Household transmission of COVID-19 cases associated with SARS-CoV-2 delta variant (B.1.617.2): national case-control study

Diagnostic stewardship and the coronavirus disease 2019 (COVID-19) pandemic: Lessons learned for prevention of emerging infectious diseases in acute-care settings

The coronavirus disease 2019 (COVID-19) pandemic has demonstrated the importance of stewardship of viral diagnostic tests to aid infection prevention efforts in healthcare facilities. We highlight diagnostic stewardship lessons learned during the COVID-19 pandemic and discuss how diagnostic stewardship principles can inform management and mitigation of future emerging pathogens in acute-care settings. Diagnostic stewardship during the COVID-19 pandemic evolved as information regarding transmission (eg, routes, timing, and efficiency of transmission) became available. Diagnostic testing approaches varied depending on the availability of tests and when supplies and resources became available. Diagnostic stewardship lessons learned from the COVID-19 pandemic include the importance of prioritizing robust infection prevention mitigation controls above universal admission testing and considering preprocedure testing, contact tracing, and surveillance in the healthcare facility in certain scenarios. In the future, optimal diagnostic stewardship approaches should be tailored to specific pathogen virulence, transmissibility, and transmission routes, as well as disease severity, availability of effective treatments and vaccines, and timing of infectiousness relative to symptoms. This document is part of a series of papers developed by the Society of Healthcare Epidemiology of America on diagnostic stewardship in infection prevention and antibiotic stewardship.1.

Source of SARS-CoV-2 infection: results from a series of 584,846 cases in France from October 2020 to August 2022

BACKGROUND

We aimed to study the source of infection for recently SARS-CoV-2-infected individuals from October 2020 to August 2022 in France.

METHODS

Participants from the nationwide ComCor case-control study who reported recent SARS-CoV-2 infection were asked to document the source and circumstances of their infection through an online questionnaire. Multivariable logistic regression was used to identify the factors associated with not identifying any source of infection.

RESULTS

Among 584,846 adults with a recent SARS-CoV-2 infection in France, 46.9% identified the source of infection and an additional 22.6% suspected an event during which they might have become infected. Known and suspected sources of infection were household members (30.8%), extended family (15.6%), work colleagues (15.0%), friends (11.0%), and possibly multiple/other sources (27.6%). When the source of infection was known, was not a household member, and involved a unique contact (n = 69,788), characteristics associated with transmission events were indoors settings (91.6%), prolonged (> 15 min) encounters (50.5%), symptomatic source case (64.9%), and neither the source of infection nor the participant wearing a mask (82.2%). Male gender, older age, lower education, living alone, using public transportation, attending places of public recreation (bars, restaurants, nightclubs), public gatherings, and cultural events, and practicing indoor sports were all independently associated with not knowing the source of infection.

CONCLUSION

Two-thirds of infections were attributed to interactions with close relatives, friends, or work colleagues. Extra-household indoor encounters without masks were commonly reported and represented avoidable circumstances of infection.

TRIAL REGISTRATION

ClinicalTrials.gov registration number: NCT04607941.

SARS-CoV-2 variants of concern in children and adolescents with COVID-19: a systematic review

OBJECTIVES

Infections by SARS-CoV-2 variants of concern (VOCs) might affect children and adolescents differently than earlier viral lineages. We aimed to address five questions about SARS-CoV-2 VOC infections in children and adolescents: (1) symptoms and severity, (2) risk factors for severe disease, (3) the risk of infection, (4) the risk of transmission and (5) long-term consequences following a VOC infection.

DESIGN

Systematic review.

DATA SOURCES

The COVID-19 Open Access Project database was searched up to 1 March 2022 and PubMed was searched up to 9 May 2022.

ELIGIBILITY CRITERIA

We included observational studies about Alpha, Beta, Gamma, Delta and Omicron VOCs among ≤18-year-olds. We included studies in English, German, French, Greek, Italian, Spanish and Turkish.

DATA EXTRACTION AND SYNTHESIS

Two reviewers extracted and verified the data and assessed the risk of bias. We descriptively synthesised the data and assessed the risks of bias at the outcome level.

RESULTS

We included 53 articles. Most children with any VOC infection presented with mild disease, with more severe disease being described with the Delta or the Gamma VOC. Diabetes and obesity were reported as risk factors for severe disease during the whole pandemic period. The risk of becoming infected with a SARS-CoV-2 VOC seemed to increase with age, while in daycare settings the risk of onward transmission of VOCs was higher for younger than older children or partially vaccinated adults. Long-term symptoms following an infection with a VOC were described in <5% of children and adolescents.

CONCLUSION

Overall patterns of SARS-CoV-2 VOC infections in children and adolescents are similar to those of earlier lineages. Comparisons between different pandemic periods, countries and age groups should be improved with complete reporting of relevant contextual factors, including VOCs, vaccination status of study participants and the risk of exposure of the population to SARS-CoV-2.

PROSPERO REGISTRATION NUMBER

CRD42022295207.

Cultivating community-based participatory research (CBPR) to respond to the COVID-19 pandemic: an illustrative example of partnership and topic prioritization in the food services industry

BACKGROUND

As an illustrative example of COVID-19 pandemic community-based participatory research (CBPR), we describe a community-academic partnership to prioritize future research most important to people experiencing high occupational exposure to COVID-19 - food service workers. Food service workers face key challenges surrounding (1) health and safety precautions, (2) stress and mental health, and (3) the long-term pandemic impact.

METHOD

Using CBPR methodologies, academic scientists partnered with community stakeholders to develop the research aims, methods, and measures, and interpret and disseminate results. We conducted a survey, three focus groups, and a rapid qualitative assessment to understand the three areas of concern and prioritize future research.

RESULTS

The survey showed that food service employers mainly supported basic droplet protections (soap, hand sanitizer, gloves), rather than comprehensive airborne protections (high-quality masks, air quality monitoring, air cleaning). Food service workers faced challenging decisions surrounding isolation, quarantine, testing, masking, vaccines, and in-home transmission, described anxiety, depression, and substance use as top mental health concerns, and described long-term physical and financial concerns. Focus groups provided qualitative examples of concerns experienced by food service workers and narrowed topic prioritization. The rapid qualitative assessment identified key needs and opportunities, with help reducing in-home COVID-19 transmission identified as a top priority. COVID-19 mitigation scientists offered recommendations for reducing in-home transmission.

CONCLUSIONS

The COVID-19 pandemic has forced food service workers to experience complex decisions about health and safety, stress and mental health concerns, and longer-term concerns. Challenging health decisions included attempting to avoid an airborne infectious illness when employers were mainly only concerned with droplet precautions and trying to decide protocols for testing and isolation without clear guidance, free tests, or paid sick leave. Key mental health concerns were anxiety, depression, and substance use. Longer-term challenges included Long COVID, lack of mental healthcare access, and financial instability. Food service workers suggest the need for more research aimed at reducing in-home COVID-19 transmission and supporting long-term mental health, physical health, and financial concerns. This research provides an illustrative example of how to cultivate community-based partnerships to respond to immediate and critical issues affecting populations most burdened by public health crises.

Index cases first identified by nasal-swab rapid COVID-19 tests had more transmission to household contacts than cases identified by other test types

At-home rapid COVID-19 tests in the U.S. utilize nasal-swab specimens and require high viral loads to reliably give positive results. Longitudinal studies from the onset of infection have found infectious virus can present in oral specimens days before nasal. Detection and initiation of infection-control practices may therefore be delayed when nasal-swab rapid tests are used, resulting in greater transmission to contacts. We assessed whether index cases first identified by rapid nasal-swab COVID-19 tests had more transmission to household contacts than index cases who used other test types (tests with higher analytical sensitivity and/or non-nasal specimen types). In this observational cohort study, 370 individuals from 85 households with a recent COVID-19 case were screened at least daily by RT-qPCR on one or more self-collected upper-respiratory specimen types. A two-level random intercept model was used to assess the association between the infection outcome of household contacts and each covariable (household size, race/ethnicity, age, vaccination status, viral variant, infection-control practices, and whether a rapid nasal-swab test was used to initially identify the household index case). Transmission was quantified by adjusted secondary attack rates (aSAR) and adjusted odds ratios (aOR). An aSAR of 53.6% (95% CI 38.8-68.3%) was observed among households where the index case first tested positive by a rapid nasal-swab COVID-19 test, which was significantly higher than the aSAR for households where the index case utilized another test type (27.2% 95% CI 19.5-35.0%, P = 0.003 pairwise comparisons of predictive margins). We observed an aOR of 4.90 (95% CI 1.65-14.56) for transmission to household contacts when a nasal-swab rapid test was used to identify the index case, compared to other test types. Use of nasal-swab rapid COVID-19 tests for initial detection of infection and initiation of infection control may be less effective at limiting transmission to household contacts than other test types.

From Emergence to Endemicity: A Comprehensive Review of COVID-19

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), later renamed coronavirus disease 2019 (COVID-19), was first identified in Wuhan, China, in early December 2019. Initially, the China office of the World Health Organization was informed of numerous cases of pneumonia of unidentified etiology in Wuhan, Hubei Province at the end of 2019. This would subsequently result in a global pandemic with millions of confirmed cases of COVID-19 and millions of deaths reported to the WHO. We have analyzed most of the data published since the beginning of the pandemic to compile this comprehensive review of SARS-CoV-2. We looked at the core ideas, such as the etiology, epidemiology, pathogenesis, clinical symptoms, diagnostics, histopathologic findings, consequences, therapies, and vaccines. We have also included the long-term effects and myths associated with some therapeutics of COVID-19. This study presents a comprehensive assessment of the SARS-CoV-2 virology, vaccines, medicines, and significant variants identified during the course of the pandemic. Our review article is intended to provide medical practitioners with a better understanding of the fundamental sciences, clinical treatment, and prevention of COVID-19. As of May 2023, this paper contains the most recent data made accessible.

Representativeness of whole-genome sequencing approaches in England: the importance for understanding inequalities associated with SARS-CoV-2 infection

Whole-genome sequencing (WGS) information has played a crucial role in the SARS-CoV-2 (COVID-19) pandemic by providing evidence about variants to inform public health policy. The purpose of this study was to assess the representativeness of sequenced cases compared with all COVID-19 cases in England, between March 2020 and August 2021, by demographic and socio-economic characteristics, to evaluate the representativeness and utility of these data in epidemiological analyses. To achieve this, polymerase chain reaction (PCR)-confirmed COVID-19 cases were extracted from the national laboratory system and linked with WGS data. During the study period, over 10% of COVID-19 cases in England had WGS data available for epidemiological analysis. With sequencing capacity increasing throughout the period, sequencing representativeness compared to all reported COVID-19 cases increased over time, allowing for valuable epidemiological analyses using demographic and socio-economic characteristics, particularly during periods with emerging novel SARS-CoV-2 variants. This study demonstrates the comprehensiveness of England's sequencing throughout the COVID-19 pandemic, rapidly detecting variants of concern, and enabling representative epidemiological analyses to inform policy.

Effects of public-health measures for zeroing out different SARS-CoV-2 variants

Targeted public health interventions for an emerging epidemic are essential for preventing pandemics. During 2020-2022, China invested significant efforts in strict zero-COVID measures to contain outbreaks of varying scales caused by different SARS-CoV-2 variants. Based on a multi-year empirical dataset containing 131 outbreaks observed in China from April 2020 to May 2022 and simulated scenarios, we ranked the relative intervention effectiveness by their reduction in instantaneous reproduction number. We found that, overall, social distancing measures (38% reduction, 95% prediction interval 31-45%), face masks (30%, 17-42%) and close contact tracing (28%, 24-31%) were most effective. Contact tracing was crucial in containing outbreaks during the initial phases, while social distancing measures became increasingly prominent as the spread persisted. In addition, infections with higher transmissibility and a shorter latent period posed more challenges for these measures. Our findings provide quantitative evidence on the effects of public-health measures for zeroing out emerging contagions in different contexts.

Household secondary attack rates and risk factors during periods of SARS-CoV-2 Delta and Omicron variant predominance in the Republic of Korea

BACKGROUND

The household secondary attack rate (SAR) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important indicator for community transmission. This study aimed to characterize transmission by comparing household SARs and identifying risk factors during the periods of Delta and Omicron variant predominance in Republic of Korea.

METHODS

We defined the period of Delta variant predominance (Delta period) as July 25, 2021 to January 15, 2022, and the period of Omicron variant predominance (Omicron period) as February 7 to September 3, 2022. The number of index cases included was 214,229 for the Delta period and 5,521,393 for the Omicron period. To identify the household SARs and risk factors for each period, logistic regression was performed to determine the adjusted odds ratio (aOR).

RESULTS

The SAR was 35.2% for the Delta period and 43.1% for the Omicron period. The aOR of infection was higher in 2 groups, those aged 0 to 18 years and ≥75 years, compared to those aged 19 to 49 years. Unvaccinated individuals (vs. vaccinated individuals) and individuals experiencing initial infection (vs. individuals experiencing a second or third infection) had an increased risk of infection with SARS-CoV-2.

CONCLUSION

This study analyzed the household SARs and risk factors. We hope that the results can help develop age-specific immunization plans and responses to reduce the SAR in preparation for emerging infectious diseases or potential new variants of SARS-CoV-2.

Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias

In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host viral burden, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part of the UK COVID-19 Infection Survey. Because viral burden distributions determined from community survey data can be biased due to the impact of variant epidemiology on the time-since-infection of samples, we developed a method to explicitly adjust observed Ct value distributions to account for the expected bias. By analysing the adjusted Ct values using partial least squares regression, we found that among unvaccinated individuals with no known prior exposure, viral burden was 44% lower among Alpha variant infections, compared to those with the predecessor strain, B.1.177. Vaccination reduced viral burden by 67%, and among vaccinated individuals, viral burden was 286% higher among Delta variant, compared to Alpha variant, infections. In addition, viral burden increased by 17% for every 10-year age increment of the infected individual. In summary, within-host viral burden increases with age, is reduced by vaccination, and is influenced by the interplay of vaccination status and viral variant.

Aerosol exchange between pressure-equilibrium rooms induced by door motion and human movement

It is now widely recognised that aerosol transport is major vector for transmission of diseases such as COVID-19, and quantification of aerosol transport in the built environment is critical to risk analysis and management. Understanding the effects of door motion and human movement on the dispersion of virus-laden aerosols under pressure-equilibrium conditions is of great significance to the evaluation of infection risks and development of mitigation strategies. This study uses novel numerical simulation techniques to quantify the impact of these motions upon aerosol transport and provides valuable insights into the wake dynamics of swinging doors and human movement. The results show that the wake flow of an opening swinging door delays aerosol escape, while that of a person walking out entrains aerosol out of the room. Aerosol escape caused by door motion mainly happens during the closing sequence which pushes the aerosols out. Parametric studies show that while an increased door swinging speed or human movement speed can enhance air exchange across the doorway, the cumulative aerosol exchange across the doorway is not clearly affected by the speeds.

Bias assessment of a test-negative design study of COVID-19 vaccine effectiveness used in national policymaking

National test-negative-case-control (TNCC) studies are used to monitor COVID-19 vaccine effectiveness in the UK. A questionnaire was sent to participants from the first published TNCC COVID-19 vaccine effectiveness study conducted by the UK Health Security Agency, to assess for potential biases and changes in behaviour related to vaccination. The original study included symptomatic adults aged ≥70 years testing for COVID-19 between 08/12/2020 and 21/02/2021. A questionnaire was sent to cases and controls tested from 1-21 February 2021. In this study, 8648 individuals responded to the questionnaire (36.5% response). Using information from the questionnaire to produce a combined estimate that accounted for all potential biases decreased the original vaccine effectiveness estimate after two doses of BNT162b2 from 88% (95% CI: 79-94%) to 85% (95% CI: 68-94%). Self-reported behaviour demonstrated minimal evidence of riskier behaviour after vaccination. These findings offer reassurance to policy makers and clinicians making decisions based on COVID-19 vaccine effectiveness TNCC studies.

The spread of the omicron variant: Identification of knowledge gaps, virus diffusion modelling, and future research needs

The World Health Organization (WHO) recognised variant B.1.1.529 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a variant of concern, termed "Omicron", on November 26, 2021. Its diffusion was attributed to its several mutations, which allow promoting its ability to diffuse worldwide and its capability in immune evasion. As a consequence, some additional serious threats to public health posed the risk to undermine the global efforts made in the last two years to control the pandemic. In the past, several works were devoted to discussing a possible contribution of air pollution to the SARS-CoV-2 spread. However, to the best of the authors' knowledge, there are still no works dealing with the Omicron variant diffusion mechanisms. This work represents a snapshot of what we know right now, in the frame of an analysis of the Omicron variant spread. The paper proposes the use of a single indicator, commercial trade data, to model the virus spread. It is proposed as a surrogate of the interactions occurring between humans (the virus transmission mechanism due to human-to-human contacts) and could be considered for other diseases. It allows also to explain the unexpected increase in infection cases in China, detected at beginning of 2023. The air quality data are also analyzed to evaluate for the first time the role of air particulate matter (PM) as a carrier of the Omicron variant diffusion. Due to emerging concerns associated with other viruses (such as smallpox-like virus diffusion in Europe and America), the proposed approach seems to be promising to model the virus spreading.

Impact of Severe Acute Respiratory Syndrome Coronavirus 2 Variants on Inpatient Clinical Outcome

BACKGROUND

Prior observation has shown differences in COVID-19 hospitalization risk between SARS-CoV-2 variants, but limited information describes hospitalization outcomes.

METHODS

Inpatients with COVID-19 at 5 hospitals in the eastern United States were included if they had hypoxia, tachypnea, tachycardia, or fever, and SARS-CoV-2 variant data, determined from whole-genome sequencing or local surveillance inference. Analyses were stratified by history of SARS-CoV-2 vaccination or infection. The average effect of SARS-CoV-2 variant on 28-day risk of severe disease, defined by advanced respiratory support needs, or death was evaluated using models weighted on propensity scores derived from baseline clinical features.

RESULTS

Severe disease or death within 28 days occurred for 977 (29%) of 3369 unvaccinated patients and 269 (22%) of 1230 patients with history of vaccination or prior SARS-CoV-2 infection. Among unvaccinated patients, the relative risk of severe disease or death for Delta variant compared with ancestral lineages was 1.30 (95% confidence interval [CI]: 1.11-1.49). Compared with Delta, the risk for Omicron patients was .72 (95% CI: .59-.88) and compared with ancestral lineages was .94 (.78-1.1). Among Omicron and Delta infections, patients with history of vaccination or prior SARS-CoV-2 infection had half the risk of severe disease or death (adjusted hazard ratio: .40; 95% CI: .30-.54), but no significant outcome difference by variant.

CONCLUSIONS

Although risk of severe disease or death for unvaccinated inpatients with Omicron was lower than with Delta, it was similar to ancestral lineages. Severe outcomes were less common in vaccinated inpatients, with no difference between Delta and Omicron infections.

Impact of COVID-19 Vaccination on Women During Pregnancy and Breastfeeding

Rapid development of anti-SARS-CoV-2 vaccinations in the late 2020s has significantly altered the trajectory in which the virus affects various patient demographics, especially the most susceptible ones. In light of ethical and conceptual safety considerations, pregnant women were initially barred from participating in clinical studies for the coronavirus disease 2019 (COVID-19) vaccination programs. However, the steady accumulation of reliable observational data from cohorts of pregnant women who received vaccinations enabled the research establishments to quickly address a number of open questions. Still, more than a year after vaccines were widely available, the safety concerns of expectant or nursing mothers are cited as the primary justification for refusing COVID-19 vaccination, and notably, the rate of vaccination in the said populations is known to be consistently lower than those of the general populace. In light of such a scenario, we have made an attempt to garner relevant studies that evaluated the effect of COVID-19 vaccination on pregnant and lactating mothers which may prove to be supporting evidence for its wide usage among the said population.

Peculiar weather patterns effects on air pollution and COVID-19 spread in Tokyo metropolis

As a pandemic hotspot in Japan, between March 1, 2020-October 1, 2022, Tokyo metropolis experienced seven COVID-19 waves. Motivated by the high rate of COVID-19 incidence and mortality during the seventh wave, and environmental/health challenges we conducted a time-series analysis to investigate the long-term interaction of air quality and climate variability with viral pandemic in Tokyo. Through daily time series geospatial and observational air pollution/climate data, and COVID-19 incidence and death cases, this study compared the environmental conditions during COVID-19 multiwaves. In spite of five State of Emergency (SOEs) restrictions associated with COVID-19 pandemic, during (2020-2022) period air quality recorded low improvements relative to (2015-2019) average annual values, namely: Aerosol Optical Depth increased by 9.13% in 2020 year, and declined by 6.64% in 2021, and 12.03% in 2022; particulate matter PM2.5 and PM10 decreased during 2020, 2021, and 2022 years by 10.22%, 62.26%, 0.39%, and respectively by 4.42%, 3.95%, 5.76%. For (2021-2022) period the average ratio of PM2.5/PM10 was (0.319 ± 0.1640), showing a higher contribution to aerosol loading of traffic-related coarse particles in comparison with fine particles. The highest rates of the daily recorded COVID-19 incidence and death cases in Tokyo during the seventh COVID-19 wave (1 July 2022-1 October 2022) may be attributed to accumulation near the ground of high levels of air pollutants and viral pathogens due to: 1) peculiar persistent atmospheric anticyclonic circulation with strong positive anomalies of geopotential height at 500 hPa; 2) lower levels of Planetary Boundary Layer (PBL) heights; 3) high daily maximum air temperature and land surface temperature due to the prolonged heat waves (HWs) in summer 2022; 4) no imposed restrictions. Such findings can guide public decision-makers to design proper strategies to curb pandemics under persistent stable anticyclonic weather conditions and summer HWs in large metropolitan areas.

Nonsystematic Reporting Biases of the SARS-CoV-2 Variant Mu Could Impact Our Understanding of the Epidemiological Dynamics of Emerging Variants

Developing a timely and effective response to emerging SARS-CoV-2 variants of concern (VOCs) is of paramount public health importance. Global health surveillance does not rely on genomic data alone to identify concerning variants when they emerge. Instead, methods that utilize genomic data to estimate the epidemiological dynamics of emerging lineages have the potential to serve as an early warning system. However, these methods assume that genomic data are uniformly reported across circulating lineages. In this study, we analyze differences in reporting delays among SARS-CoV-2 VOCs as a plausible explanation for the timing of the global response to the former VOC Mu. Mu likely emerged in South America in mid-2020, where its circulation was largely confined. In this study, we demonstrate that Mu was designated as a VOC ∼1 year after it emerged and find that the reporting of genomic data for Mu differed significantly than that of other VOCs within countries, states, and individual laboratories. Our findings suggest that nonsystematic biases in the reporting of genomic data may have delayed the global response to Mu. Until they are resolved, the surveillance gaps that affected the global response to Mu could impede the rapid and accurate assessment of future emerging variants.

Clustering of SARS-CoV-2 in Households in New York City: A Building-Level Analysis, March-December 2020

OBJECTIVES

To identify the proportion of coronavirus disease 2019 (COVID-19) cases that occurred within households or buildings in New York City (NYC) beginning in March 2020 during the first stay-at-home order to determine transmission attributable to these settings and inform targeted prevention strategies.

DESIGN

The residential addresses of cases were geocoded (converting descriptive addresses to latitude and longitude coordinates) and used to identify clusters of cases residing in unique buildings based on building identification number (BIN), a unique building identifier. Household clusters were defined as 2 or more cases within 2 weeks of onset or diagnosis date in the same BIN with the same unit number, last name, or in a single-family home. Building clusters were defined as 3 or more cases with onset date or diagnosis date within 2 weeks in the same BIN who do not reside in the same household.

SETTING

NYC from March to December 2020.

PARTICIPANTS

NYC residents with a positive SARS-CoV-2 nucleic acid amplification or antigen test result with a specimen collected during March 1, 2020, to December 31, 2020.

MAIN OUTCOME MEASURE

The proportion of NYC COVID-19 cases in a household or building cluster.

RESULTS

The BIN analysis identified 65 343 building and household clusters: 17 139 (26%) building clusters and 48 204 (74%) household clusters. A substantial proportion of NYC COVID-19 cases (43%) were potentially attributable to household transmission in the first 9 months of the pandemic.

CONCLUSIONS

Geocoded address matching assisted in identifying COVID-19 household clusters. Close contact transmission within a household or building cluster was found in 43% of noncongregate cases with a valid residential NYC address. The BIN analysis should be utilized to identify disease clustering for improved surveillance.

Risk factors for SARS-CoV-2 infection in primary and secondary school students and staff in England in the 2020/2021 school year: a longitudinal study

OBJECTIVES

Investigate risk factors for SARS-CoV-2 infections in school students and staff.

METHODS

In the 2020/2021 school year, we administered polymerase chain reaction, antibody tests, and questionnaires to a sample of primary and secondary school students and staff, with data linkage to COVID-19 surveillance. We fitted logistic regression models to identify the factors associated with infection.

RESULTS

We included 6799 students and 5090 staff in the autumn and 11,952 students and 4569 staff in the spring/summer terms. Infections in students in autumn 2020 were related to the percentage of students eligible for free school meals. We found no statistical association between infection risk in primary and secondary schools and reported contact patterns between students and staff in either period in our study. Using public transports was associated with increased risk in autumn in students (adjusted odds ratio = 1.72; 95% confidence interval 1.31-2.25) and staff. One or more infections in the same household during either period was the strongest risk factor for infection in students and more so among staff.

CONCLUSION

Deprivation, community, and household factors were more strongly associated with infection than contacts patterns at school; this suggests that the additional school-based mitigation measures in England in 2020/2021 likely helped reduce transmission risk in schools.

The case fatality rate of COVID-19 during the Delta and the Omicron epidemic phase: A meta-analysis

As coronavirus variants are constantly occurring, we tried to understand more about the omicron and delta variants that have hit the world. We provided dynamic information on the case fatality rate (CFR) of the Omicron variant over time and to compare it with that of the Delta variant through meta-analysis. Twenty-four countries were selected by submission counts, submission dates, and confirmed cases. We defined the Delta or the Omicron epidemic period for individual countries as when each variant is over 90%. We further analyzed the Omicron period by dividing it into the initial plateau, increasing, and decreasing phases according to the number of newly confirmed daily cases. Finally, the meta-analysis examined the summary and between-study heterogeneity. The CFR of COVID-19 during the Omicron epidemic was lower than that during the Delta epidemic (odds ratio [OR]: 0.252, 95% confidence interval [CI] 0.205-0.309). The CFR of COVID-19 during the initial plateau phase of Omicron was higher than during other phases. (OR: 1.962, 95% CI 1.607-2.397). The CFR of COVID-19 during the increasing phase was lower than during the decreasing phases (OR: 0.412, 95% CI 0.342-0.498). The Omicron variant had lower CFR compared to the Delta variant, and the initial plateau phase had higher CFR compared to the noninitial phases. These results can help establish global health policies for COVID-19 in the future.

Histopathological Lung Findings in COVID-19 B.1.617.2 SARS-CoV-2 Delta Variant

BACKGROUND

The Delta variant (Pango lineage B.1.617.2) is one of the most significant and aggressive variants of SARS-CoV-2. To the best of our knowledge, this is the first paper specifically studying pulmonary morphopathology in COVID-19 caused by the B.1.617.2 Delta variant.

METHODS

The study included 10 deceased patients (40-83 years) with the COVID-19 Delta variant. The necrotic lung fragments were obtained either by biopsy (six cases) or autopsy (four cases). Tissue samples were subjected to virology analysis for identification of the SARS-CoV-2 variant, histopathology, and immunohistochemistry (anti-SARS coronavirus mouse anti-virus antibody).

RESULTS

Virology analysis identified B.1.617.2 through genetic sequencing in eight cases, and in two cases, specific mutations of B.1.617.2 were identified. Macroscopically, in all autopsied cases, the lung had a particular appearance, purple in color, with increased consistency on palpation and abolished crepitations. Histopathologically, the most frequently observed lesions were acute pulmonary edema (70%) and diffuse alveolar damage at different stages. The immunohistochemical examination was positive for proteins of SARS-CoV-2 in 60% of cases on alveolocytes and in endothelial cells.

CONCLUSIONS

The histopathological lung findings in the B.1.617.2 Delta variant are similar to those previously described in COVID-19. Spike protein-binding antibodies were identified immunohistochemically both on alveolocytes and in the endothelial cells, showing the potential of indirect damage from thrombosis.

Twice evasions of Omicron variants explain the temporal patterns in six Asian and Oceanic countries

BACKGROUND

The ongoing coronavirus 2019 (COVID-19) pandemic has emerged and caused multiple pandemic waves in the following six countries: India, Indonesia, Nepal, Malaysia, Bangladesh and Myanmar. Some of the countries have been much less studied in this devastating pandemic. This study aims to assess the impact of the Omicron variant in these six countries and estimate the infection fatality rate (IFR) and the reproduction number [Formula: see text] in these six South Asia, Southeast Asia and Oceania countries.

METHODS

We propose a Susceptible-Vaccinated-Exposed-Infectious-Hospitalized-Death-Recovered model with a time-varying transmission rate [Formula: see text] to fit the multiple waves of the COVID-19 pandemic and to estimate the IFR and [Formula: see text] in the aforementioned six countries. The level of immune evasion and the intrinsic transmissibility advantage of the Omicron variant are also considered in this model.

RESULTS

We fit our model to the reported deaths well. We estimate the IFR (in the range of 0.016 to 0.136%) and the reproduction number [Formula: see text] (in the range of 0 to 9) in the six countries. Multiple pandemic waves in each country were observed in our simulation results.

CONCLUSIONS

The invasion of the Omicron variant caused the new pandemic waves in the six countries. The higher [Formula: see text] suggests the intrinsic transmissibility advantage of the Omicron variant. Our model simulation forecast implies that the Omicron pandemic wave may be mitigated due to the increasing immunized population and vaccine coverage.

The predictive role of parental attitudes toward COVID-19 vaccines and child vulnerability: A multi-country study on the relationship between parental vaccine hesitancy and financial well-being

Background and purpose

Recent new mutations and increases in transmission of COVID-19 among adolescents and children highlight the importance of identifying which factors influence parental decisions regarding vaccinating their children. The current study aims to explore whether child vulnerability and parents' attitudes toward vaccines mediate the association between perceived financial well-being and vaccine hesitancy among parents.

Method

A predictive, cross-sectional, multi-country online questionnaire was administered with a convenience sample of 6,073 parents (Australia, 2,734; Iran, 2,447; China, 523; Turkey, 369). Participants completed the Parent Attitude About Child Vaccines (PACV), the Child Vulnerability Scale (CVS), a Financial Well-being (FWB) measure, and Parental Vaccine Hesitancy (PVH) questionnaire.

Results

The current study revealed that perceived financial well-being had significant and negative associations with parents' attitudes toward COVID-19 vaccines and child vulnerability among the Australian sample. Contrary to the Australian findings, results from Chinese participants indicated that financial well-being had significant and positive predictive effects on parent attitudes toward vaccines, child vulnerability, and parental vaccine hesitancy. The results of the Iranian sample revealed that parents' attitudes toward vaccines and child vulnerability significantly and negatively predicted parental vaccine hesitancy.

Conclusion

The current study revealed that a parents' perceived financial well-being had a significant and negative relationship with parental attitudes about vaccines and child vulnerability; however, it did not significantly predict parental vaccine hesitancy among Turkish parents as it did for parents in Australia, Iran, and China. Findings of the study have policy implications for how certain countries may tailor their vaccine-related health messages to parents with low financial wellbeing and parents with vulnerable children.

Association of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection With Maternal Mortality and Neonatal Birth Outcomes in Botswana by Human Immunodeficiency Virus Status

OBJECTIVE

To evaluate the combined association of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human immunodeficiency virus (HIV) infection on adverse birth outcomes in an HIV-endemic region.

METHODS

The Tsepamo Study abstracts data from antenatal and obstetric records in government maternity wards across Botswana. We assessed maternal mortality and adverse birth outcomes for all singleton pregnancies from September 2020 to mid-November 2021 at 13 Tsepamo sites among individuals with documented SARS-CoV-2 screening tests and known HIV status.

RESULTS

Of 20,410 individuals who gave birth, 11,483 (56.3%) were screened for SARS-CoV-2 infection; 4.7% tested positive. People living with HIV were more likely to test positive (144/2,421, 5.9%) than those without HIV (392/9,030, 4.3%) (P=.001). Maternal deaths occurred in 3.7% of those who had a positive SARS-CoV-2 test result compared with 0.1% of those who tested negative (adjusted relative risk [aRR] 31.6, 95% CI 15.4-64.7). Maternal mortality did not differ by HIV status. The offspring of individuals with SARS-CoV-2 infection experienced more overall adverse birth outcomes (34.5% vs 26.6%; aRR 1.2, 95% CI 1.1-1.4), severe adverse birth outcomes (13.6% vs 9.8%; aRR 1.2, 95% CI 1.0-1.5), preterm delivery (21.4% vs 13.4%; aRR 1.4, 95% CI 1.2-1.7), and stillbirth (5.6% vs 2.7%; aRR 1.7 95% CI 1.2-2.5). Neonates exposed to SARS-CoV-2 and HIV infection had the highest prevalence of adverse birth outcomes (43.1% vs 22.6%; aRR 1.7, 95% CI 1.4-2.0).

CONCLUSION

Infection with SARS-CoV-2 at the time of delivery was associated with 3.7% maternal mortality and 5.6% stillbirth in Botswana. Most adverse birth outcomes were worse among neonates exposed to both SARS-CoV-2 and HIV infection.

The infected and the affected: A longitudinal study of the impact of the COVID-19 pandemic on schoolchildren in Florida

Objectives

To identify risk factors associated with symptoms of anxiety, depression, and obsessive-compulsive disorder (OCD) among children during the 1st year of the COVID-19 pandemic.

Methods

A longitudinal study with three cross-sectional timepoints [April 2020 (n = 273), October 2020 (n = 180), and April 2021 (n = 116)] was conducted at a K-12 public school in Florida. Infection and sero-positivity for SARS-CoV-2 was determined by molecular and serologic approaches. Adjusted odds ratios using mixed effect logistic regression models for symptom-derived indicators of anxiety, depression, and OCD in children in April 2021 are presented; past infection and seropositivity were included in the models.

Results

The prevalence of anxiety, depression, or OCD moved from 47.1, to 57.2, to 42.2% across the three timepoints during the study. By endline of the study, in April 2021, non-white children were at higher risk for depression and OCD. Risk for anxiety, depression, and OCD was associated with students who lost a family member due to COVID-19 and who were identified as at-risk in previous timepoints. Rates of SARS-CoV-2 infection and seropositivity were low and not statistically associated with assessed outcomes.

Conclusions

In situations like the COVID-19 pandemic, targeted mental health interventions and screenings are needed in children and adolescents, especially among minority children.

Effective pandemic policy design through feedback does not need accurate predictions

The COVID-19 pandemic has had an enormous toll on human health and well-being and led to major social and economic disruptions. Public health interventions in response to burgeoning case numbers and hospitalizations have repeatedly bent down the epidemic curve, effectively creating a feedback control system. Worst case scenarios have been avoided in many places through this responsive feedback. We aim to formalize and illustrate how to incorporate principles of feedback control into pandemic projections and decision-making, and ultimately shift the focus from prediction to the design of interventions. Starting with an epidemiological model for COVID-19, we illustrate how feedback control can be incorporated into pandemic management using a simple design that couples recent changes in case numbers or hospital occupancy with explicit policy restrictions. We demonstrate robust ability to control a pandemic using a design that responds to hospital cases, despite simulating large uncertainty in reproduction number R0 (range: 1.04-5.18) and average time to hospital admission (range: 4-28 days). We show that shorter delays, responding to case counts versus hospital measured infections, reduce both the cumulative case count and the average level of interventions. Finally, we show that feedback is robust to changing compliance to public health directives and to systemic changes associated with variants of concern and with the introduction of a vaccination program. The negative impact of a pandemic on human health and societal disruption can be reduced by coupling models of disease propagation with models of the decision-making process. In contrast to highly varying open-loop projections, incorporating feedback explicitly in the decision-making process is more reflective of the real-world challenge facing public health decision makers. Using feedback principles, effective control strategies can be designed even if the pandemic characteristics are highly uncertain, encouraging earlier and smaller actions that reduce both case counts and the extent of interventions.

The frequency of defective genomes in Omicron differs from that of the Alpha, Beta and Delta variants

The SARS-CoV-2 Omicron variant emerged showing higher transmissibility and possibly higher resistance to current COVID-19 vaccines than other variants dominating the global pandemic. In March 2020 we performed a study in clinical samples, where we found that a portion of genomes in the SARS-CoV-2 viral population accumulated deletions immediately before the S1/S2 cleavage site (furin-like cleavage site, PRRAR/S) of the spike gene, generating a frameshift and appearance of a premature stop codon. The main aim of this study was to determine the frequency of defective deletions in prevalent variants from the first to sixth pandemic waves in our setting and discuss whether the differences observed might support epidemiological proposals. The complete SARS-CoV-2 spike gene was deeply studied by next-generation sequencing using the MiSeq platform. More than 90 million reads were obtained from respiratory swab specimens of 78 COVID-19 patients with mild infection caused by the predominant variants circulating in the Barcelona city area during the six pandemic waves: B.1.5, B.1.1, B.1.177, Alpha, Beta, Delta, and Omicron. The frequency of defective genomes found in variants dominating the first and second waves was similar to that seen in Omicron, but differed from the frequencies seen in the Alpha, Beta and Delta variants. The changing pattern of mutations seen in the various SARS-CoV-2 variants driving the pandemic waves over time can affect viral transmission and immune escape. Here we discuss the putative biological effects of defective deletions naturally occurring before the S1/S2 cleavage site during adaption of the virus to human infection.

Primary and Secondary Attack Rates by Vaccination Status after a SARS-CoV-2 B.1.617.2 (Delta) Variant Outbreak at a Youth Summer Camp-Texas, June 2021

Children are capable of initiating COVID-19 transmission into households, but many questions remain about the impact of vaccination on transmission. Data from a COVID-19 Delta variant outbreak at an overnight camp in Texas during June 23-27, 2021, were analyzed. The camp had 451 attendees, including 364 youths aged  < 18 years and 87 adults. Detailed interviews were conducted with 92 (20.4%) of consenting attendees and 117 household members of interviewed attendees with COVID-19. Among 450 attendees with known case status, the attack rate was 41%, including 42% among youths; attack rates were lower among vaccinated (13%) than among unvaccinated youths (48%). The secondary attack rate was 51% among 115 household contacts of 55 interviewed index patients. Secondary infections occurred in 67% of unvaccinated household members and 33% of fully or partially vaccinated household members. Analyses suggested that household member vaccination and camp attendee masking at home protected against household transmission.

The SARS-CoV-2 Delta (B.1.617.2) variant with spike N501Y mutation in the shadow of Omicron emergence

Circulation of the Omicron variant with the reemergence of the N501Y mutation along with many others in the spike protein has once again stirred the academic community. Interestingly, tracing the genetic diversity of SARS-CoV-2 shed light on a less frequent N501Y + Delta variant which has been in the global circulation for some time before the Omicron appearance. This paper aims to present the molecular characteristics of the SARS-CoV-2 Spike_N501Y + Delta variant detected in Bosnia and Herzegovina. The study was conducted during November and December 2021. All patients were tested using real-time RT-PCR for detection of SARS-CoV-2. A representative number of SARS-CoV-2 positive samples was pre-screened using VirSNiP SARS-CoV-2 Spike N501Y kit. The characterization of the viruses was carried out with Illumina RNA Prep with enrichment and the Respiratory Virus Oligo Panel kit. Among the analyzed sequences, we found two isolates of the Delta variant that differ from their most related clade- GK AY.4.3 in additional mutations N501Y and L54F. In this study, we described the presence of a rare form of Delta variant with Spike_N501Y mutation in the shadow of the Omicron emergence. Despite the set of mutations in the Spike protein, this form of Delta variant does not indicate the large-scale consequences for the general population. Further functional studies of this form could provide more information about its antigenicity and infectivity.

Real-world effectiveness of casirivimab and imdevimab among patients diagnosed with COVID-19 in the ambulatory setting: a retrospective cohort study using a large claims database

OBJECTIVE

To assess the real-world effectiveness of casirivimab and imdevimab (CAS+IMD) versus no COVID-19 antibody treatment among patients diagnosed with COVID-19 in the ambulatory setting, including patients diagnosed during the Delta-dominant period prior to Omicron emergence.

DESIGN

Retrospective cohort study.

SETTING

Komodo Health closed claims database.

PARTICIPANTS

13 273 128 patients diagnosed with COVID-19 (December 2020 through September 2021) were treated with CAS+IMD or untreated but treatment eligible under the Emergency Use Authorization (EUA). Each treated patient was exact and propensity score matched without replacement to up to five untreated EUA-eligible patients.

INTERVENTIONS

CAS+IMD.

PRIMARY AND SECONDARY OUTCOME MEASURES

Composite endpoint of 30-day all-cause mortality or COVID-19-related hospitalisation. Kaplan-Meier estimators were used to calculate outcome risks overall and across subgroups: age, COVID-19 vaccination status, immunocompromised status, and timing of diagnosis (December 2020 to June 2021, and July to September 2021). Cox proportional hazards models were used to estimate adjusted HRs (aHRs) and 95% CIs.

RESULTS

Among 75 159 CAS+IMD-treated and 1 670 338 EUA-eligible untreated patients, 73 759 treated patients were matched to 310 688 untreated patients; matched patients were ~50 years, ~60% were women and generally well balanced across risk factors. The 30-day risk of the composite outcome was 2.1% and 5.2% in the CAS+IMD-treated and CAS+IMD-untreated patients, respectively; equivalent to a 60% lower risk (aHR 0.40; 95% CI, 0.38 to 0.42). The effect of CAS+IMD was consistent across subgroups, including those who received a COVID-19 vaccine (aHR 0.48, 95% CI, 0.41 to 0.56), and those diagnosed during the Delta-dominant period (aHR 0.40, 95% CI, 0.38 to 0.42).

CONCLUSIONS

The real-world effectiveness of CAS+IMD is consistent with the efficacy for reducing all-cause mortality or COVID-19-related hospitalisation reported in clinical trials. Effectiveness is maintained across patient subgroups, including those prone to breakthrough infections, and was effective against susceptible variants including Delta. .

Mutations in SARS-CoV-2 structural proteins: a global analysis

BACKGROUND

Emergence of new variants mainly variants of concerns (VOC) is caused by mutations in main structural proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, we aimed to investigate the mutations among structural proteins of SARS-CoV-2 globally.

METHODS

We analyzed samples of amino-acid sequences (AASs) for envelope (E), membrane (M), nucleocapsid (N), and spike (S) proteins from the declaration of the coronavirus 2019 (COVID-19) as pandemic to January 2022. The presence and location of mutations were then investigated by aligning the sequences to the reference sequence and categorizing them based on frequency and continent. Finally, the related human genes with the viral structural genes were discovered, and their interactions were reported.

RESULTS

The results indicated that the most relative mutations among the E, M, N, and S AASs occurred in the regions of 7 to 14, 66 to 88, 164 to 205, and 508 to 635 AAs, respectively. The most frequent mutations in E, M, N, and S proteins were T9I, I82T, R203M/R203K, and D614G. D614G was the most frequent mutation in all six geographical areas. Following D614G, L18F, A222V, E484K, and N501Y, respectively, were ranked as the most frequent mutations in S protein globally. Besides, A-kinase Anchoring Protein 8 Like (AKAP8L) was shown as the linkage unit between M, E, and E cluster genes.

CONCLUSION

Screening the structural protein mutations can help scientists introduce better drug and vaccine development strategies.

Analysis of a German blood donor cohort reveals a high number of undetected SARS-CoV-2 infections and sex-specific differences in humoral immune response

Seroprevalence studies can contribute to a better assessment of the actual incidence of infection. Since long-term data for Germany are lacking, we determined the seroprevalence of immunoglobulin G (IgG) antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in residual plasma samples of 3,759 German regular blood donors between July 2020 and June 2021. Over almost the entire study period, the incidences determined based on our data were higher than those officially reported by the Robert Koch Institute, the public health institute in Germany. Using our serological testing strategy, we retrospectively detected natural infection in 206/3,759 (5.48%; 95% confidence interval (CI): 4.77-6.25) individuals. The IgG seroprevalence ranked from 5.15% (95% CI: 3.73-6.89) in Lower Saxony to 5.62% (95% CI: 4.57-6.84) in North Rhine Westphalia. The analyses of follow-up samples of 88 seropositive blood donors revealed a comparable fast decay of binding and neutralizing anti-SARS-CoV-2 IgG antibodies. The antibody avidity remained at a low level throughout the whole follow-up period of up to 181 days. Interestingly, female donors seem to express a stronger and longer lasting humoral immunity against the new coronavirus when compared to males. Conclusion: Overall, our data emphasizes that seroprevalence measurements can and should be used to understand the true incidence of infection better. Further characterization of follow-up samples from seropositive donors indicated rapid antibody waning with sex-specific differences concerning the strength and persistence of humoral immune response.

The COVID-19 hospitalization metric in the pre- and postvaccination eras as a measure of pandemic severity: A retrospective, nationwide cohort study

BACKGROUND

Coronavirus disease 2019 (COVID-19) hospitalization definitions do not include a disease severity assessment. Thus, we sought to identify a simple and objective mechanism for identifying hospitalized severe cases and to measure the impact of vaccination on trends.

METHODS

All admissions to a Veterans' Affairs (VA) hospital, where routine inpatient screening is recommended, between March 1, 2020, and November 22, 2021, with laboratory-confirmed severe acute respiratory coronavirus virus 2 (SARS-CoV-2) were included. Moderate-to-severe COVID-19 was defined as any oxygen supplementation or any oxygen saturation (SpO₂) <94% between 1 day before and 2 weeks after the positive SARS-CoV-2 test. Admissions with moderate-to-severe disease were divided by the total number of admissions, and the proportion of admissions with moderate-to-severe COVID-19 was modelled using a penalized spline in a Poisson regression and stratified by vaccination status. Dexamethasone receipt and its correlation with moderate-to-severe cases was also assessed.

RESULTS

Among 67,025 admissions with SARS-CoV-2, the proportion with hypoxemia or supplemental oxygen fell from 64% prior to vaccine availability to 56% by November 2021, driven in part by lower rates in vaccinated patients (vaccinated, 52% versus unvaccinated, 58%). The proportion of cases of moderate-to-severe disease identified using SpO₂ levels and oxygen supplementation was highly correlated with dexamethasone receipt (correlation coefficient, 0.95), and increased after July 1, 2021, concurrent with δ (delta) variant predominance.

CONCLUSIONS

A simple and objective definition of COVID-19 hospitalizations using SpO₂ levels and oxygen supplementation can be used to track pandemic severity. This metric could be used to identify risk factors for severe breakthrough infections, to guide clinical treatment algorithms, and to detect trends in changes in vaccine effectiveness over time and against new variants.

Elevated ubiquitination contributes to protective immunity against severe SARS-CoV-2 infection

BACKGROUND

The crosstalk between the ubiquitin-proteasome and the immune system plays an important role in the health and pathogenesis of viral infection. However, there have been few studies of ubiquitin activation in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.

METHODS

We investigated the effect of ubiquitination on SARS-CoV-2 infection and patient prognosis by integrating published coronavirus disease 2019 (COVID-19) multi-transcriptome data and bioinformatics methods.

RESULTS

The differential expression of COVID-19 samples revealed changed ubiquitination in most solid and hollow organs, and it was activated in lymphatic and other immune tissues. In addition, in the respiratory system of COVID-19 patients, the immune response was mainly focused on the alveoli, and the expression of ubiquitination reflected increasing immune infiltration. Ubiquitination stratification could significantly differentiate patients' prognosis and inflammation levels through the general transcriptional analysis of the peripheral blood of patients with COVID-19. Moreover, high ubiquitination levels were associated with a favourable prognosis, low inflammatory response, and reduced mechanical ventilation and intensive care unit. Moreover, high ubiquitination promoted a beneficial immune response while inhibiting immune damage. Finally, prognostic stratification and biomarker screening based on ubiquitination traits played an important role in clinical management and drug development.

CONCLUSION

Ubiquitination characteristics provides new ideas for clinical intervention and prognostic guidance for COVID-19 patients.

Increased pathogenicity and aerosol transmission for one SARS-CoV-2 B.1.617.2 Delta variant over the wild-type strain in hamsters

During the two-year pandemic of coronavirus disease 2019 (COVID-19), its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been evolving. SARS-CoV-2 Delta, a variant of concern, has become the dominant circulating strain worldwide within just a few months. Here, we performed a comprehensive analysis of a new B.1.617.2 Delta strain (Delta630) compared with the early WIV04 strain (WIV04) in vitro and in vivo, in terms of replication, infectivity, pathogenicity, and transmission in hamsters. When inoculated intranasally, Delta630 led to more pronounced weight loss and more severe disease in hamsters. Moreover, 40% mortality occurred about one week after infection with 10⁴ ​PFU of Delta630, whereas no deaths occurred even after infection with 10⁵ ​PFU of WIV04 or other strains belonging to the Delta variant. Moreover, Delta630 outgrew over WIV04 in the competitive aerosol transmission experiment. Taken together, the Delta630 strain showed increased replication ability, pathogenicity, and transmissibility over WIV04 in hamsters. To our knowledge, this is the first SARS-CoV-2 strain that causes death in a hamster model, which could be an asset for the efficacy evaluation of vaccines and antivirals against infections of SARS-CoV-2 Delta strains. The underlying molecular mechanisms of increased virulence and transmission await further analysis.

mRNA vaccine effectiveness against SARS-CoV-2 B.1.617.2 (Delta) and B.1.1.529 (Omicron) variant transmission from home care cases to household contacts in South Korea

OBJECTIVES

Household contacts of confirmed cases of coronavirus disease 2019 (COVID-19) areexposed to a high risk of viral transmission, and secondary incidence is an important indicatorof community transmission. This study analyzed the secondary attack rate and mRNA vaccineeffectiveness against transmission (VET) for index cases (patients treated at home) confirmedto be infected with the Delta and Omicron variants.

METHODS

The subjects of the study were 4,450 index cases and 10,382 household contacts.Logistic regression analysis was performed to compare the secondary attack rate byvaccination status, and adjusted relative risk and 95% confidence intervals were identified.

RESULTS

The secondary attack rate of the Delta variant was 27.3%, while the secondary attackrate of the Omicron variant was 29.8%. For the Delta variant, groups with less than 90 daysand more than 90 days after 2 doses of mRNA vaccination both showed a VET of 37%. For theOmicron variant, a 64% VET was found among those with less than 90 days after 2 doses ofmRNA vaccination.

CONCLUSION

This study provides useful data on the secondary attack rate and VET of mRNAvaccines for household contacts of COVID-19 cases in South Korea.

Prediction of infectivity of SARS-CoV2: Mathematical model with analysis of docking simulation for spike proteins and angiotensin-converting enzyme 2

OBJECTIVES

Variants of a coronavirus (SARS-CoV-2) have been spreading in a global pandemic. Improved understanding of the infectivity of future new variants is important so that effective countermeasures against them can be quickly undertaken. In our research reported here, we aimed to predict the infectivity of SARS-CoV-2 by using a mathematical model with molecular simulation analysis, and we used phylogenetic analysis to determine the evolutionary distance of the spike protein gene (S gene) of SARS-CoV-2.

METHODS

We subjected the six variants and the wild type of spike protein and human angiotensin-converting enzyme 2 (ACE2) to molecular docking simulation analyses to understand the binding affinity of spike protein and ACE2. We then utilized regression analysis of the correlation coefficient of the mathematical model and the infectivity of SARS-CoV-2 to predict infectivity.

RESULTS

The evolutionary distance of the S gene correlated with the infectivity of SARS-CoV-2 variants. The calculated biding affinity for the mathematical model obtained with results of molecular docking simulation also correlated with the infectivity of SARS-CoV-2 variants. These results suggest that the data from the docking simulation for the receptor binding domain of variant spike proteins and human ACE2 were valuable for prediction of SARS-CoV-2 infectivity.

CONCLUSION

We developed a mathematical model for prediction of SARS-CoV-2 variant infectivity by using binding affinity obtained via molecular docking and the evolutionary distance of the S gene.

Research progress on vaccine efficacy against SARS-CoV-2 variants of concern

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate worldwide and a variety of variants have emerged. Variants of concern (VOC) designated by the World Health Organization (WHO) have triggered epidemic waves due to their strong infectivity or pathogenicity and potential immune escape, among other reasons. Although large-scale vaccination campaigns undertaken globally have contributed to the improved control of SARS-CoV-2, the efficacies of current vaccines against VOCs have declined to various degrees. In particular, the highly infectious Delta and Omicron variants have caused recent epidemics and prompted concerns about control measures. This review summarizes current VOCs, the protective efficacy of vaccines against VOCs, and the shortcomings in methods for evaluating vaccine efficacy. In addition, strategies for responding to variants are proposed for future epidemic prevention and control as well as for vaccine research and development.

Factors Associated with the Antibiotic Treatment of Children Hospitalized for COVID-19 during the Lockdown in Serbia

Unselective use of antibiotics to treat children with COVID-19 is one of the major issues during the pandemic in Serbia. Thus far, there has been no evidence about the predictors of multiple antibiotic use in the treatment of children with COVID-19. The purpose of this study was to assess the prevalence of antibiotic use, as well as to examine demographic and clinical factors associated with a greater number of antibiotics and with a longer antibiotic treatment administered to hospitalized children with COVID-19 during the lockdown in Serbia. This study included all children who were hospitalized from 6 March to 31 May 2020 at the only pediatric COVID-19 hospital, and who were confirmed to have SARS-CoV-2 infection. Demographic, clinical, and laboratory data were collected from medical records. The antibiotic treatment included the use of azithromycin, cephalosporin (ceftriaxone), ampicillin-amikacin, and hydroxychloroquine. The overall prevalence of antibiotics use in children hospitalized with COVID-19 regardless of age was 47.2% (43.3% in children aged 1-5 years and 44.4% in those aged 5-17 years). In children aged 1-5 years, not having a family member affected by COVID-19 (B = -1.38, 95% confidence interval [CI] -2.43, -0.34, p = 0.011), having pneumonia on chest X-ray (B = 0.81, 95%CI 0.34, 1.29, p = 0.002), being a boy (B = -0.65, 95%CI -1.17, -0.13, p = 0.018), and having higher C-reactive protein (CRP) values on admission (B = 0.12, 95%CI 0.07, 0.17, p = 0.001) were associated with the administration of a higher number of antibiotics. These factors, along with having fever (B = 3.20, 95%CI 1.03, 5.37, p = 0.006), were associated with a longer duration of antibiotic treatment in children aged 1-5 years. In children aged 5-17 years, having pharyngeal erythema (B = 1.37, 95%CI 0.61, 2.13, p = 0.001), fever (B = 0.43, 95%CI 0.07, 0.79, p = 0.018), and pneumonia on chest X-ray (B = 0.91, 95%CI 0.53, 1.29, p = 0.001), not having rhinorrhea (B = -1.27, 95%CI -2.47, -0.08, p = 0.037), being a girl (B = 0.52, 95%CI 0.08, 0.97, p = 0.021), and having higher CRP values on admission (B = 0.04, 95%CI 0.01, 0.06, p = 0.006) were associated with the administration of a higher number of antibiotics. These factors, not including the absence of rhinorrhea, were associated with a longer duration of antibiotics treatment in children aged 5-17 years. Demographic, epidemiological, clinical, and laboratory parameters were associated with the use of multiple antibiotics and a longer duration of antibiotic treatment both among children aged 1-5 years and those aged 5-17 years.

The variant-specific burden of SARS-CoV-2 in Michigan: March 2020 through November 2021

Accurate estimates of the total burden of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to inform policy, planning, and response. We sought to quantify SARS-CoV-2 cases, hospitalizations, and deaths by age in Michigan. Coronavirus disease 2019 cases reported to the Michigan Disease Surveillance System were multiplied by age and time-specific adjustment factors to correct for under-detection. Adjustment factors were estimated in a model fit to incidence data and seroprevalence estimates. Age-specific incidence of SARS-CoV-2 hospitalization, death, vaccination, and variant proportions were estimated from publicly available data. We estimated substantial under-detection of infection that varied by age and time. Accounting for under-detection, we estimate the cumulative incidence of infection in Michigan reached 75% by mid-November 2021, and over 87% of Michigan residents were estimated to have had ≥1 vaccination dose and/or previous infection. Comparing pandemic waves, the relative burden among children increased over time. In general, the proportion of cases who were hospitalized or who died decreased over time. Our results highlight the ongoing risk of periods of high SARS-CoV-2 incidence despite widespread prior infection and vaccination. This underscores the need for long-term planning for surveillance, vaccination, and other mitigation measures amidst continued response to the acute pandemic.

Differential Infectivity of Original and Delta Variants of SARS-CoV-2 in Children Compared to Adults

Although children of all ages are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, they have not been implicated as major drivers of transmission thus far. However, it is still unknown if this finding holds true with new variants of concern (VOC), such as Delta (B.1.617.2). This study aimed to examine differences in both viral RNA (as measured by cycle threshold [CT]) and viable-virus levels from children infected with Delta and those infected with original variants (OV). Furthermore, we aimed to compare the pediatric population infection trends to those in adults. We obtained 690 SARS-CoV-2 RT-PCR positive nasopharyngeal swabs from across Manitoba, Canada, which were further screened for mutations characteristic of VOC. Aliquots of sample were then provided for TCID50 (50% tissue culture infective dose) assays to determine infectious titers. Using a variety of statistical analyses we compared CT and infectivity of VOC in different age demographics. Comparing 122 Delta- to 175 OV-positive nasopharyngeal swab samples from children, we found that those infected with Delta are 2.7 times more likely to produce viable SARS-CoV-2 with higher titers (in TCID50 per milliliter), regardless of viral RNA levels. Moreover, comparing the pediatric samples to 130 OV- and 263 Delta-positive samples from adults, we found only that the Delta pediatric culture-positive samples had titers (TCID50 per milliliter) similar to those of culture-positive adult samples. IMPORTANCE These important findings show that children may play a larger role in viral transmission of Delta than for previously circulating SARS-CoV-2 variants. Additionally, they may suggest a mechanism for why Delta has evolved to be the predominant circulating variant.

SARS-CoV-2 Infections in Icelandic Children: Close Follow-up of All Confirmed Cases in a Nationwide Study

INTRODUCTION

Children are less likely to acquire SARS-CoV-2 infections than adults and when infected, usually have milder disease. True infection and complication rates are, however, difficult to ascertain. In Iceland, a strict test, trace and isolate policy was maintained from the start of the pandemic and offers more accurate information of the number of truly infected children in a nationwide study.

MATERIAL AND METHODS

All children with positive PCR for SARS-CoV-2 infections from February 28, 2020 to August 31, 2021 were followed up through telephone consultations for at least 14 days and their symptoms were registered. Symptom severity and duration were categorized based on age groups and the source of infection was registered.

RESULTS

A total of 1749 children were infected with SARS-CoV-2 in 3 waves of infections. All waves had similar disease severity whereas the incidence was 5-fold higher in the third wave (3.5 vs. 0.73/1000 children/month). No children had severe symptoms, 81 (4.6%) had moderate symptoms, 1287 (73.9%) had mild and 374 (21.5%) were asymptomatic. Symptoms from upper (n = 839, 48%) and lower respiratory tract (n = 744, 43%) were most common. Median duration of symptoms was 5 days and adolescents had a higher risk of prolonged duration [OR:1.84 (1.39-2.43)]. Nineteen (1.1%) children needed medical attention, but no child was hospitalized. The source of infection was a household member in 65% of cases.

DISCUSSION

During the first 3 waves of the pandemic, SARS-CoV-2 infections in Icelandic children were mild and none were hospitalized. The most common symptoms were respiratory symptoms followed by fever, headache and tiredness. This study helps shed light on true complication rates of children with confirmed SARS-CoV-2 infection.

Household secondary attack rate in SARS-CoV-2 infection during the second wave of the COVID-19 pandemic in South India

Background

Coronavirus disease 2019 (COVID-19) has become a major public health problem since its inception disrupting public life and crippling health systems. The mutated variant of the causative virus, Delta, has been notorious in causing rapid upsurge in cases compared to the Alpha variant. The current study tries to find out the household secondary attack rate (HSAR) of COVID-19 and factors associated with it during the second wave of cases in Kerala.

Methodology

A retrospective cohort study was performed among 313 household contacts of 76 COVID-19 patients who had been admitted in Government Medical College, Thrissur, in the southern state of India, Kerala. Data from the participants were collected via phone using a semi-structured interview schedule, and analysis was performed with SPSS software.

Results

The HSAR among household contacts was 59.1% (53.4-64.6%). The risk of acquiring COVID infection among household contacts was higher among contacts of symptomatic index cases with a P value of 0.001 and an odds ratio of 11 (3.7-32.4). index cases were having a home isolation P value of 0.001 and an odds ratio of 3.2 (2-5.1), with delay in COVID-19 testing for index cases with a P value of 0.006. Regarding characteristics of household contacts, higher age groups (p = 0.048), groups living in the same room with an index case P value of 0.021 and an odds ratio of [1.71 (1-2.8)], groups having physical contact with an index case P value of 0.001 and an odds ratio of [3.7 (2.1-7)], groups with touched or cleaned linen/articles with an index case P value of 0.02 and an odds ratio of [1.8 (1-3.1)], and groups having co-morbidities, especially diabetes mellitus (p = 0.0020), were significantly associated with chances of acquiring infection. However, the history of previous COVID positivity in household contacts was a protective factor against the infection P value of 0.009 with an odds ratio of [0.09 (0.01-0.78)].

Conclusion

The study concludes that the second wave of COVID-19 in Kerala was primarily caused by a high SAR, especially among household contacts, and this could have been the reason for the difficulty in control measures during the wave.

Delta Variant: Partially Sensitive To Vaccination, but Still Worth Global Attention

The pandemic coronavirus disease 2019 (COVID-19) has rapidly spread to all countries worldwide. The emergence of its variants has exacerbated this problem. To date, many variants have been identified across the viral genome; the variants of concern are the focus of attention due to their higher transmissibility and resistance to vaccines, especially the delta variant. The delta variant has become the dominant severe acute respiratory syndrome novel coronavirus (SARS-CoV-2) variant worldwide, causing severe panic as it is highly infectious. A better understanding of these variants may help in the development of possible treatments and save more lives. In this study, we summarize the characteristics of the variants of concern. More importantly, we summarize the results of previous studies on the delta variant. The delta variant has a high transmissibility rate and increases the risk of hospitalization and death. However, it is partially sensitive to vaccines. In addition, nonpharmaceutical interventions are valuable during epidemics. These interventions can be used against the delta variant, but managing this variant should still be taken seriously.

Viable SARS-CoV-2 Delta variant detected in aerosols in a residential setting with a self-isolating college student with COVID-19

The B.1.617.2 (Delta) variant of SARS-CoV-2 emerged in India in October of 2020 and spread widely to over 145 countries, comprising over 99% of genome sequence-confirmed virus in COVID-19 cases of the United States (US) by September 2021. The rise in COVID-19 cases due to the Delta variant coincided with a return to in-person school attendance, straining COVID-19 mitigation plans implemented by educational institutions. Some plans required sick students to self-isolate off-campus, resulting in an unintended consequence: exposure of co-inhabitants of dwellings used by the sick person during isolation. We assessed air and surface samples collected from the bedroom of a self-isolating university student with mild COVID-19 for the presence of SARS-CoV-2. That virus' RNA was detected by real-time reverse-transcription quantitative polymerase chain reaction (rRT-qPCR) in air samples from both an isolation bedroom and a distal, non-isolation room of the same dwelling. SARS-CoV-2 was detected and viable virus was isolated in cell cultures from aerosol samples as well as from the surface of a mobile phone. Genomic sequencing revealed that the virus was a Delta variant SARS-CoV-2 strain. Taken together, the results of this work confirm the presence of viable SARS-CoV-2 within a residential living space of a person with COVID-19 and show potential for transportation of virus-laden aerosols beyond a designated isolation suite to other areas of a single-family home.

Predicting SARS-CoV-2 Variant Spread in a Completely Seropositive Population Using Semi-Quantitative Antibody Measurements in Blood Donors

SARS-CoV-2 serologic surveys estimate the proportion of the population with antibodies against historical variants, which nears 100% in many settings. New approaches are required to fully exploit serosurvey data. Using a SARS-CoV-2 anti-Spike (S) protein chemiluminescent microparticle assay, we attained a semi-quantitative measurement of population IgG titers in serial cross-sectional monthly samples of blood donations across seven Brazilian state capitals (March 2021−November 2021). Using an ecological analysis, we assessed the contributions of prior attack rate and vaccination to antibody titer. We compared anti-S titer across the seven cities during the growth phase of the Delta variant and used this to predict the resulting age-standardized incidence of severe COVID-19 cases. We tested ~780 samples per month, per location. Seroprevalence rose to >95% across all seven capitals by November 2021. Driven by vaccination, mean antibody titer increased 16-fold over the study, with the greatest increases occurring in cities with the highest prior attack rates. Mean anti-S IgG was strongly correlated (adjusted R2 = 0.89) with the number of severe cases caused by Delta. Semi-quantitative anti-S antibody titers are informative about prior exposure and vaccination coverage and may also indicate the potential impact of future SARS-CoV-2 variants.

COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have been key drivers of new coronavirus disease 2019 (COVID-19) pandemic waves. To better understand variant epidemiologic characteristics, here we apply a model-inference system to reconstruct SARS-CoV-2 transmission dynamics in South Africa, a country that has experienced three VOC pandemic waves (i.e. Beta, Delta, and Omicron BA.1) by February 2022. We estimate key epidemiologic quantities in each of the nine South African provinces during March 2020 to February 2022, while accounting for changing detection rates, infection seasonality, nonpharmaceutical interventions, and vaccination. Model validation shows that estimated underlying infection rates and key parameters (e.g. infection-detection rate and infection-fatality risk) are in line with independent epidemiological data and investigations. In addition, retrospective predictions capture pandemic trajectories beyond the model training period. These detailed, validated model-inference estimates thus enable quantification of both the immune erosion potential and transmissibility of three major SARS-CoV-2 VOCs, that is, Beta, Delta, and Omicron BA.1. These findings help elucidate changing COVID-19 dynamics and inform future public health planning.

One year on: What we have learned about the psychological effects of COVID-19 social restrictions: A meta-analysis

This article reports on the first meta-analysis of studies on the association between government-imposed social restrictions and mental health outcomes published during the initial year of the COVID-19 pandemic. Thirty-three studies (N = 131,844) were included. Social restrictions were significantly associated with increased mental health symptoms overall (d = .41 [CI 95% .17-.65]), including depression (d = .83 [CI 95% .30-1.37]), stress (d = .21 [CI 95% .01-.42]) and loneliness (d = .30 [CI 95% .07-.52]), but not anxiety (d= .26 [CI 95% -.04-.56]). Subgroup analyses demonstrated that the strictness and length of restrictions had divergent effects on mental health outcomes, but there are concerns regarding study quality. The findings provide critical insights for future research on the effects of COVID-19 social restrictions.

Transmissibility of SARS-CoV-2 B.1.1.214 and Alpha Variants during 4 COVID-19 Waves, Kyoto, Japan, January 2020-June 2021

Household transmission is a primary source of SARS-CoV-2 spread. We used COVID-19 epidemiologic investigation data and viral genome analysis data collected in the city of Kyoto, Japan, during January 2020–June 2021 to evaluate the effects of different settings and viral strains on SARS-CoV-2 transmission. Epidemiologic investigations of 5,061 COVID-19 cases found that the most common category for close contact was within households (35.3%); this category also had the highest reverse transcription PCR positivity. The prevalent viral lineage shifted from B.1.1.214 in the third wave to the Alpha variant in the fourth wave. The proportion of secondary cases associated with households also increased from the third to fourth waves (27% vs. 29%). Among 564 contacts from 206 households, Alpha variant was significantly associated with household transmission (odds ratio 1.52, 95% CI 1.06–2.18) compared with B.1.1.214. Public health interventions targeting household contacts and specific variants could help control SARS-CoV-2 transmission.

SARS-CoV-2 Delta AY.1 Variant Cluster in an Accommodation Facility for COVID-19: Cluster Report

Background: This study aimed to examine the cause of and effective measures against cluster infections, including the delta AY.1 variant of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that occurred in an accommodation facility. Methods: We surveyed the zoning and ventilation systems of the cluster accommodation, examined the staff’s working conditions, conducted an interview, and administered a SARS-CoV-2 test (positive samples were further tested with molecular biological test). Results: Among the 99 employees working at the accommodation, 10 were infected with the delta AY.1 variant. The causes of the cluster infections were close-distance conversations without an unwoven-three-layer mask and contact for approximately five minutes with an unwoven mask under hypoventilated conditions. Conclusions: The Delta AY.1 infection may occur via aerosols and an unwoven mask might not prevent infection in poorly ventilated small spaces. Routine infection detection and responding quickly and appropriately to positive results helps to prevent clusters from spreading.