Predictors of SARS-CoV-2 infection following high-risk exposure

Nasopharyngeal angiotensin converting enzyme 2 (ACE2) expression as a risk-factor for SARS-CoV-2 transmission in concurrent hospital associated outbreaks

BACKGROUND

Widespread human-to-human transmission of the severe acute respiratory syndrome coronavirus two (SARS-CoV-2) stems from a strong affinity for the cellular receptor angiotensin converting enzyme two (ACE2). We investigate the relationship between a patient's nasopharyngeal ACE2 transcription and secondary transmission within a series of concurrent hospital associated SARS-CoV-2 outbreaks in British Columbia, Canada.

METHODS

Epidemiological case data from the outbreak investigations was merged with public health laboratory records and viral lineage calls, from whole genome sequencing, to reconstruct the concurrent outbreaks using infection tracing transmission network analysis. ACE2 transcription and RNA viral load were measured by quantitative real-time polymerase chain reaction. The transmission network was resolved to calculate the number of potential secondary cases. Bivariate and multivariable analyses using Poisson and Negative Binomial regression models was performed to estimate the association between ACE2 transcription the number of SARS-CoV-2 secondary cases.

RESULTS

The infection tracing transmission network provided n = 76 potential transmission events across n = 103 cases. Bivariate comparisons found that on average ACE2 transcription did not differ between patients and healthcare workers (P = 0.86). High ACE2 transcription was observed in 98.6% of transmission events, either the primary or secondary case had above average ACE2. Multivariable analysis found that the association between ACE2 transcription (log2 fold-change) and the number of secondary transmission events differs between patients and healthcare workers. In health care workers Negative Binomial regression estimated that a one-unit change in ACE2 transcription decreases the number of secondary cases (β = -0.132 (95%CI: -0.255 to -0.0181) adjusting for RNA viral load. Conversely, in patients a one-unit change in ACE2 transcription increases the number of secondary cases (β = 0.187 (95% CI: 0.0101 to 0.370) adjusting for RNA viral load. Sensitivity analysis found no significant relationship between ACE2 and secondary transmission in health care workers and confirmed the positive association among patients.

CONCLUSION

Our study suggests that ACE2 transcription has a positive association with SARS-CoV-2 secondary transmission in admitted inpatients, but not health care workers in concurrent hospital associated outbreaks, and it should be further investigated as a risk-factor for viral transmission.

Association between face mask use and risk of SARS-CoV-2 infection: Cross-sectional study

We examined the association between face masks and risk of infection with SARS-CoV-2 using cross-sectional data from 3,209 participants in a randomized trial exploring the effectiveness of glasses in reducing the risk of SARS-CoV-2 infection. Face mask use was based on participants' response to the end-of-follow-up survey. We found that the incidence of self-reported COVID-19 was 33% (aRR 1.33; 95% CI 1.03-1.72) higher in those wearing face masks often or sometimes, and 40% (aRR 1.40; 95% CI 1.08-1.82) higher in those wearing face masks almost always or always, compared to participants who reported wearing face masks never or almost never. We believe the observed increase in the incidence of infection associated with wearing a face mask is likely due to unobservable and hence nonadjustable differences between those wearing and not wearing a mask. Observational studies reporting on the relationship between face mask use and risk of respiratory infections should be interpreted cautiously, and more randomized trials are needed.

Effectiveness of face masks for reducing transmission of SARS-CoV-2: a rapid systematic review

This rapid systematic review of evidence asks whether (i) wearing a face mask, (ii) one type of mask over another and (iii) mandatory mask policies can reduce the transmission of SARS-CoV-2 infection, either in community-based or healthcare settings. A search of studies published 1 January 2020-27 January 2023 yielded 5185 unique records. Due to a paucity of randomized controlled trials (RCTs), observational studies were included in the analysis. We analysed 35 studies in community settings (three RCTs and 32 observational) and 40 in healthcare settings (one RCT and 39 observational). Ninety-five per cent of studies included were conducted before highly transmissible Omicron variants emerged. Ninety-one per cent of observational studies were at 'critical' risk of bias (ROB) in at least one domain, often failing to separate the effects of masks from concurrent interventions. More studies found that masks (n = 39/47; 83%) and mask mandates (n = 16/18; 89%) reduced infection than found no effect (n = 8/65; 12%) or favoured controls (n = 1/65; 2%). Seven observational studies found that respirators were more protective than surgical masks, while five found no statistically significant difference between the two mask types. Despite the ROB, and allowing for uncertain and variable efficacy, we conclude that wearing masks, wearing higher quality masks (respirators), and mask mandates generally reduced SARS-CoV-2 transmission in these study populations. This article is part of the theme issue 'The effectiveness of non-pharmaceutical interventions on the COVID-19 pandemic: the evidence'.

Masks During Pandemics Caused by Respiratory Pathogens-Evidence and Implications for Action

Importance

As demonstrated by the influenza virus and SARS-CoV-2, viruses spread by the respiratory route can cause deadly pandemics, and face masks can reduce the spread of these pathogens. The effectiveness of responses to future epidemics and pandemics will depend at least in part on whether evidence on masks, including from the COVID-19 pandemic, is utilized.

Observations

Well-designed observational studies have demonstrated the association of mask use with reduced transmission of SARS-CoV-2 in community settings, and rigorous evaluations of mask mandates have found substantial protection. Disagreement about whether face masks reduce the spread of SARS-CoV-2 has been exacerbated by a focus on randomized trials, which are limited in number, scope, and statistical power. Many effective public health policies have never been assessed in randomized clinical trials; such trials are not the gold standard of evidence for the efficacy of all interventions. Masking in the community to reduce the spread of SARS-CoV-2 is supported by robust evidence from diverse settings and populations. Data on the epidemiologic, environmental, and mask design parameters that influence the effectiveness of masking provide insights on when and how masks should be used to prevent transmission.

Conclusions and Relevance

During the next epidemic or pandemic caused by a respiratory pathogen, decision-makers will need to rely on existing evidence as they implement interventions. High-quality studies have shown that use of face masks in the community is associated with reduced transmission of SARS-CoV-2 and is likely to be an important component of an effective response to a future respiratory threat.

A chronological review of COVID-19 case fatality rate and its secular trend and investigation of all-cause mortality and hospitalization during the Delta and Omicron waves in the United States: a retrospective cohort study

Introduction

Coronavirus disease 2019 (COVID-19) has caused more than 690 million deaths worldwide. Different results concerning the death rates of the Delta and Omicron variants have been recorded. We aimed to assess the secular trend of case fatality rate (CFR), identify risk factors associated with mortality following COVID-19 diagnosis, and investigate the risks of mortality and hospitalization during Delta and Omicron waves in the United States.

Methods

This study assessed 2,857,925 individuals diagnosed with COVID-19 in the United States from January 2020, to June 2022. The inclusion criterion was the presence of COVID-19 diagnostic codes in electronic medical record or a positive laboratory test of the SARS-CoV-2. Statistical analysis was bifurcated into two components, longitudinal analysis and comparative analysis. To assess the discrepancies in hospitalization and mortality rates for COVID-19, we identified the prevailing periods for the Delta and Omicron variants.

Results

Longitudinal analysis demonstrated four sharp surges in the number of deaths and CFR. The CFR was persistently higher in males and older age. The CFR of Black and White remained higher than Asians since January 2022. In comparative analysis, the adjusted hazard ratios for all-cause mortality and hospitalization were higher in Delta wave compared to the Omicron wave. Risk of all-cause mortality was found to be greater 14-30 days after a COVID-19 diagnosis, while the likelihood of hospitalization was higher in the first 14 days following a COVID-19 diagnosis in Delta wave compared with Omicron wave. Kaplan-Meier analysis revealed the cumulative probability of mortality was approximately 2-fold on day 30 in Delta than in Omicron cases (log-rank p < 0.001). The mortality risk ratio between the Delta and Omicron variants was 1.671 (95% Cl 1.615-1.729, log-rank p < 0.001). Delta also had a significantly increased mortality risk over Omicron in all age groups. The CFR of people aged above 80 years was extremely high as 17.33%.

Conclusion

Male sex and age seemed to be strong and independent risk factors of mortality in COVID-19. The Delta variant appears to cause more hospitalization and death than the Omicron variant.

The hidden inequality: the disparities in the quality of daily use masks associated with family economic status

Wearing high-quality masks plays a critical role in reducing COVID-19 transmission. However, no study has investigated socioeconomic inequality in the quality of masks. Addressing this gap, this paper explored the relationships between mask's quality and family economic status. The cross-sectional survey was conducted in two Chinese universities by distributing structured questionnaires to assess participants' characteristics including family economic status, and meanwhile collecting their masks to evaluate the quality by measuring particle filtration efficiency. The valid responses were obtained from 912 students with mean age of 19.556 ± 1.453  years and were analyzed by using fractional or binary logistic regression. Three main findings were presented. First, inequality existed in the quality of masks. 36.07% of students were using unqualified masks with average filtration efficiency of 0.795 ± 0.119, which was much lower than China's national standard (0.9). Of those masks with identified production date, 11.43% were manufactured during COVID-19 outbreak when market was flooded with counterfeit production, and thus were of poor quality with average filtration efficiency of 0.819 ± 0.152. Second, better family economic status was associated with better masks' filtration efficiency and greater probability of using qualified masks. Third, students with better family economic status tend to use masks with individual packaging, and unique patterns and special designs, which may lead to inequality on a psychological level. Our analysis reveals the hidden socioeconomic inequality that exist behind cheap masks. In facing the challenges of future emerging infectious diseases, it is important to address the inequity to ensure equal access to affordable qualified personal protection equipment.

Real-world uptake of COVID-19 vaccination among individuals expressing vaccine hesitancy: A registry-linkage study

INTRODUCTION

Uptake of COVID-19 vaccination remains suboptimal in the United States and other settings. Though early reports indicated that a strong majority of people were interested in receiving the COVID-19 vaccine, the association between vaccine intention and uptake is not yet fully understood. Ourobjective was todescribe predictors of vaccine uptake, and estimate the sensitivity, specificity, and predictive values of self-reported COVID-19 vaccine status compared to a comprehensive statewide COVID-19 vaccine registry.

METHODS

A cohort of California residents that received a molecular test for SARS-CoV-2 infection during 24 February-5 December 2021 were enrolled in a telephone-administered survey. Survey participants were matched with records in a statewide immunization registry. Cox proportional hazards model were used to compare time to vaccination among those unvaccinated at survey enrollment by self-reported COVID-19 vaccination intention.

RESULTS

Among 864 participants who were unvaccinated at the time of interview, 272 (31%) had documentation of receipt of COVID-19 vaccination at a later date; including 194/423 (45.9%) who had initially reported being willing to receive vaccination, 41/185 (22.2%) who reported being unsure about vaccination, and 37/278 (13.3%) who reported unwillingness to receive vaccination.Adjusted hazard ratios (aHRs) for registry-confirmed COVID-19 vaccination were 0.49 (95% confidence interval: 0.32-0.76) and 0.21 (0.12-0.36) for participants expressing uncertainty and unwillingness to receive vaccination, respectively, as compared with participants who reported being willing to receive vaccination. Time to vaccination was shorter among participants from higher-income households (aHR = 3.30 [2.02-5.39]) and who reported co-morbidities or immunocompromising conditions (aHR = 1.54 [1.01-2.36]).Sensitivity of self-reported COVID-19 vaccination status was 82% (80-85%) overall, and 98% (97-99%) among those referencing vaccination records; specificity was 87% (86-89%).

CONCLUSION

Willingness to receive COVID-19 vaccination was an imperfect predictor of real-world vaccine uptake. Improved messaging about COVID-19 vaccination regardless of previous SARS-CoV-2 infection status may help improve uptake.

Association between self-reported masking behavior and SARS-CoV-2 infection wanes from Pre-Delta to Omicron-predominant periods - North Carolina COVID-19 Community Research Partnership (NC-CCRP)

BACKGROUND

Wearing a face mask is a primary public health method to reduce SARS-CoV-2 transmission.

METHODS

We performed a nested case-control analysis within the North Carolina COVID-19 Community Research Partnership (NC-CCRP) of adults who completed daily surveillance surveys, April 2020 - February 2022. We assessed the association between self-reported mask wearing behavior during nonhousehold interactions and COVID-19 infection during 3 pandemic periods using conditional logistic regression models of risk of infection that were adjusted for demographics, vaccination status, and recent known exposure to COVID-19.

RESULTS

Among 3,901 cases and 27,813 date-matched controls, there was a significant interaction between mask use and time period (P < .001). Prior to July 2021, the odds of a reported infection were 66% higher (aOR = 1.66, 95% CI = 1.43-1.91) among participants reporting ≥1 day not wearing a mask compared to those who reported no days (1,592 cases, 11,717 controls). During the Delta-predominant period, the results were similar (aOR = 1.53, 95% CI = 1.23-1.89; 659 cases, 4,649 controls). This association was attenuated during the Omicron-predominant period, where odds of an infection was 16% higher (aOR = 1.16, 95% CI = 1.03-1.32; 1,563 cases, 10,960 controls).

CONCLUSIONS

While the effect of not wearing a mask remains significant, during the Omicron-predominant period we observed a decrease in the association between self-reported mask wearing and risk of SARS-CoV-2 infection.

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.

Lifting Universal Masking in Schools - Covid-19 Incidence among Students and Staff

BACKGROUND

In February 2022, Massachusetts rescinded a statewide universal masking policy in public schools, and many Massachusetts school districts lifted masking requirements during the subsequent weeks. In the greater Boston area, only two school districts - the Boston and neighboring Chelsea districts - sustained masking requirements through June 2022. The staggered lifting of masking requirements provided an opportunity to examine the effect of universal masking policies on the incidence of coronavirus disease 2019 (Covid-19) in schools.

METHODS

We used a difference-in-differences analysis for staggered policy implementation to compare the incidence of Covid-19 among students and staff in school districts in the greater Boston area that lifted masking requirements with the incidence in districts that sustained masking requirements during the 2021-2022 school year. Characteristics of the school districts were also compared.

RESULTS

Before the statewide masking policy was rescinded, trends in the incidence of Covid-19 were similar across school districts. During the 15 weeks after the statewide masking policy was rescinded, the lifting of masking requirements was associated with an additional 44.9 cases per 1000 students and staff (95% confidence interval, 32.6 to 57.1), which corresponded to an estimated 11,901 cases and to 29.4% of the cases in all districts during that time. Districts that chose to sustain masking requirements longer tended to have school buildings that were older and in worse condition and to have more students per classroom than districts that chose to lift masking requirements earlier. In addition, these districts had higher percentages of low-income students, students with disabilities, and students who were English-language learners, as well as higher percentages of Black and Latinx students and staff. Our results support universal masking as an important strategy for reducing Covid-19 incidence in schools and loss of in-person school days. As such, we believe that universal masking may be especially useful for mitigating effects of structural racism in schools, including potential deepening of educational inequities.

CONCLUSIONS

Among school districts in the greater Boston area, the lifting of masking requirements was associated with an additional 44.9 Covid-19 cases per 1000 students and staff during the 15 weeks after the statewide masking policy was rescinded.

Effectiveness of two and three mRNA COVID-19 vaccine doses against Omicron- and Delta-Related outpatient illness among adults, October 2021-February 2022

Background

We estimated SARS-CoV-2 Delta- and Omicron-specific effectiveness of two and three mRNA COVID-19 vaccine doses in adults against symptomatic illness in US outpatient settings.

Methods

Between October 1, 2021, and February 12, 2022, research staff consented and enrolled eligible participants who had fever, cough, or loss of taste or smell and sought outpatient medical care or clinical SARS-CoV-2 testing within 10 days of illness onset. Using the test-negative design, we compared the odds of receiving two or three mRNA COVID-19 vaccine doses among SARS-CoV-2 cases versus controls using logistic regression. Regression models were adjusted for study site, age, onset week, and prior SARS-CoV-2 infection. Vaccine effectiveness (VE) was calculated as (1 - adjusted odds ratio) × 100%.

Results

Among 3847 participants included for analysis, 574 (32%) of 1775 tested positive for SARS-CoV-2 during the Delta predominant period and 1006 (56%) of 1794 participants tested positive during the Omicron predominant period. When Delta predominated, VE against symptomatic illness in outpatient settings was 63% (95% CI: 51% to 72%) among mRNA two-dose recipients and 96% (95% CI: 93% to 98%) for three-dose recipients. When Omicron predominated, VE was 21% (95% CI: -6% to 41%) among two-dose recipients and 62% (95% CI: 48% to 72%) among three-dose recipients.

Conclusions

In this adult population, three mRNA COVID-19 vaccine doses provided substantial protection against symptomatic illness in outpatient settings when the Omicron variant became the predominant cause of COVID-19 in the United States. These findings support the recommendation for a third mRNA COVID-19 vaccine dose.

COVID-19 and isolation: Risks and implications in the scenario of new variants

With the emergence of new variants of SARS-CoV-2, questions about transmissibility, vaccine efficacy, and impact on mortality are important to support decision-making in public health measures. Modifications related to transmissibility combined with the fact that much of the population has already been partially exposed to infection and/or vaccination, have stimulated recommendations to reduce the isolation period for COVID-19. However, these new guidelines have raised questions about their effectiveness in reducing contamination and minimizing impact in work environments. Therefore, a collaborative task force was developed to review the subject in a non-systematic manner, answering questions about SARS-CoV-2 variants, COVID-19 vaccines, isolation/quarantine periods, testing to end the isolation period, and the use of masks as mitigation procedures. Overall, COVID-19 vaccines are effective in preventing severe illness and death but are less effective in preventing infection in the case of the Omicron variant. Any strategy that is adopted to reduce the isolation period should take into consideration the epidemiological situation of the geographical region, individual clinical characteristics, and mask for source control. The use of tests for isolation withdrawal should be evaluated with caution, due to results depending on various conditions and may not be reliable.

Limitations of Molecular and Antigen Test Performance for SARS-CoV-2 in Symptomatic and Asymptomatic COVID-19 Contacts

COVID-19 has brought unprecedented attention to the crucial role of diagnostics in pandemic control. We compared severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) test performance by sample type and modality in close contacts of SARS-CoV-2 cases. Close contacts of SARS-CoV-2-positive individuals were enrolled after informed consent. Clinician-collected nasopharyngeal (NP) swabs in viral transport media (VTM) were tested with a routine clinical reference nucleic acid test (NAT) and PerkinElmer real-time reverse transcription-PCR (RT-PCR) assay; positive samples were tested for infectivity using a VeroE6TMPRSS2 cell culture model. Self-collected passive drool was also tested using the PerkinElmer RT-PCR assay. For the first 4 months of study, midturbinate swabs were tested using the BD Veritor rapid antigen test. Between 17 November 2020 and 1 October 2021, 235 close contacts of SARS-CoV-2 cases were recruited, including 95 with symptoms (82% symptomatic for ≤5 days) and 140 asymptomatic individuals. Reference NATs were positive for 53 (22.6%) participants; 24/50 (48%) were culture positive. PerkinElmer testing of NP and saliva samples identified an additional 28 (11.9%) SARS-CoV-2 cases who tested negative by reference NAT. Antigen tests performed for 99 close contacts showed 83% positive percent agreement (PPA) with reference NAT among early symptomatic persons, but 18% PPA in others; antigen tests in 8 of 11 (72.7%) culture-positive participants were positive. Contacts of SARS-CoV-2 cases may be falsely negative early after contact, but more sensitive platforms may identify these cases. Repeat or serial SARS-CoV-2 testing with both antigen and molecular assays may be warranted for individuals with high pretest probability for infection.

Antigen Test Positivity After COVID-19 Isolation - Yukon-Kuskokwim Delta Region, Alaska, January-February 2022

Isolation is recommended during acute infection with SARS-CoV-2, the virus that causes COVID-19, but the duration of infectiousness varies among individual persons. Rapid antigen test results have been correlated with detection of viable virus (1-3) and might inform isolation guidance, but data are limited for the recently emerged SARS-CoV-2 B.1.1.529 (Omicron) variant. On January 5, 2022, the Yukon-Kuskokwim Health Corporation (YKHC) recommended that persons with SARS-CoV-2 infection isolate for 10 days after symptom onset (or, for asymptomatic persons, 10 days after a positive nucleic acid amplification or antigen test result). However, isolation could end after 5-9 days if symptoms were resolving or absent, fever was absent for ≥24 hours without fever-reducing medications, and an Abbott BinaxNOW COVID-19 Ag (BinaxNOW) rapid antigen test result was negative. Antigen test results and associated individual characteristics were analyzed among 3,502 infections reported to YKHC during January 1-February 9, 2022. After 5-9 days, 396 of 729 persons evaluated (54.3%) had a positive antigen test result, with a declining percentage positive over time. In a multivariable model, a positive antigen test result was more likely after 5 days compared with 9 days (adjusted odds ratio [aOR] = 6.39) or after symptomatic infection (aOR = 9.63), and less likely after previous infection (aOR = 0.30), receipt of a primary COVID-19 vaccination series (aOR = 0.60), or after both previous infection and receipt of a primary COVID-19 vaccination series (aOR = 0.17). Antigen tests might be a useful tool to guide recommendations for isolation after SARS-CoV-2 infection. During the 10 days after infection, persons might be infectious to others and are recommended to wear a well-fitting mask when around others, even if ending isolation after 5 days.

Limitations of molecular and antigen test performance for SARS-CoV-2 in symptomatic and asymptomatic COVID-19 contacts

OBJECTIVES

COVID-19 has brought unprecedented attention to the crucial role of diagnostics in pandemic control. We compared SARS-CoV-2 test performance by sample type and modality in close contacts of SARS-CoV-2 cases.

METHODS

Close contacts of SARS-CoV-2 positive individuals were enrolled after informed consent. Clinician-collected nasopharyngeal (NP) swabs in viral transport media (VTM) were tested with a nucleic acid test (NAT). NP VTM and self-collected passive drool were tested using the PerkinElmer real-time reverse transcription PCR (RT-PCR) assay. For the first 4 months of study, mid-turbinate swabs were tested using the BD Veritor rapid antigen test. NAT positive NP samples were tested for infectivity using a VeroE6TMPRSS2 cell culture model.

RESULTS

Between November 17, 2020, and October 1, 2021, 235 close contacts of SARS-CoV-2 cases were recruited, including 95 with symptoms (82% symptomatic for < 5 days) and 140 asymptomatic individuals. NP swab reference tests were positive for 53 (22.6%) participants; 24/50 (48%) were culture positive. PerkinElmer testing of NP and saliva samples identified an additional 28 (11.9%) SARS-CoV-2 cases who tested negative by clinical NAT. Antigen tests performed for 99 close contacts showed 83% positive percent agreement (PPA) with reference NAT among early symptomatic persons, but 18% PPA in others; antigen tests in 8 of 11 (72.7%) culture-positive participants were positive.

CONCLUSIONS

Contacts of SARS-CoV-2 cases may be falsely negative early after contact, which more sensitive platforms may identify. Repeat or serial SARS-CoV-2 testing with both antigen and molecular assays may be warranted for individuals with high pretest probability for infection.