SARS-CoV-2 incidence and risk factors in a national, community-based prospective cohort of U.S. adults

The changing contributory role to infections of work, public transport, shopping, hospitality and leisure activities throughout the SARS-CoV-2 pandemic in England and Wales

Background

Understanding how non-household activities contributed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections under different levels of national health restrictions is vital.

Methods

Among adult Virus Watch participants in England and Wales, we used multivariable logistic regressions and adjusted-weighted population attributable fractions (aPAF) assessing the contribution of work, public transport, shopping, and hospitality and leisure activities to infections.

Results

Under restrictions, among 17,256 participants (502 infections), work [adjusted odds ratio (aOR) 2.01 (1.65-2.44), (aPAF) 30% (22-38%)] and transport [(aOR 1.15 (0.94-1.40), aPAF 5% (-3-12%)], were risk factors for SARS-CoV-2 but shopping, hospitality and leisure were not. Following the lifting of restrictions, among 11,413 participants (493 infections), work [(aOR 1.35 (1.11-1.64), aPAF 17% (6-26%)] and transport [(aOR 1.27 (1.04-1.57), aPAF 12% (2-22%)] contributed most, with indoor hospitality [(aOR 1.21 (0.98-1.48), aPAF 7% (-1-15%)] and leisure [(aOR 1.24 (1.02-1.51), aPAF 10% (1-18%)] increasing. During the Omicron variant, with individuals more socially engaged, among 11,964 participants (2335 infections), work [(aOR 1.28 (1.16-1.41), aPAF (11% (7-15%)] and transport [(aOR 1.16 (1.04-1.28), aPAF 6% (2-9%)] remained important but indoor hospitality [(aOR 1.43 (1.26-1.62), aPAF 20% (13-26%)] and leisure [(aOR 1.35 (1.22-1.48), aPAF 10% (7-14%)] dominated.

Conclusions

Work and public transport were important to transmissions throughout the pandemic with hospitality and leisure's contribution increasing as restrictions were lifted, highlighting the importance of restricting leisure and hospitality alongside advising working from home, when facing a highly infectious and virulent respiratory infection.

Protection against SARS-CoV-2 BA.4 and BA.5 subvariants via vaccination and natural infection: A modeling study

With continuing emergence of new SARS-CoV-2 variants, understanding the proportion of the population protected against infection is crucial for public health risk assessment and decision-making and so that the general public can take preventive measures. We aimed to estimate the protection against symptomatic illness caused by SARS-CoV-2 Omicron variants BA.4 and BA.5 elicited by vaccination against and natural infection with other SARS-CoV-2 Omicron subvariants. We used a logistic model to define the protection rate against symptomatic infection caused by BA.1 and BA.2 as a function of neutralizing antibody titer values. Applying the quantified relationships to BA.4 and BA.5 using two different methods, the estimated protection rate against BA.4 and BA.5 was 11.3% (95% confidence interval [CI]: 0.01-25.4) (method 1) and 12.9% (95% CI: 8.8-18.0) (method 2) at 6 months after a second dose of BNT162b2 vaccine, 44.3% (95% CI: 20.0-59.3) (method 1) and 47.3% (95% CI: 34.1-60.6) (method 2) at 2 weeks after a third BNT162b2 dose, and 52.3% (95% CI: 25.1-69.2) (method 1) and 54.9% (95% CI: 37.6-71.4) (method 2) during the convalescent phase after infection with BA.1 and BA.2, respectively. Our study indicates that the protection rate against BA.4 and BA.5 are significantly lower compared with those against previous variants and may lead to substantial morbidity, and overall estimates were consistent with empirical reports. Our simple yet practical models enable prompt assessment of public health impacts posed by new SARS-CoV-2 variants using small sample-size neutralization titer data to support public health decisions in urgent situations.

Racial/Ethnic Disparities in Exposure, Disease Susceptibility, and Clinical Outcomes during COVID-19 Pandemic in National Cohort of Adults, United States

We examined racial/ethnic disparities for COVID-19 seroconversion and hospitalization within a prospective cohort (n = 6,740) in the United States enrolled in March 2020 and followed-up through October 2021. Potential SARS-CoV-2 exposure, susceptibility to COVID-19 complications, and access to healthcare varied by race/ethnicity. Hispanic and Black non-Hispanic participants had more exposure risk and difficulty with healthcare access than white participants. Participants with more exposure had greater odds of seroconversion. Participants with more susceptibility and more barriers to healthcare had greater odds of hospitalization. Race/ethnicity positively modified the association between susceptibility and hospitalization. Findings might help to explain the disproportionate burden of SARS-CoV-2 infections and complications among Hispanic/Latino/a and Black non-Hispanic persons. Primary and secondary prevention efforts should address disparities in exposure, vaccination, and treatment for COVID-19.

Settings for non-household transmission of SARS-CoV-2 during the second lockdown in England and Wales - analysis of the Virus Watch household community cohort study

Background: "Lockdowns" to control serious respiratory virus pandemics were widely used during the coronavirus disease 2019 (COVID-19) pandemic.  However, there is limited information to understand the settings in which most transmission occurs during lockdowns, to support refinement of similar policies for future pandemics.  Methods: Among Virus Watch household cohort participants we identified those infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outside the household.  Using survey activity data, we undertook multivariable logistic regressions assessing the contribution of activities on non-household infection risk.  We calculated adjusted population attributable fractions (APAF) to estimate which activity accounted for the greatest proportion of non-household infections during the pandemic's second wave. Results: Among 10,858 adults, 18% of cases were likely due to household transmission.  Among 10,475 participants (household-acquired cases excluded), including 874 non-household-acquired infections, infection was associated with: leaving home for work or education (AOR 1.20 (1.02 - 1.42), APAF 6.9%); public transport (more than once per week AOR 1.82 (1.49 - 2.23), public transport APAF 12.42%); and shopping (more than once per week AOR 1.69 (1.29 - 2.21), shopping APAF 34.56%).  Other non-household activities were rare and not significantly associated with infection. Conclusions: During lockdown, going to work and using public or shared transport independently increased infection risk, however only a minority did these activities.  Most participants visited shops, accounting for one-third of non-household transmission.  Transmission in restricted hospitality and leisure settings was minimal suggesting these restrictions were effective.   If future respiratory infection pandemics emerge these findings highlight the value of working from home, using forms of transport that minimise exposure to others, minimising exposure to shops and restricting non-essential activities.

Understanding the social determinants of health and genetic factors contributing to the differences observed in COVID-19 incidence and mortality between underrepresented and other communities

COVID-19 has been a devastating disease, especially in underserved communities. Data has shown that Indigenous peoples, Latinx communities, and Black Americans have a 3.3, 2.4, and 2 times higher mortality rate than White communities, respectively, due to COVID-19. Therefore, in this paper, we sought to understand how Social Determinants of Health and genetic factors influence COVID-19 incidence, mortality rates, and complications by assessing existing literature. Studies showed that identifying with a racial/ethnic minority, being homeless, housing insecurity, lower household median income, and living in an area with decreased air quality were associated with higher incidence and mortality from COVID-19. Analyses of these studies also showed a lack of resources to collect patients' social determinants of health, revealing an urgent need to create databases with information on local support programs and operationalize the referral and tracking outcomes to address the health inequities for Black, Indigenous, and Latinx communities.

State-wide random seroprevalence survey of SARS-CoV-2 past infection in a southern US State, 2020

The purpose of this cross-sectional study was to estimate the proportion of Arkansas residents who were infected with the SARS-CoV-2 virus between May and December 2020 and to assess the determinants of infection. To estimate seroprevalence, a state-wide population-based random-digit dial sample of non-institutionalized adults in Arkansas was surveyed. Exposures were age, sex, race/ethnicity, education, occupation, contact with infected persons, comorbidities, height, and weight. The outcome was past COVID-19 infection measured by serum antibody test. We found a prevalence of 15.1% (95% CI: 11.1%, 20.2%) by December 2020. Seropositivity was significantly elevated among participants who were non-Hispanic Black, Hispanic (prevalence ratio [PRs]:1.4 [95% CI: 0.8, 2.4] and 2.3 [95% CI: 1.3, 4.0], respectively), worked in high-demand essential services (PR: 2.5 [95% CI: 1.5, 4.1]), did not have a college degree (PR: 1.6 [95% CI: 1.0, 2.4]), had an infected household or extra-household contact (PRs: 4.7 [95% CI: 2.1, 10.1] and 2.6 [95% CI: 1.2, 5.7], respectively), and were contacted in November or December (PR: 3.6 [95% CI: 1.9, 6.9]). Our results indicate that by December 2020, one out six persons in Arkansas had a past SARS-CoV-2 infection.

Cohort profile: a national, community-based prospective cohort study of SARS-CoV-2 pandemic outcomes in the USA-the CHASING COVID Cohort study

PURPOSE

The Communities, Households and SARS-CoV-2 Epidemiology (CHASING) COVID Cohort Study is a community-based prospective cohort study launched during the upswing of the USA COVID-19 epidemic. The objectives of the cohort study are to: (1) estimate and evaluate determinants of the incidence of SARS-CoV-2 infection, disease and deaths; (2) assess the impact of the pandemic on psychosocial and economic outcomes and (3) assess the uptake of pandemic mitigation strategies.

PARTICIPANTS

We began enrolling participants from 28 March 2020 using internet-based strategies. Adults≥18 years residing anywhere in the USA or US territories were eligible. 6740 people are enrolled in the cohort, including participants from all 50 US states, the District of Columbia, Puerto Rico and Guam. Participants are contacted regularly to complete study assessments, including interviews and dried blood spot specimen collection for serologic testing.

FINDINGS TO DATE

Participants are geographically and sociodemographically diverse and include essential workers (19%). 84.2% remain engaged in cohort follow-up activities after enrolment. Data have been used to assess SARS-CoV-2 cumulative incidence, seroincidence and related risk factors at different phases of the US pandemic; the role of household crowding and the presence of children in the household as potential risk factors for severe COVID-19 early in the US pandemic; to describe the prevalence of anxiety symptoms and its relationship to COVID-19 outcomes and other potential stressors; to identify preferences for SARS-CoV-2 diagnostic testing when community transmission is on the rise via a discrete choice experiment and to assess vaccine hesitancy over time and its relationship to vaccine uptake.

FUTURE PLANS

The CHASING COVID Cohort Study has outlined a research agenda that involves ongoing monitoring of the incidence and determinants of SARS-CoV-2 outcomes, mental health outcomes and economic outcomes. Additional priorities include assessing the incidence, prevalence and correlates of long-haul COVID-19.

Development and Evaluation of Quantitative Immunoglobulin G Enzyme-Linked Immunosorbent Assay for the Diagnosis of Coronavirus Disease 2019 Using Truncated Recombinant Nucleocapsid Protein as Assay Antigen

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Real-time RT-PCR is the most commonly used method for COVID-19 diagnosis. However, serological assays are urgently needed as complementary tools to RT-PCR. Hachim et al. 2020 and Burbelo et al. 2020 demonstrated that anti-nucleocapsid(N) SARS-CoV-2 antibodies are higher and appear earlier than the spike antibodies. Additionally, cross-reactive antibodies against N protein are more prevalent than those against spike protein. We developed a less cross-reactive immunoglobulin G (IgG) indirect ELISA by using a truncated recombinant SARS-CoV-2 N protein as assay antigen. A highly conserved region of coronaviruses N protein was deleted and the protein was prepared using an E. coli protein expression system. A total of 177 samples collected from COVID-19 suspected cases and 155 negative control sera collected during the pre-COVID-19 period were applied to evaluate the assay's performance, with the plaque reduction neutralization test and the commercial SARS-CoV-2 spike protein IgG ELISA as gold standards. The SARS-CoV-2 N truncated protein-based ELISA showed similar sensitivity (91.1% vs. 91.9%) and specificity (93.8% vs. 93.8%) between the PRNT and spike IgG ELISA, as well as also higher specificity compared to the full-length N protein (93.8% vs. 89.9%). Our ELISA can be used for the diagnosis and surveillance of COVID-19.

Exposures associated with SARS-CoV-2 infection in France: A nationwide online case-control study

BACKGROUND

We aimed to assess the role of different setting and activities in acquiring SARS-CoV-2 infection.

METHODS

In this nationwide case-control study, cases were SARS-CoV-2 infected adults recruited between 27 October and 30 November 2020. Controls were individuals from the Ipsos market research database matched to cases by age, sex, region, population density and time period. Participants completed an online questionnaire on recent activity-related exposures.

FINDINGS

Among 3426 cases and 1713 controls, in multivariable analysis, we found an increased risk of infection associated with any additional person living in the household (adjusted-OR: 1•16; 95%CI: 1•11-1•21); having children attending day-care (aOR: 1•31; 95%CI: 1•02-1•62), kindergarten (aOR: 1•27; 95%CI: 1•09-1•45), middle school (aOR: 1•30; 95%CI: 1•15-1•47), or high school (aOR: 1•18; 95%CI: 1•05-1•34); with attending professional (aOR: 1•15; 95%CI: 1•04-1•26) or private gatherings (aOR: 1•57; 95%CI: 1•45-1•71); and with having frequented bars and restaurants (aOR: 1•95; 95%CI: 1•76-2•15), or having practiced indoor sports activities (aOR: 1•36; 95%CI: 1•15-1•62). We found no increase in risk associated with frequenting shops, cultural or religious gatherings, or with transportation, except for carpooling (aOR: 1•47; 95%CI: 1•28-1•69). Teleworking was associated with decreased risk of infection (aOR: 0•65; 95%CI: 0•56-0•75).

INTERPRETATION

Places and activities during which infection prevention and control measures may be difficult to fully enforce were those with increased risk of infection. Children attending day-care, kindergarten, middle and high schools, but not primary schools, were potential sources of infection for the household.

FUNDING

Institut Pasteur, Research & Action Emerging Infectious Diseases (REACTing), Fondation de France (Alliance" Tous unis contre le virus").

The emergence, surge and subsequent wave of the SARS-CoV-2 pandemic in New York metropolitan area: The view from a major region-wide urgent care provider

BACKGROUND

Describing SARS-CoV-2 testing and positivity trends among urgent care users is crucial for understanding the trajectory of the pandemic.

OBJECTIVE

To describe demographic and clinical characteristics, positivity rates, and repeat testing patterns among patients tested for SARS-CoV-2 at CityMD, an urgent care provider in the New York City metropolitan area.

DESIGN

Retrospective study of all persons testing for SARS-CoV-2 between March 1, 2020 and January 8, 2021 at 115 CityMD locations in the New York metropolitan area.

PATIENTS

Individuals receiving a SARS-CoV-2 diagnostic or serologic test.

MEASUREMENTS

Test and individual level SARS-CoV-2 positivity by PCR, rapid antigen, or serologic tests.

RESULTS

During the study period, 3.4 million COVID tests were performed on 1.8 million individuals. In New York City, CityMD diagnosed 268,298 individuals, including 17% of all reported cases. Testing levels were higher among 20-29 year olds, non-Hispanic Whites, and females compared with other groups. About 24.8% (n=464,902) were repeat testers. Test positivity was higher in non-Hispanic Black (6.4%), Hispanic (8.0%), and Native American (8.0%) patients compared to non-Hispanic White (5.4%) patients. Overall seropositivity was estimated to be 21.7% (95% Confidence Interval [CI]: 21.6-21.8) and was highest among 10-14 year olds (27.3%). Seropositivity was also high among non-Hispanic Black (24.5%) and Hispanic (30.6%) testers, and residents of the Bronx (31.3%) and Queens (30.5%). Using PCR as the gold standard, SARS-CoV-2 rapid tests had a false positive rate of 5.4% (95%CI 5.3-5.5).

CONCLUSION

Urgent care centers can provide broad access to critical evaluation, diagnostic testing and treatment of a substantial number of ambulatory patients during pandemics, especially in population-dense, urban epicenters.