deployment, herd-immunity, viral evolution and the possibility of vaccine escape. From the perspective of mathematical epidemiology, we highlight the important properties, findings, and, of course, deficiencies, that all these models have.

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.

Screening for Severe Acute Respiratory Syndrome Coronavirus 2 in Close Contacts of Individuals With Confirmed Infection: Performance and Operational Considerations

BACKGROUND

Point-of-care and decentralized testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to inform public health responses. Performance evaluations in priority use cases such as contact tracing can highlight trade-offs in test selection and testing strategies.

METHODS

A prospective diagnostic accuracy study was conducted among close contacts of coronavirus disease 2019 (COVID-19) cases in Brazil. Two anterior nares swabs (ANS), a nasopharyngeal swab (NPS), and saliva were collected at all visits. Vaccination history and symptoms were assessed. Household contacts were followed longitudinally. Three rapid antigen tests and 1 molecular method were evaluated for usability and performance against reference reverse-transcription polymerase chain reaction (RT-PCR) on nasopharyngeal swab specimens.

RESULTS

Fifty index cases and 214 contacts (64 household) were enrolled. Sixty-five contacts were RT-PCR positive during ≥1 visit. Vaccination did not influence viral load. Gamma variants were most prevalent; Delta variants emerged increasingly during implementation. The overall sensitivity of evaluated tests ranged from 33% to 76%. Performance was higher among symptomatic cases and those with cycle threshold (Ct) values <34 and lower among oligosymptomatic or asymptomatic cases. Assuming a 24-hour time to results for RT-PCR, the cumulative sensitivity of an anterior nares swab rapid antigen test was >70% and almost 90% after 4 days.

CONCLUSIONS

The near-immediate time to results for antigen tests significantly offsets lower analytical sensitivity in settings where RT-PCR results are delayed or unavailable.

Occurrence and transmission potential of asymptomatic and presymptomatic SARS-CoV-2 infections: Update of a living systematic review and meta-analysis

BACKGROUND

Debate about the level of asymptomatic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection continues. The amount of evidence is increasing and study designs have changed over time. We updated a living systematic review to address 3 questions: (1) Among people who become infected with SARS-CoV-2, what proportion does not experience symptoms at all during their infection? (2) What is the infectiousness of asymptomatic and presymptomatic, compared with symptomatic, SARS-CoV-2 infection? (3) What proportion of SARS-CoV-2 transmission in a population is accounted for by people who are asymptomatic or presymptomatic?

METHODS AND FINDINGS

The protocol was first published on 1 April 2020 and last updated on 18 June 2021. We searched PubMed, Embase, bioRxiv, and medRxiv, aggregated in a database of SARS-CoV-2 literature, most recently on 6 July 2021. Studies of people with PCR-diagnosed SARS-CoV-2, which documented symptom status at the beginning and end of follow-up, or mathematical modelling studies were included. Studies restricted to people already diagnosed, of single individuals or families, or without sufficient follow-up were excluded. One reviewer extracted data and a second verified the extraction, with disagreement resolved by discussion or a third reviewer. Risk of bias in empirical studies was assessed with a bespoke checklist and modelling studies with a published checklist. All data syntheses were done using random effects models. Review question (1): We included 130 studies. Heterogeneity was high so we did not estimate a mean proportion of asymptomatic infections overall (interquartile range (IQR) 14% to 50%, prediction interval 2% to 90%), or in 84 studies based on screening of defined populations (IQR 20% to 65%, prediction interval 4% to 94%). In 46 studies based on contact or outbreak investigations, the summary proportion asymptomatic was 19% (95% confidence interval (CI) 15% to 25%, prediction interval 2% to 70%). (2) The secondary attack rate in contacts of people with asymptomatic infection compared with symptomatic infection was 0.32 (95% CI 0.16 to 0.64, prediction interval 0.11 to 0.95, 8 studies). (3) In 13 modelling studies fit to data, the proportion of all SARS-CoV-2 transmission from presymptomatic individuals was higher than from asymptomatic individuals. Limitations of the evidence include high heterogeneity and high risks of selection and information bias in studies that were not designed to measure persistently asymptomatic infection, and limited information about variants of concern or in people who have been vaccinated.

CONCLUSIONS

Based on studies published up to July 2021, most SARS-CoV-2 infections were not persistently asymptomatic, and asymptomatic infections were less infectious than symptomatic infections. Summary estimates from meta-analysis may be misleading when variability between studies is extreme and prediction intervals should be presented. Future studies should determine the asymptomatic proportion of SARS-CoV-2 infections caused by variants of concern and in people with immunity following vaccination or previous infection. Without prospective longitudinal studies with methods that minimise selection and measurement biases, further updates with the study types included in this living systematic review are unlikely to be able to provide a reliable summary estimate of the proportion of asymptomatic infections caused by SARS-CoV-2.

REVIEW PROTOCOL

Open Science Framework (https://osf.io/9ewys/).

SARS-CoV-2 Molecular Epidemiology Can Be Enhanced by Occupational Health: The Experience of Monitoring Variants of Concern in Workplaces in Rio de Janeiro, Brazil

The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to extra caution in workplaces to avoid the coronavirus disease 2019 (COVID-19). In the occupational environment, SARS-CoV-2 testing is a powerful approach in providing valuable information to detect, monitor, and mitigate the spread of the virus and preserve productivity. Here a centralized Occupational Health Center provided molecular diagnosis and genomic sequences for companies and industries in Rio de Janeiro, Brazil. From May to August 2021, around 20% of the SARS-CoV-2 positive nasopharyngeal swabs from routinely tested workers were sequenced and reproduced the replacement of Gamma with Delta variant observed in regular surveillance programs. Moreover, as a proof-of-concept on the sensibility of the occupational health genomic surveillance program described here, it was also found: i) the primo-identification of B.1.139 and A.2.5 viral genomes in Brazil and ii) an improved dating of Delta VoC evolution, by identifying earlier cases associated with AY-related genomes. We interpret that SARS-CoV-2 molecular testing of workers, independent of symptom presentation, provides an earlier opportunity to identify variants. Thus, considering the continuous monitoring of SARS-CoV-2 in workplaces, positive samples from occupation health programs should be regarded as essential to improve the knowledge on virus genetic diversity and VoC emergence.

Comparison of Saliva and Midturbinate Swabs for Detection of SARS-CoV-2

Saliva is an attractive sample for detecting SARS-CoV-2. However, contradictory reports exist concerning the sensitivity of saliva versus nasal swabs. We followed close contacts of COVID-19 cases for up to 14 days from the last exposure and collected self-reported symptoms, midturbinate swabs (MTS), and saliva every 2 or 3 days. Ct values, viral load, and frequency of viral detection by MTS and saliva were compared. Fifty-eight contacts provided 200 saliva-MTS pairs, and 14 contacts (13 with symptoms) had one or more positive samples. Saliva and MTS had similar rates of viral detection (P = 0.78) and substantial agreement (κ = 0.83). However, sensitivity varied significantly with time since symptom onset. Early on (days -3 to 2), saliva had 12 times (95% CI: 1.2, 130) greater likelihood of viral detection and 3.2 times (95% CI: 2.8, 3.8) higher RNA copy numbers compared to MTS. After day 2 of symptoms, there was a nonsignificant trend toward greater sensitivity using MTS. Saliva and MTS demonstrated high agreement making saliva a suitable alternative to MTS for SARS-CoV-2 detection. Saliva was more sensitive early in the infection when the transmission was most likely to occur, suggesting that it may be a superior and cost-effective screening tool for COVID-19. IMPORTANCE The findings of this manuscript are increasingly important with new variants that appear to have shorter incubation periods emerging, which may be more prone to detection in saliva before detection in nasal swabs. Therefore, there is an urgent need to provide the science to support the use of a detection method that is highly sensitive and widely acceptable to the public to improve screening rates and early detection. The manuscript presents the first evidence that saliva-based RT-PCR is more sensitive than MTS-based RT-PCR in detecting SARS-CoV-2 during the presymptomatic period - the critical period for unwitting onward transmission. Considering other advantages of saliva samples, including the lower cost, greater acceptability within the general population, and less risk to health care workers, our findings further supported the use of saliva to identify presymptomatic infection and prevent transmission of the virus.

Epidemiological, Radiographical, and Laboratorial Characteristics of Chinese Asymptomatic Cases With COVID-19: A Systematic Review and Meta-Analysis

The comprehensive understanding of the characteristics of asymptomatic cases are helpful for the identification and management of patients with asymptomatic COVID-19 infection. Four electronic databases were searched from December 1, 2019 to February 8, 2022 for relevant articles. Data synthesis, subgroup analysis, and sensitivity analysis were performed on the included studies. I² and Q tests were applied to evaluate heterogeneity across studies. The risk of publication bias was assessed and visualized using a funnel plot. A total of 45 studies consisting of 2,655 patients with no symptoms at the screening point were included. Pooled results showed that in China, 65% of initial no-symptoms COVID-19 patients did not present any COVID-19-related symptom during follow-up or by end of disease course (asymptomatic infections). High proportions of initial no-symptoms COVID-19 patients (76%) and patients with asymptomatic infection (55%) had abnormal CT features at the screening point. High proportion of patients with asymptomatic infection had been detected Ig G⁺ (72%) and/or Ig M⁺ (57%) at the screening point. The chest CT scan and SARS-CoV-2-specific antibody testing could serve as effective supplementary methods to identify asymptomatic cases in the early stage of SARS-CoV-2 infection. However, the chest CT scan and the SARS-CoV-2-specific IgM and IgG testing should not replace reverse transcription–polymerase chain reaction (RT-PCR) for screening in asymptomatic patients. The combination of repeated RT-PCR, chest CT scans, and the SARS-CoV-2-specific IgM and IgG testing should be performed for those highly suspected SARS-CoV-2 infections.

Evaluating the impacts of tiered restrictions introduced in England, during October and December 2020 on COVID-19 cases: a synthetic control study

OBJECTIVES

To analyse the impact on SARS-CoV-2 transmission of tier 3 restrictions introduced in October and December 2020 in England, compared with tier 2 restrictions. We further investigate whether these effects varied between small areas by deprivation.

DESIGN

Synthetic control analysis.

SETTING

We identified areas introducing tier 3 restrictions in October and December, constructed a synthetic control group of places under tier 2 restrictions and compared changes in weekly infections over a 4-week period. Using interaction analysis, we estimated whether this effect varied by deprivation and the prevalence of a new variant (B.1.1.7).

INTERVENTIONS

In both October and December, no indoor between-household mixing was permitted in either tier 2 or 3. In October, no between-household mixing was permitted in private gardens and pubs and restaurants remained open only if they served a 'substantial meal' in tier 3, while in tier 2 meeting with up to six people in private gardens were allowed and all pubs and restaurants remained open. In December, in tier 3, pubs and restaurants were closed, while in tier 2, only those serving food remained open. The differences in restrictions between tier 2 and 3 on meeting outside remained the same as in October.

MAIN OUTCOME MEASURE

Weekly reported cases adjusted for changing case detection rates for neighbourhoods in England.

RESULTS

Introducing tier 3 restrictions in October and December was associated with a 14% (95% CI 10% to 19%) and 20% (95% CI 13% to 29%) reduction in infections, respectively, compared with the rates expected with tier 2 restrictions only. The effects were similar across levels of deprivation and by the prevalence of the new variant.

CONCLUSIONS

Compared with tier 2 restrictions, additional restrictions in tier 3 areas in England had a moderate effect on transmission, which did not appear to increase socioeconomic inequalities in COVID-19 cases.

Household transmission of SARS-CoV-2 from unvaccinated asymptomatic and symptomatic household members with confirmed SARS-CoV-2 infection: an antibody-surveillance study

BACKGROUND

Household transmission contributes to SARS-CoV-2 spread, but the role of children in transmission is unclear. We conducted a study that included symptomatic and asymptomatic children and adults exposed to SARS-CoV-2 in their households with the objective of determining how SARS-CoV-2 is transmitted within households.

METHODS

In this case-ascertained antibody-surveillance study, we enrolled households in Ottawa, Ontario, in which at least 1 household member had tested positive for SARS-CoV-2 on reverse transcription polymerase chain reaction testing. The enrolment period was September 2020 to March 2021. Potentially eligible participants were identified if they had tested positive for SARS-CoV-2 at an academic emergency department or affiliated testing centre; people who learned about the study through the media could also self-identify for participation. At least 2 participants were required for a household to be eligible for study participation, and at least 1 enrolled participant per household had to be a child (age < 18 yr). Enzyme-linked immunosorbent assays were used to evaluate SARS-CoV-2-specific IgA, IgM and IgG against the spike-trimer and nucleocapsid protein. The primary outcome was household secondary attack rate, defined as the proportion of household contacts positive for SARS-CoV-2 antibody among the total number of household contacts participating in the study. We performed descriptive statistics at both the individual and household levels. To estimate and compare outcomes between patient subgroups, and to examine predictors of household transmission, we fitted a series of multivariable logistic regression with robust standard errors to account for clustering of individuals within households.

RESULTS

We enrolled 695 participants from 180 households: 180 index participants (74 children, 106 adults) and 515 of their household contacts (266 children, 249 adults). A total of 487 household contacts (94.6%) (246 children, 241 adults) had SARS-CoV-2 antibody testing, of whom 239 had a positive result (secondary attack rate 49.1%, 95% confidence interval [CI] 42.9%-55.3%). Eighty-eight (36.8%, 95% CI 29.3%-43.2%) of the 239 were asymptomatic; asymptomatic rates were similar for children (51/130 [39.2%, 95% CI 30.7%-48.5%]) and adults (37/115 [32.2%, 95% CI 24.2%-41.4%]) (odds ratio [OR] 1.3, 95% CI 0.8-2.1). Adults were more likely than children to transmit SARS-CoV-2 (OR 2.2, 95% CI 1.3-3.6). The odds of transmission from asymptomatic (OR 0.6, 95% CI 0.2-1.4) versus symptomatic (OR 0.9, 95% CI 0.6-1.4) index participants to household contacts was uncertain. Predictors of household transmission included household density (number of people per bedroom), relationship to index participant and number of cases in the household.

INTERPRETATION

The rate of SARS-CoV-2 transmission within households was nearly 50% during the study period, and children were an important source of spread. The findings suggest that children are an important driver of the COVID-19 pandemic; this should inform public health policy.

Factors influencing the acquisition of COVID infection among high-risk contacts of COVID-19 patients in Madurai district-A case control study

Introduction

COVID is a new disease; understanding the transmission dynamics and epidemiological characteristics may help in developing the effective control measures. The study is done 1. To determine the various factors influencing the acquisition of COVID-19 infection among high-risk contacts 2. To estimate the secondary attack rate among high-risk contacts 3. To determine the factors in COVID index cases influencing their secondary attack rate.

Methodology

Unmatched case control study was conducted from March to August 2020 among 139 COVID index cases in Madurai district from March-May (Reference period) and their 50 COVID positive (cases), 551 COVID negative (controls) high-risk contacts. Case investigation form* and contact tracing Proforma*were used to collect data. Chi-square test and independent sample t test were used to find out the association. Univariate* and Multivariate logistic regression* were used to predict the risk of various factors in acquisition of COVID infection with the help of adjusted and unadjusted odds ratio. P value < 0.05 was considered statistically significant.

Results

Male contacts (P = 0.005, OR = 2.520), overcrowding (P = 0.007, OR = 3.810), and duration of exposure to index case (for 4-7 days P = 0.014, OR = 2.902, for >7 days P = 0.001, OR = 6.748 and for > 12 hours/day P = 0.000, OR = 5.543) were significant factors predicted to be associated with acquisition of COVID infection among high-risk contacts. Reproductive number (R0)* estimated was 1.3. Secondary attack rate (SAR)* estimated among high-risk contacts was 8.32%. Index cases whose outcome was death (P = 0.026); symptomatic index cases (P = 0.000), cases with fever (P = 0.001); sorethroat (P = 0.019); breathlessness (P = 0.010); cough (P = 0.006) and running nose (P = 0.002) had significantly higher mean SAR than their counterparts.

Conclusion

Contacts with above said risk factors who were found to be more prone to infection could be given special focus to prevent the transmission in them.

VSV-Based Vaccines Reduce Virus Shedding and Viral Load in Hamsters Infected with SARS-CoV-2 Variants of Concern

The continued progression of the COVID-19 pandemic can partly be attributed to the ability of SARS-CoV-2 to mutate and introduce new viral variants. Some of these variants with the potential to spread quickly and conquer the globe are termed variants of concern (VOC). The existing vaccines implemented on a global scale are based on the ancestral strain, which has resulted in increased numbers of breakthrough infections as these VOC have emerged. It is imperative to show protection against VOC infection with newly developed vaccines. Previously, we evaluated two vesicular stomatitis virus (VSV)-based vaccines expressing the SARS-CoV-2 spike protein alone (VSV-SARS2) or in combination with the Ebola virus glycoprotein (VSV-SARS2-EBOV) and demonstrated their fast-acting potential. Here, we prolonged the time to challenge; we vaccinated hamsters intranasally (IN) or intramuscularly 28 days prior to infection with three SARS-CoV-2 VOC-the Alpha, Beta, and Delta variants. IN vaccination with either the VSV-SARS2 or VSV-SARS2-EBOV resulted in the highest protective efficacy as demonstrated by decreased virus shedding and lung viral load of vaccinated hamsters. Histopathologic analysis of the lungs revealed the least amount of lung damage in the IN-vaccinated animals regardless of the challenge virus. This data demonstrates the ability of a VSV-based vaccine to not only protect from disease caused by SARS-CoV-2 VOC but also reduce viral shedding.

The changing epidemiology of SARS-CoV-2

We have come a long way since the start of the COVID-19 pandemic-from hoarding toilet paper and wiping down groceries to sending our children back to school and vaccinating billions. Over this period, the global community of epidemiologists and evolutionary biologists has also come a long way in understanding the complex and changing dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19. In this Review, we retrace our steps through the questions that this community faced as the pandemic unfolded. We focus on the key roles that mathematical modeling and quantitative analyses of empirical data have played in allowing us to address these questions and ultimately to better understand and control the pandemic.

Vaccine efficacy and SARS-CoV-2 control in California and U.S. during the session 2020-2026: A modeling study

BACKGROUND

Besides maintaining health precautions, vaccination has been the only prevention from SARS-CoV-2, though no clinically proved 100% effective vaccine has been developed till date. At this stage, to withhold the debris of this pandemic-experts need to know the impact of the vaccine efficacy rates, the threshold level of vaccine effectiveness and how long this pandemic may extent with vaccines that have different efficacy rates. In this article, a mathematical model study has been done on the importance of vaccination and vaccine efficiency rate during an ongoing pandemic.

METHODS

We simulated a five compartment mathematical model to analyze the pandemic scenario in both California, and whole U.S. We considered four vaccines, Pfizer (95%), Moderna (94%), AstraZeneca (79%), and Johnson & Johnson (72%), which are being used rigorously to control the SARS-CoV-2 pandemic, in addition with two special cases: a vaccine with 100% efficacy rate and no vaccine under use. SARS-CoV-2 related data of California, and U.S. were used in this study.

FINDINGS

Both the infection and death rates are very high in California. Our model suggests that the pandemic situation in California will be under control in the last quartile of the year 2023 if vaccination program is continued with the Pfizer vaccine. During this time, six waves may happen from the beginning of the immunization where the case fatality and recovery rates will be 1.697% and 98.30%, respectively. However, according to the considered model, this period might be extended to the mid of 2024 when vaccines with lower efficacy rates are used. On the other hand, the daily cases and deaths in the U.S. will be under control at the end of 2026 with multiple waves. Although the number of susceptible people will fall down to none in the beginning of 2027, there is less chance to stop the vaccination program if vaccinated with a vaccine other than a 100% effective vaccine or Pfizer, and at that case vaccination program must run till the mid of 2028. According to this study, the unconfirmed-infectious and infected cases will be under control at the end of 2027 and at the mid of 2028, respectively.

INTERPRETATION

The more effective a vaccine is, the less people suffer from this malign infection. Vaccines which are less than 90% effective do not have notable contribution to control the pandemic besides hard immunity. Furthermore, specific groups of people are getting prioritized initially, mass vaccination and quick responses are required to control the spread of this disease.

Advances in nucleic acid amplification techniques (NAATs): COVID-19 point-of-care diagnostics as an example

Achieving superhigh sensitivity is the ultimate goal for bio-detection in modern analytical science and life science. Among variable signal amplification strategies, nucleic acid amplification technologies are revolutionizing the field of bio-detection, providing greater possibilities in novel diagnosis achieving high efficiency, specificity, and cost-effectiveness. Nucleic acid amplification techniques (NAATs), such as Polymerase Chain Reaction (PCR), Rolling Circle Amplification (RCA), Loop-Mediated Isothermal Amplification (LAMP), Recombinase Polymerase Amplification (RPA), CRISPR-related amplification, and others are dominating methods employed in research and clinical settings. They each provide distinctively unique features that can offer desirable performance in terms of sensitivity, specificity, simplicity, stability, and cost. NAATs are in unmet demand in molecular diagnosis, especially in point-of-care scenario. This review will discuss the principles and recent advancements of each NAAT, respectively, revealing their strengths and challenges in achieving rapid and accurate bio-detection with a focus on point-of-care diagnosis. Furthermore, this review will explore the application of each of the technologies through the contemporary COVID-19 pandemic, analyzing their ability in point-of-care diagnosis of the COVID-19 with high sensitivity to emphasize significance of developing NAATs based methods in battling COVID-19. Finally, advantages and potentials of each NAAT in enhancements of sensitivity and specificity in bio-detection from bench side to the bedside will be discussed, aiming for full exploitation of capability of each NAAT. This review will provide novel aspects in the selection and combination of usages of various NAATs based on their distinctive characteristics and limitations. A possible advancing direction of future accurate POCT is also proposed.

Human Nasal Epithelial Cells Sustain Persistent SARS-CoV-2 Infection In Vitro, despite Eliciting a Prolonged Antiviral Response

The dynamics of SARS-CoV-2 infection in COVID-19 patients are highly variable, with a subset of patients demonstrating prolonged virus shedding, which poses a significant challenge for disease management and transmission control. In this study, the long-term dynamics of SARS-CoV-2 infection were investigated using a human well-differentiated nasal epithelial cell (NEC) model of infection. NECs were observed to release SARS-CoV-2 virus onto the apical surface for up to 28 days postinfection (dpi), further corroborated by viral antigen staining. Single-cell transcriptome sequencing (sc-seq) was utilized to explore the host response from infected NECs after short-term (3-dpi) and long-term (28-dpi) infection. We identified a unique population of cells harboring high viral loads present at both 3 and 28 dpi, characterized by expression of cell stress-related genes DDIT3 and ATF3 and enriched for genes involved in tumor necrosis factor alpha (TNF-α) signaling and apoptosis. Remarkably, this sc-seq analysis revealed an antiviral gene signature within all NEC cell types even at 28 dpi. We demonstrate increased replication of basal cells, absence of widespread cell death within the epithelial monolayer, and the ability of SARS-CoV-2 to replicate despite a continuous interferon response as factors likely contributing to SARS-CoV-2 persistence. This study provides a model system for development of therapeutics aimed at improving viral clearance in immunocompromised patients and implies a crucial role for immune cells in mediating viral clearance from infected epithelia. IMPORTANCE Increasing medical attention has been drawn to the persistence of symptoms (long-COVID syndrome) or live virus shedding from subsets of COVID-19 patients weeks to months after the initial onset of symptoms. In vitro approaches to model viral or symptom persistence are needed to fully dissect the complex and likely varied mechanisms underlying these clinical observations. We show that in vitro differentiated human NECs are persistently infected with SARS-CoV-2 for up to 28 dpi. This viral replication occurred despite the presence of an antiviral gene signature across all NEC cell types even at 28 dpi. This indicates that epithelial cell intrinsic antiviral responses are insufficient for the clearance of SARS-CoV-2, implying an essential role for tissue-resident and infiltrating immune cells for eventual viral clearance from infected airway tissue in COVID-19 patients.

Estimating local outbreak risks and the effects of non-pharmaceutical interventions in age-structured populations: SARS-CoV-2 as a case study

During the COVID-19 pandemic, non-pharmaceutical interventions (NPIs) including school closures, workplace closures and social distancing policies have been employed worldwide to reduce transmission and prevent local outbreaks. However, transmission and the effectiveness of NPIs depend strongly on age-related factors including heterogeneities in contact patterns and pathophysiology. Here, using SARS-CoV-2 as a case study, we develop a branching process model for assessing the risk that an infectious case arriving in a new location will initiate a local outbreak, accounting for the age distribution of the host population. We show that the risk of a local outbreak depends on the age of the index case, and we explore the effects of NPIs targeting individuals of different ages. Social distancing policies that reduce contacts outside of schools and workplaces and target individuals of all ages are predicted to reduce local outbreak risks substantially, whereas school closures have a more limited impact. In the scenarios considered here, when different NPIs are used in combination the risk of local outbreaks can be eliminated. We also show that heightened surveillance of infectious individuals reduces the level of NPIs required to prevent local outbreaks, particularly if enhanced surveillance of symptomatic cases is combined with efforts to find and isolate nonsymptomatic infected individuals. Our results reflect real-world experience of the COVID-19 pandemic, during which combinations of intense NPIs have reduced transmission and the risk of local outbreaks. The general modelling framework that we present can be used to estimate local outbreak risks during future epidemics of a range of pathogens, accounting fully for age-related factors.

Asymptomatic and pre-symptomatic infection in Coronavirus Disease 2019 pandemic

With the presence of Coronavirus Disease 2019 (COVID-19) asymptomatic infections detected, their proportion, transmission potential, and other aspects such as immunity and related emerging challenges have attracted people's attention. We have found that based on high-quality research, asymptomatic infections account for at least one-third of the total cases, whereas based on systematic review and meta-analysis, the proportion is about one-fifth. Evaluating the true transmission potential of asymptomatic cases is difficult but critical, since it may affect national policies in response to COVID-19. We have summarized the current evidence and found, compared with symptomatic cases, the transmission capacity of asymptomatic individuals is weaker, even though they have similar viral load and relatively short virus shedding duration. As the outbreak progresses, asymptomatic infections have also been found to develop long COVID-19. In addition, the role of asymptomatic infection in COVID-19 remains to be further revealed as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge. Nevertheless, as asymptomatic infections transmit the SARS-CoV-2 virus silently, they still pose a substantial threat to public health. Therefore, it is essential to conduct screening to obtain more knowledge about the asymptomatic infections and to detect them as soon as possible; meanwhile, management of them is also a key point in the fight against COVID-19 community transmission. The different management of asymptomatic infections in various countries are compared and the experience in China is displayed in detail.

A Multi-center Retrospective Analysis of Healthcare Workers after COVID-19: Epidemiological and Clinical Features

Objective: Concerns regarding the high-level risk of infection among healthcare workers (HCWs) increased after COVID19 was declared as a pandemic in March 2020. Inadequate infection control owing to a shortage of personal protective equipment or an inconvenient usage of infection control measures may play a significant role in transmission to/among healthcare personnel. The study aimed to determine the characteristics and outcomes of COVID-19 patients who are healthcare workers along with possible transmission routes of COVID-19 in four different healthcare facilities in Istanbul. Methods: All hospital records were reviewed retrospectively. Demographic and clinical characteristics of HCWs were documented, and all infected HCWs were subjected to a phone-based mini-questionnaire and three-dimensional test (TDT). All statistical analyses were done using statistical packages SPSS Demo Ver 22 (SPSS Inc. Chicago, IL, USA). Results: Clinical features of COVID-19 were similar to the general public’s characteristics. The most frequent symptoms were cough, fever, and headache. HCWs with the O blood group tend to have asymptomatic COVID-19 infection. Hospital workers other than medical professionals have a lack of convenience of infection control measures. The median duration of PCR negativity was 9 days. HCWs who had a sore throat at the beginning of COVID-19 have a longer PCR-positive duration. Conclusion: Understanding the clinical features or characteristics of asymptomatic COVID-19 carriers may aid in the implementation of a feasible screening program for early detection. It is strongly advised that proper infection control precautions, education, and auditing of nonclinical staff be implemented. As a result, transmission among healthcare workers can be avoided.

Impact of close interpersonal contact on COVID-19 incidence: Evidence from 1 year of mobile device data

Close contact between people is the primary route for transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). We quantified interpersonal contact at the population level using mobile device geolocation data. We computed the frequency of contact (within 6 feet) between people in Connecticut during February 2020 to January 2021 and aggregated counts of contact events by area of residence. When incorporated into a SEIR-type model of COVID-19 transmission, the contact rate accurately predicted COVID-19 cases in Connecticut towns. Contact in Connecticut explains the initial wave of infections during March to April, the drop in cases during June to August, local outbreaks during August to September, broad statewide resurgence during September to December, and decline in January 2021. The transmission model fits COVID-19 transmission dynamics better using the contact rate than other mobility metrics. Contact rate data can help guide social distancing and testing resource allocation.

Demographic, Virological Characteristics and Prognosis of Asymptomatic COVID-19 Patients in South China

BACKGROUND

Asymptomatic transmission is a major concern for SARS-CoV-2 community spread; however, little information is available on demographic, virological characteristics and prognosis of asymptomatic cases.

METHODS

All COVID-19 patients hospitalized in Guangdong Province from September 1, 2020 to February 28, 2021, were included and were divided into asymptomatic and symptomaticgroup. The source country of all patients, clinical laboratory test results, the genotype of virus and the time of SARS-CoV-2 RNA turning negative or hospitalization were confirmed.

RESULTS

Total 233 patients from 57 different countries or regions were included, with 83 (35.6%) asymptomatic and 150 (64.4%) symptomatic patients. Asymptomatic cases were younger (P = 0.019), lower rate in comorbidities (P = 0.021) such as hypertension (P = 0.083) and chronic liver disease (P = 0.045), lower PCT (P = 0.021), DDI (P < 0.001) and ALT (P = 0.029), but higher WBC count (P = 0.002) and lymphocyte (P = 0.011) than symptomatic patients. As for SARS-CoV-2 subtypes, patients infected with B.1.1 (53.8%), B.1.351 (81.8%) and B.1.524 (60%) are mainly asymptomatic, while infected with B, B.1, B.1.1.63, B.1.1.7, B.1.36, B.1.36.1, B.1.36.16, B.1.5 and B.6 were inclined to be symptomatic. Patients infected with variant B.1.351 and B.1.524 spent longer time in SARS-CoV-2 RNA turn negative (26 days, P = 0.085; 41 days, P = 0.007) and hospitalization (28 days, P = 0.085; 43 days, P = 0.004).

CONCLUSIONS

The asymptomatic cases are prone to develop in patients with younger age, less comorbidities andinfected with B.1.1 and B.1.524 variants. More attention should be paid for lineage B.1.524 because it can significantly prolong the SARS-CoV-2 RNA negative conversion time and hospitalization in infected cases.