Seroprevalence and infection fatality rate of the SARS-CoV-2 Omicron variant in Denmark: A nationwide serosurveillance study

A data science pipeline applied to Australia's 2022 COVID-19 Omicron waves

The field of software engineering is advancing at astonishing speed, with packages now available to support many stages of data science pipelines. These packages can support infectious disease modelling to be more robust, efficient and transparent, which has been particularly important during the COVID-19 pandemic. We developed a package for the construction of infectious disease models, integrated it with several open-source libraries and applied this composite pipeline to multiple data sources that provided insights into Australia's 2022 COVID-19 epidemic. We aimed to identify the key processes relevant to COVID-19 transmission dynamics and thereby develop a model that could quantify relevant epidemiological parameters. The pipeline's advantages include markedly increased speed, an expressive application programming interface, the transparency of open-source development, easy access to a broad range of calibration and optimisation tools and consideration of the full workflow from input manipulation through to algorithmic generation of the publication materials. Extending the base model to include mobility effects slightly improved model fit to data, with this approach selected as the model configuration for further epidemiological inference. Under our assumption of widespread immunity against severe outcomes from recent vaccination, incorporating an additional effect of the main vaccination programs rolled out during 2022 on transmission did not further improve model fit. Our simulations suggested that one in every two to six COVID-19 episodes were detected, subsequently emerging Omicron subvariants escaped 30-60% of recently acquired natural immunity and that natural immunity lasted only one to eight months on average. We documented our analyses algorithmically and present our methods in conjunction with interactive online code notebooks and plots. We demonstrate the feasibility of integrating a flexible domain-specific syntax library with state-of-the-art packages in high performance computing, calibration, optimisation and visualisation to create an end-to-end pipeline for infectious disease modelling. We used the resulting platform to demonstrate key epidemiological characteristics of the transition from the emergency to the endemic phase of the COVID-19 pandemic.

Zero-covid advocacy during the COVID-19 pandemic: a case study of views on Twitter/X

During the COVID-19 pandemic, many advocacy groups and individuals criticized governments on social media for doing either too much or too little to mitigate the pandemic. In this article, we review advocacy for COVID-19 elimination or "zero-covid" on the social media platform X (Twitter). We present a thematic analysis of tweets by 20 influential co-signatories of the World Health Network letter on ten themes, covering six topics of science and mitigation (zero-covid, epidemiological data on variants, long-term post-acute sequelae (Long COVID), vaccines, schools and children, views on monkeypox/Mpox) and four advocacy methods (personal advice and promoting remedies, use of anecdotes, criticism of other scientists, and of authorities). The advocacy, although timely and informative, often appealed to emotions and values using anecdotes and strong criticism of authorities and other scientists. Many tweets received hundreds or thousands of likes. Risks were emphasized about children's vulnerability, Long COVID, variant severity, and Mpox, and via comparisons with human immunodeficiency viruses (HIV). Far-reaching policies and promotion of remedies were advocated without systematic evidence review, or sometimes, core field expertise. We identified potential conflicts of interest connected to private companies. Our study documents a need for public health debates to be less polarizing and judgmental, and more factual. In order to protect public trust in science during a crisis, we suggest the development of mechanisms to ensure ethical guidelines for engagement in "science-based" advocacy, and consideration of cost-benefit analysis of recommendations for public health decision-making.

Detection of Nucleocapsid Antibodies Associated with Primary SARS-CoV-2 Infection in Unvaccinated and Vaccinated Blood Donors

Nucleocapsid antibody assays can be used to estimate SARS-CoV-2 infection prevalence in regions implementing spike-based COVID-19 vaccines. However, poor sensitivity of nucleocapsid antibody assays in detecting infection after vaccination has been reported. We derived a lower cutoff for identifying previous infections in a large blood donor cohort (N = 142,599) by using the Ortho VITROS Anti-SARS-CoV-2 Total-N Antibody assay, improving sensitivity while maintaining specificity >98%. We validated sensitivity in samples donated after self-reported swab-confirmed infections diagnoses. Sensitivity for first infections in unvaccinated donors was 98.1% (95% CI 98.0-98.2) and for infection after vaccination was 95.6% (95% CI 95.6-95.7) based on the standard cutoff. Regression analysis showed sensitivity was reduced in the Delta compared with Omicron period, in older donors, in asymptomatic infections, <30 days after infection, and for infection after vaccination. The standard Ortho N antibody threshold demonstrated good sensitivity, which was modestly improved with the revised cutoff.

Seroepidemiological assessment of the spread of SARS-CoV-2 among 25 and 28 year-old adult women in Finland between March 2020-June 2022

INTRODUCTION

Serological surveys of the prevalence of SARS-CoV-2 are instrumental to understanding the course of the COVID-19 epidemic. We evaluate the seroprevalence of SARS-CoV-2 among young adult Finnish females residing in 25 communities all over Finland from 2020 until 2022.

METHODS

Between 1st March 2020 and 30th June 2022, 3589 blood samples were collected from 3583 women born in 1992-95 when aged 25 or 28 years old attending the follow-up of an ongoing population-based trial of cervical screening strategies. The crude and population standardized SARS-CoV-2 seroprevalence was measured using nucleocapsid (induced by infection) and spike wild-type (WT) protein (induced both by infection and by vaccination) antigens over time and stratified by place of residence (inside or outside the Helsinki metropolitan region).

RESULTS

During 2020 (before vaccinations), spike-WT and nucleocapsid IgG antibodies followed each other closely, at very low levels (<5%). Spike-WT seropositivity increased rapidly concomitant with mass vaccinations in 2021 and reached 96.3% in the 2nd quartile of 2022. Antibodies to nucleocapsid IgG remained relatively infrequent throughput 2020-2021, increasing rapidly in the 1st and 2nd quartiles of 2022 (to 19.7% and 56.6% respectively). The nucleocapsid IgG seropositivity increased more profoundly in participants residing in the Helsinki metropolitan region (4.5%, 8.4% and 43.9% in 2020, 2021 and 2022 respectively) compared to those residing in communities outside the capital region (4.5%, 4.3% and 34.7%).

CONCLUSIONS

Low SARS-CoV-2 infection-related seroprevalence during 2020-2021 suggest a comparatively successful infection control. Antibodies to the SARS-CoV-2 WT spike protein became extremely common among young women by the end of 2021, in line with the high uptake of SARS-CoV-2 vaccination. Finally, the rapid increase of seroprevalences to the SARS-CoV-2 nucleocapsid protein during the first and second quartile of 2022, imply a high incidence of infections with SARS-CoV-2 variants able to escape vaccine-induced protection.

Ethics of Nudging in the COVID-19 Crisis and the Necessary Return to the Principles of Shared Decision Making: A Critical Review

Nudging, a controversial technique for modifying people's behavior in a predictable way, is claimed to preserve freedom of choice while simultaneously influencing it. Nudging had been largely confined to situations such as promoting healthy eating choices but has been employed in the coronavirus disease 2019 (COVID-19) crisis in a shift towards measures that involve significantly less choice, such as shoves and behavioral prods. Shared decision making (SDM), a method for direct involvement and autonomy, is an alternative approach to communicate risk. Predominantly peer-reviewed scientific publications from standard literature databases like PubMed, PsycInfo, and Psyndex were evaluated in a narrative review. The so-called fear nudges, as well as the dissemination of strongly emotionalizing or moralizing messages can lead to intense psycho-physical stress. The use of these nudges by specialized units during the COVID-19 pandemic generated a societal atmosphere of fear that precipitated a deterioration of the mental and physical health of the population. Major recommendations of the German COVID-19 Snapshot Monitoring (COSMO) study, which are based on elements of nudging and coercive measures, do not comply with ethical principles, basic psychological principles, or evidence-based data. SDM was misused in the COVID-19 crisis, which helped to achieve one-sided goals of governments. The emphasis on utilitarian thinking is criticized and the unethical behavior of decision makers is explained by both using the concept of moral disengagement and the maturity level of coping strategies. There should be a return to an open-ended, democratic, and pluralistic scientific debate without using nudges. It is therefore necessary to return to the origins of SDM.

Effectiveness of a fourth SARS-CoV-2 vaccine dose in previously infected individuals from Austria

INTRODUCTION

Evidence is limited on the effectiveness of a fourth vaccine dose against coronavirus disease 2019 (COVID-19) in populations with prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. We estimated the risk of COVID-19 deaths and SARS-CoV-2 infections according to vaccination status in previously infected individuals in Austria.

METHODS

This is a nationwide retrospective observational study. We calculated age and gender adjusted Cox proportional hazard ratios (HRs) of COVID-19 deaths (primary outcome) and SARS-CoV-2 infections (secondary outcome) from 1 November to 31 December 2022, primarily comparing individuals with four versus three vaccine doses. Relative vaccine effectiveness (rVE) was calculated as (1-HR) X 100.

RESULTS

Among 3,986,312 previously infected individuals, 281,291 (7,1%) had four and 1,545,242 (38.8%) had three vaccinations at baseline. We recorded 69 COVID-19 deaths and 89,056 SARS-CoV-2 infections. rVE for four versus three vaccine doses was -24% (95% CI: -120 to 30) against COVID-19 deaths, and 17% (95% CI: 14-19) against SARS-CoV-2 infections. This latter effect rapidly diminished over time and infection risk with four vaccinations was higher compared to less vaccinated individuals during extended follow-up until June 2023. Adjusted HR (95% CI) for all-cause mortality for four versus three vaccinations was 0.79 (0.74-0.85).

DISCUSSION

In previously infected individuals, a fourth vaccination was not associated with COVID-19 death risk, but with transiently reduced risk of SARS-CoV-2 infections and reversal of this effect in longer follow-up. All-cause mortality data suggest healthy vaccinee bias.

Clinical outcomes in hospitalized plasma and platelet transfusion recipients prior to and following widespread blood donor SARS-CoV-2 infection and vaccination

BACKGROUND

The safety of transfusion of SARS-CoV-2 antibodies in high plasma volume blood components to recipients without COVID-19 is not established. We assessed whether transfusion of plasma or platelet products during periods of increasing prevalence of blood donor SARS-CoV-2 infection and vaccination was associated with changes in outcomes in hospitalized patients without COVID-19.

METHODS

We conducted a retrospective cohort study of hospitalized adults who received plasma or platelet transfusions at 21 hospitals during pre-COVID-19 (3/1/2018-2/29/2020), COVID-19 pre-vaccine (3/1/2020-2/28/2021), and COVID-19 post-vaccine (3/1/2021-8/31/2022) study periods. We used multivariable logistic regression with generalized estimating equations to adjust for demographics and comorbidities to calculate odds ratios (ORs) and 95% confidence intervals (CIs).

RESULTS

Among 21,750 hospitalizations of 18,584 transfusion recipients without COVID-19, there were 697 post-transfusion thrombotic events, and oxygen requirements were increased in 1751 hospitalizations. Intensive care unit length of stay (n = 11,683) was 3 days (interquartile range 1-5), hospital mortality occurred in 3223 (14.8%), and 30-day rehospitalization in 4144 (23.7%). Comparing the pre-COVID, pre-vaccine and post-vaccine study periods, there were no trends in thromboses (OR 0.9 [95% CI 0.8, 1.1]; p = .22) or oxygen requirements (OR 1.0 [95% CI 0.9, 1.1]; p = .41). In parallel, there were no trends across study periods for ICU length of stay (p = .83), adjusted hospital mortality (OR 1.0 [95% CI 0.9-1.0]; p = .36), or 30-day rehospitalization (p = .29).

DISCUSSION

Transfusion of plasma and platelet blood components collected during the pre-vaccine and post-vaccine periods of the COVID-19 pandemic was not associated with increased adverse outcomes in transfusion recipients without COVID-19.

Epidemiological features of SARS-CoV-2 Omicron infection under new control strategy: a cross-sectional study of the outbreak since December 2022 in Sichuan, China

BACKGROUND

A major shift in the "dynamic zero-COVID" policy was announced by China's National Health Commission on December 7, 2022, and the subsequent immediate large-scale outbreak of SARS-CoV-2 infections in the entire country has caused worldwide concern. This observational cross-sectional study aimed to describe the epidemiological characteristics of this outbreak in Sichuan, China.

METHODS

All data were self-reported online by volunteers. We described the epidemic by characterizing the infection, symptoms, clinical duration, severity, spatiotemporal clustering, and dynamic features of the disease. Prevalence ratio (PR), Odds ratios (ORs) and adjusted ORs were calculated to analyze the associations between risk factors and infection and the associations of risk factors with clinical severity using log-binomial and multivariable logistic regression models; 95% confidence intervals (CIs) and Wald test results were reported. The prevalence rates and clinical severity among different subgroups were compared using the Chi-square and trend Chi-square tests.

RESULTS

Between January 6 and 12, 2023, 138,073 volunteers were enrolled in this survey, and 102,645 were infected with COVID-19, holding a prevalence rate of 74.34%; the proportion of asymptomatic infections was 1.58%. Log-binomial regression revealed that the risk of infection increased among those living in urban areas. Multivariable logistic regression analysis showed that female sex, chronic diseases, older age and the fewer doses of vaccine received were associated with an increased risk of severe clinical outcomes after infection. We estimated the mean reproduction number during this pandemic was 1.83. The highest time-dependent reproduction number was 4.15; this number decreased below 1 after 11 days from December 7, 2022. Temporal trends revealed a single peak curve with a plateau pattern of incidence during the outbreak, whereas spatiotemporal clustering analysis showed that the onset in 21 cities in the Sichuan province had four-wave peaks.

CONCLUSIONS

The peak of the first wave of Omicron infection in Sichuan Province had passed and could be considered a snapshot of China under the new control strategy. There were significant increases in the risk of severe clinical outcomes after infection among females, with chronic diseases, and the elderly. The vaccines have been effective in reducing poor clinical outcomes.

Monovalent vaccination with inactivated SARS-CoV-2 BA.5 protects hamsters against Omicron but not non-Omicron variants

We compared the protective effects of inactivated SARS-CoV-2 vaccines derived from the ancestral and the currently circulating BA.5.2 strains against infection with multiple variants in Syrian golden hamsters. Vaccination with BA.5.2 effectively protected against infection with the Omicron subvariants including XBB.1, but not the Alpha or Delta variant. In contrast, hamsters vaccinated with the ancestral strain demonstrated decent neutralization activity against both the Omicron and non-Omicron variants. Our findings might instruct future design and formulation of SARS-CoV-2 vaccines.

Risk of hospital admission and death from first-ever SARS-CoV-2 infection by age group during the Delta and Omicron periods in British Columbia, Canada

BACKGROUND

Population-based cross-sectional serosurveys within the Lower Mainland, British Columbia, Canada, showed about 10%, 40% and 60% of residents were infected with SARS-CoV-2 by the sixth (September 2021), seventh (March 2022) and eighth (July 2022) serosurveys. We conducted the ninth (December 2022) and tenth (July 2023) serosurveys and sought to assess risk of severe outcomes from a first-ever SARS-CoV-2 infection during intersurvey periods.

METHODS

Using increments in cumulative infection-induced seroprevalence, population census, discharge abstract and vital statistics data sets, we estimated infection hospitalization and fatality ratios (IHRs and IFRs) by age and sex for the sixth to seventh (Delta/Omicron-BA.1), seventh to eighth (Omicron-BA.2/BA.5) and eighth to ninth (Omicron-BA.5/BQ.1) intersurvey periods. As derived, IHR and IFR estimates represent the risk of severe outcome from a first-ever SARS-CoV-2 infection acquired during the specified intersurvey period.

RESULTS

The cumulative infection-induced seroprevalence was 74% by December 2022 and 79% by July 2023, exceeding 80% among adults younger than 50 years but remaining less than 60% among those aged 80 years and older. Period-specific IHR and IFR estimates were consistently less than 0.3% and 0.1% overall. By age group, IHR and IFR estimates were less than 1.0% and up to 0.1%, respectively, except among adults aged 70-79 years during the sixth to seventh intersurvey period (IHR 3.3% and IFR 1.0%) and among those aged 80 years and older during all periods (IHR 4.7%, 2.2% and 3.5%; IFR 3.3%, 0.6% and 1.3% during the sixth to seventh, seventh to eighth and eighth to ninth periods, respectively). The risk of severe outcome followed a J-shaped age pattern. During the eighth to ninth period, we estimated about 1 hospital admission for COVID-19 per 300 newly infected children younger than 5 years versus about 1 per 30 newly infected adults aged 80 years and older, with no deaths from COVID-19 among children but about 1 death per 80 newly infected adults aged 80 years and older during that period.

INTERPRETATION

By July 2023, we estimated about 80% of residents in the Lower Mainland, BC, had been infected with SARS-CoV-2 overall, with low risk of hospital admission or death; about 40% of the oldest adults, however, remained uninfected and at highest risk of a severe outcome. First infections among older adults may still contribute substantial burden from COVID-19, reinforcing the need to continue to prioritize this age group for vaccination and to consider them in health care system planning.

SARS-CoV-2 sero-immunity and quality of life in children and adolescents in relation to infections and vaccinations: the IMMUNEBRIDGE KIDS cross-sectional study, 2022

PURPOSE

The study evaluates the effects on sero-immunity, health status and quality of life of children and adolescents after the upsurge of the Omicron variant in Germany.

METHODS

This multicenter cross-sectional study (IMMUNEBRIDGE Kids) was conducted within the German Network University Medicine (NUM) from July to October 2022. SARS-CoV-2- antibodies were measured and data on SARS-CoV-2 infections, vaccinations, health and socioeconomic factors as well as caregiver-reported evaluation on their children's health and psychological status were assessed.

RESULTS

497 children aged 2-17 years were included. Three groups were analyzed: 183 pre-schoolchildren aged 2-4 years, 176 schoolchildren aged 5-11 years and 138 adolescents aged 12-18 years. Positive antibodies against the S- or N-antigen of SARS-CoV-2 were detected in 86.5% of all participants (70.0% [128/183] of pre-schoolchildren, 94.3% of schoolchildren [166/176] and 98.6% of adolescents [136/138]). Among all children, 40.4% (201/497) were vaccinated against COVID-19 (pre-schoolchildren 4.4% [8/183], schoolchildren 44.3% [78/176] and adolescents 83.3% [115/138]). SARS-CoV-2 seroprevalence was lowest in pre-school. Health status and quality of life reported by the parents were very positive at the time of the survey (Summer 2022).

CONCLUSION

Age-related differences on SARS-CoV-2 sero-immunity could mainly be explained by differences in vaccination rates based on the official German vaccination recommendations as well as differences in SARS-CoV-2 infection rates in the different age groups. Health status and quality of life of almost all children were very good independent of SARS-CoV-2 infection and/or vaccination.

TRIAL REGISTRATION

German Registry for Clinical Trials Identifier Würzburg: DRKS00025546 (registration: 11.09.2021), Bochum: DRKS00022434 (registration:07.08.2020), Dresden: DRKS 00022455 (registration: 23.07.2020).

Infection-Induced SARS-CoV-2 Seroprevalence among Blood Donors, Japan, 2022

A nationwide survey of SARS-CoV-2 antinucleocapsid seroprevalence among blood donors in Japan revealed that, as of November 2022, infection-induced seroprevalence of the population was 28.6% (95% CI 27.6%-29.6%). Seroprevalence studies might complement routine surveillance and ongoing monitoring efforts to provide a more complete real-time picture of COVID-19 burden.

Policies on children and schools during the SARS-CoV-2 pandemic in Western Europe

During the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), mitigation policies for children have been a topic of considerable uncertainty and debate. Although some children have co-morbidities which increase their risk for severe coronavirus disease (COVID-19), and complications such as multisystem inflammatory syndrome and long COVID, most children only get mild COVID-19. On the other hand, consistent evidence shows that mass mitigation measures had enormous adverse impacts on children. A central question can thus be posed: What amount of mitigation should children bear, in response to a disease that is disproportionally affecting older people? In this review, we analyze the distinct child versus adult epidemiology, policies, mitigation trade-offs and outcomes in children in Western Europe. The highly heterogenous European policies applied to children compared to adults did not lead to significant measurable differences in outcomes. Remarkably, the relative epidemiological importance of transmission from school-age children to other age groups remains uncertain, with current evidence suggesting that schools often follow, rather than lead, community transmission. Important learning points for future pandemics are summarized.

Booster vaccinations and Omicron: the effects on SARS-CoV-2 antibodies in Dutch blood donors

INTRODUCTION

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) booster vaccination campaign and the emergence of SARS-CoV-2 Omicron variants impact the prevalence and levels of SARS-CoV-2 antibodies in the Netherlands. In this study we determined antibody levels across age groups, the impact of Omicron variant infections, and the effect of booster vaccinations on antibody levels.

METHODS

In September and December 2021 and in February 2022, over 2000 Dutch blood donors were tested for presence of SARS-CoV-2 antibodies. Donations were selected based on age, sex, and region of residence, to provide an optimal coverage and representation of the Dutch population.

RESULTS

Levels of vaccination-induced spike antibodies decreased over time in all age groups. Donors vaccinated with Janssen or AstraZeneca had significantly lower antibody levels than donors vaccinated with Pfizer or Moderna vaccine. Boostering with an mRNA vaccine elevated antibody levels in all age-groups irrespective of the initial vaccine. In donors aged < 56 years, the proportion of infected donors almost doubled between December 2021 and February 2022.

CONCLUSION

The booster vaccination campaign increased antibody levels in all age-groups. After a booster vaccination, donors initially vaccinated with AstraZeneca or Janssen vaccine showed antibody levels similar to donors initially vaccinated with an mRNA vaccine. The emergence of the SARS-CoV-2 Omicron variant in the Netherlands caused a substantial increase in donors with infection-induced antibodies, especially among younger donors.

Outcomes and characteristics of patients hospitalized for COVID-19 in British Columbia, Ontario and Quebec during the Omicron wave

BACKGROUND

Omicron is the current predominant variant of concern of SARS-CoV-2. We hypothesized that vaccination alters outcomes of patients hospitalized with COVID-19 during the Omicron wave and that these patients have different characteristics and outcomes than in previous waves.

METHODS

This is a substudy of the Host Response Mediators in Coronavirus (COVID-19) Infection (ARBs CORONA I) trial, which included adults admitted to hospital with acute COVID-19 up to July 2022 from 9 hospitals in British Columbia, Ontario and Quebec. We excluded emergency department visits without hospital admission, readmissions and admissions for another reason. Using adjusted regression analysis, we compared mortality and organ dysfunction between vaccinated (≥ 2 doses) and unvaccinated patients during the Omicron wave, as well as between all patients in the Omicron and first 3 waves of the COVID-19 pandemic.

RESULTS

During the Omicron wave, 28-day mortality was significantly lower in vaccinated (n = 19/237) than unvaccinated hospitalized patients (n = 12/127) (adjusted odds ratio [OR] 0.36, 95% confidence interval [CI] 0.15-0.89); vaccinated patients had lower risk of admission to the intensive care unit, invasive ventilation and acute respiratory distress syndrome and shorter hospital length of stay. Patients hospitalized during the Omicron wave had more comorbidities than in previous waves, and lower 28-day mortality than in waves 1 and 2 (adjusted OR 0.38, 95% CI 0.24-0.59; and 0.42, 95% CI 0.26-0.65) but not wave 3 (adjusted OR 0.81, 95% CI 0.43-1.51) and had less organ dysfunction than in the first 2 waves.

INTERPRETATION

Patients who were at least double vaccinated had lower mortality than unvaccinated patients hospitalized during the Omicron wave. Patients hospitalized during the Omicron wave had more chronic disease and lower mortality than in the first 2 waves, but not wave 3. Changes in vaccination, treatments and predominant SARS-CoV-2 variant may have decreased mortality in patients hospitalized during the Omicron wave.

Serosurveillance of SARS-CoV-2 in Welsh Blood Donors: Establishment of the surveillance system and results up to November 2022

BackgroundIn 2020, Wales experienced some of the highest rates of confirmed COVID-19 cases in Europe. We set up a serosurveillance scheme using residual samples from blood donations to inform the pandemic response in Wales.AimTo identify changes in SARS-CoV-2 antibody seroprevalence in Wales by time, demography and location.MethodsResidual samples from blood donations made in Wales between 29 June 2020 and 20 November 2022 were tested for antibodies to the nucleocapsid antigen (anti-N) of SARS-CoV-2, resulting from natural infection. Donations made between 12 April 2021 and 20 November 2022 were also tested for antibodies to the spike antigen (anti-S) occurring as a result of natural infection and vaccination.ResultsAge-standardised seroprevalence of anti-N antibodies in donors remained stable (4.4-5.5%) until November 2020 before increasing to 16.7% by February 2021. Trends remained steady until November 2021 before increasing, peaking in November 2022 (80.2%). For anti-S, seroprevalence increased from 67.1% to 98.6% between May and September 2021, then remained above 99%. Anti-N seroprevalence was highest in younger donors and in donors living in urban South Wales. In contrast, seroprevalence of anti-S was highest in older donors and was similar across regions. No significant difference was observed by sex. Seroprevalence of anti-N antibodies was higher in Black, Asian and other minority ethnicities (self-reported) compared with White donors, with the converse observed for anti-S antibodies.ConclusionWe successfully set up long-term serological surveillance of SARS-CoV-2 using residual samples from blood donations, demonstrating variation based on age, ethnicity and location.

Impact of hybrid immunity booster vaccination and Omicron breakthrough infection on SARS-CoV-2 VOCs cross-neutralization

The elicitation of cross-variant neutralizing antibodies against SARS-CoV-2 represents a major goal for current COVID-19 vaccine strategies. Additionally, natural infection may also contribute to broaden neutralizing responses. To assess the contribution of vaccines and natural infection, we cross-sectionally analyzed plasma neutralization titers of six groups of individuals, organized according to the number of vaccines they received and their SARS-CoV-2 infection history. Two doses of vaccine had a limited capacity to generate cross-neutralizing antibodies against Omicron variants of concern (VOCs) in uninfected individuals, but efficiently synergized with previous natural immunization in convalescent individuals. In contrast, booster dose had a critical impact on broadening the cross-neutralizing response in uninfected individuals, to level similar to hybrid immunity, while still improving cross-neutralizing responses in convalescent individuals. Omicron breakthrough infection improved cross-neutralization of Omicron subvariants in non-previously infected vaccinated individuals. Therefore, ancestral Spike-based immunization, via infection or vaccination, contributes to broaden SARS-CoV-2 humoral immunity.

Temporal dynamics and fatality of SARS-CoV-2 variants in Bangladesh

Background and Aims

Since the beginning of the SARS-CoV-2 pandemic, multiple new variants have emerged posing an increased risk to global public health. This study aimed to investigate SARS-CoV-2 variants, their temporal dynamics, infection rate (IFR) and case fatality rate (CFR) in Bangladesh by analyzing the published genomes.

Methods

We retrieved 6610 complete whole genome sequences of the SARS-CoV-2 from the GISAID (Global Initiative on Sharing all Influenza Data) platform from March 2020 to October 2022, and performed different in-silico bioinformatics analyses. The clade and Pango lineages were assigned by using Nextclade v2.8.1. SARS-CoV-2 infections and fatality data were collected from the Institute of Epidemiology Disease Control and Research (IEDCR), Bangladesh. The average IFR was calculated from the monthly COVID-19 cases and population size while average CFR was calculated from the number of monthly deaths and number of confirmed COVID-19 cases.

Results

SARS-CoV-2 first emerged in Bangladesh on March 3, 2020 and created three pandemic waves so far. The phylogenetic analysis revealed multiple introductions of SARS-CoV-2 variant(s) into Bangladesh with at least 22 Nextstrain clades and 107 Pangolin lineages with respect to the SARS-CoV-2 reference genome of Wuhan/Hu-1/2019. The Delta variant was detected as the most predominant (48.06%) variant followed by Omicron (27.88%), Beta (7.65%), Alpha (1.56%), Eta (0.33%) and Gamma (0.03%) variant. The overall IFR and CFR from circulating variants were 13.59% and 1.45%, respectively. A time-dependent monthly analysis showed significant variations in the IFR (p = 0.012, Kruskal-Wallis test) and CFR (p = 0.032, Kruskal-Wallis test) throughout the study period. We found the highest IFR (14.35%) in 2020 while Delta (20A) and Beta (20H) variants were circulating in Bangladesh. Remarkably, the highest CFR (1.91%) from SARS-CoV-2 variants was recorded in 2021.

Conclusion

Our findings highlight the importance of genomic surveillance for careful monitoring of variants of concern emergence to interpret correctly their relative IFR and CFR, and thus, for implementation of strengthened public health and social measures to control the spread of the virus. Furthermore, the results of the present study may provide important context for sequence-based inference in SARS-CoV-2 variant(s) evolution and clinical epidemiology beyond Bangladesh.

Trajectories of Seroprevalence and Neutralizing Activity of Antibodies against SARS-CoV-2 in Southern Switzerland between July 2020 and July 2021: An Ongoing, Prospective Population-Based Cohort Study

OBJECTIVES

The COVID-19 pandemic continues, and evidence on infection- and vaccine-induced immunity is key. We assessed COVID-19 immunity and the neutralizing antibody response to virus variants across age groups in the Swiss population.

STUDY DESIGN

We conducted a cohort study in representative community-dwelling residents aged five years or older in southern Switzerland (total population 353,343), and we collected blood samples in July 2020 (in adults only, N = 646), November-December 2020 (N = 1457), and June-July 2021 (N = 885).

METHODS

We used a previously validated Luminex assay to measure antibodies targeting the spike (S) and the nucleocapsid (N) proteins of the virus and a high-throughput cell-free neutralization assay optimized for multiple spike protein variants. We calculated seroprevalence with a Bayesian logistic regression model accounting for the population's sociodemographic structure and the test performance, and we compared the neutralizing activity between vaccinated and convalescent participants across virus variants.

RESULTS

The overall seroprevalence was 7.8% (95% CI: 5.4-10.4) by July 2020 and 20.2% (16.4-24.4) by December 2020. By July 2021, the overall seroprevalence increased substantially to 72.5% (69.1-76.4), with the highest estimates of 95.6% (92.8-97.8) among older adults, who developed up to 10.3 more antibodies via vaccination than after infection compared to 3.7 times more in adults. The neutralizing activity was significantly higher for vaccine-induced than infection-induced antibodies for all virus variants (all p values < 0.037).

CONCLUSIONS

Vaccination chiefly contributed to the reduction in immunonaive individuals, particularly those in older age groups. Our findings on the greater neutralizing activity of vaccine-induced antibodies than infection-induced antibodies are greatly informative for future vaccination campaigns.

Seroprevalence of Anti-SARS-CoV-2 Antibodies Following the Omicron BA.1 Wave

We conducted a seroprevalence study using convenient residual sera samples from the Slovenian population collected after the end of the Omicron BA.1 pandemic wave. Serum samples were tested for spike glycoprotein (anti-S) and nucleocapsid protein (anti-N) antibodies. Participants' data regarding confirmed infection and vaccination was obtained from national registries. Anti-S antibodies were detected in 2439 (84.1%) of 2899 sera from persons aged 0-90 years, with the lowest prevalence in the 0-17 age group. The proportion of anti-N positives was the lowest in the ≥70 age group. The proportion of anti-N positives was significantly higher among participants with confirmed past infection and among those who had never been vaccinated. In participants who had not been notified as infected and who had never been vaccinated, the seroprevalence of anti-S and anti-N antibodies was 53% and 35.5%, respectively. From the time of serum collection to mid-November 2022, 445 participants (15.3%) tested positive for SARS-CoV-2, with higher odds in seronegative participants, participants in the 40-59 age group, and those without notified previous infection. Vaccination status and gender had no significant effects on infection risk. This study underlines the importance of serosurveys in understanding the development of the pandemic.

Wild-type SARS-CoV-2 neutralizing immunity decreases across variants and over time but correlates well with diagnostic testing

Importance

The degree of immune protection against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants provided by infection versus vaccination with wild-type virus remains unresolved, which could influence future vaccine strategies. The gold-standard for assessing immune protection is viral neutralization; however, few studies involve a large-scale analysis of viral neutralization against the Omicron variant by sera from individuals infected with wild-type virus.

Objectives

1) To define the degree to which infection versus vaccination with wild-type SARS-CoV-2 induced neutralizing antibodies against Delta and Omicron variants.2) To determine whether clinically available data, such as infection/vaccination timing or antibody status, can predict variant neutralization.

Methods

We examined a longitudinal cohort of 653 subjects with sera collected three times at 3-to-6-month intervals from April 2020 to June 2021. Individuals were categorized according to SARS-CoV-2 infection and vaccination status. Spike and nucleocapsid antibodies were detected via ADVIA Centaur^® (Siemens) and Elecsys^® (Roche) assays, respectively. The Healgen Scientific^® lateral flow assay was used to detect IgG and IgM spike antibody responses. Pseudoviral neutralization assays were performed on all samples using human ACE2 receptor-expressing HEK-293T cells infected with SARS-CoV-2 spike protein pseudotyped lentiviral particles for wild-type (WT), B.1.617.2 (Delta), and B.1.1.529 (Omicron) variants.

Results

Vaccination after infection led to the highest neutralization titers at all timepoints for all variants. Neutralization was also more durable in the setting of prior infection versus vaccination alone. Spike antibody clinical testing effectively predicted neutralization for wild-type and Delta. However, nucleocapsid antibody presence was the best independent predictor of Omicron neutralization. Neutralization of Omicron was lower than neutralization of either wild-type or Delta virus across all groups and timepoints, with significant activity only present in patients that were first infected and later immunized.

Conclusions

Participants having both infection and vaccination with wild-type virus had the highest neutralizing antibody levels against all variants and had persistence of activity. Neutralization of WT and Delta virus correlated with spike antibody levels against wild-type and Delta variants, but Omicron neutralization was better correlated with evidence of prior infection. These data help explain why 'breakthrough' Omicron infections occurred in previously vaccinated individuals and suggest better protection is observed in those with both vaccination and previous infection. This study also supports the concept of future SARS-CoV-2 Omicron-specific vaccine boosters.

Real-world COVID-19 vaccine effectiveness against the Omicron BA.2 variant in a SARS-CoV-2 infection-naive population

The SARS-CoV-2 Omicron variant has demonstrated enhanced transmissibility and escape of vaccine-derived immunity. Although first-generation vaccines remain effective against severe disease and death, robust evidence on vaccine effectiveness (VE) against all Omicron infections, irrespective of symptoms, remains sparse. We used a community-wide serosurvey with 5,310 subjects to estimate how vaccination histories modulated risk of infection in infection-naive Hong Kong during a large wave of Omicron BA.2 epidemic in January-July 2022. We estimated that Omicron infected 45% (41-48%) of the local population. Three and four doses of BNT162b2 or CoronaVac were effective against Omicron infection 7 days after vaccination (VE of 48% (95% credible interval 34-64%) and 69% (46-98%) for three and four doses of BNT162b2, respectively; VE of 30% (1-66%) and 56% (6-97%) for three and four doses of CoronaVac, respectively). At 100 days after immunization, VE waned to 26% (7-41%) and 35% (10-71%) for three and four doses of BNT162b2, and to 6% (0-29%) and 11% (0-54%) for three and four doses of CoronaVac. The rapid waning of VE against infection conferred by first-generation vaccines and an increasingly complex viral evolutionary landscape highlight the necessity for rapidly deploying updated vaccines followed by vigilant monitoring of VE.

Does natural and hybrid immunity obviate the need for frequent vaccine boosters against SARS-CoV-2 in the endemic phase?

The coronavirus disease 2019 (COVID-19) pandemic has entered its endemic phase and we observe significantly declining infection fatality rates due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). On this background, it is crucial but challenging to define current and future vaccine policy in a population with a high immunity against SARS-CoV-2 conferred by previous infections and/or vaccinations. Vaccine policy must consider the magnitude of the risks conferred by new infection(s) with current and evolving SARS-CoV-2 variants, how these risks vary in different groups of individuals, how to balance these risks against the apparently small, but existent, risks of harms of vaccination, and the cost-benefit of different options. More evidence from randomized controlled trials and continuously accumulating national health data is required to inform shared decision-making with people who consider vaccination options. Vaccine policy makers should cautiously weight what vaccination schedules are needed, and refrain from urging frequent vaccine boosters unless supported by sufficient evidence.

Clinical outcomes of myocarditis after SARS-CoV-2 mRNA vaccination in four Nordic countries: population based cohort study

Objective

To investigate the clinical outcomes of myocarditis associated with mRNA vaccines against the SARS-CoV-2 virus compared with other types of myocarditis.

Design

Population based cohort study.

Setting

Nationwide register data from four Nordic countries (Denmark, Finland, Norway, and Sweden), from 1 January 2018 to the latest date of follow-up in 2022.

Participants

The Nordic myocarditis cohort; 7292 individuals aged ≥12 years who had an incident diagnosis of myocarditis as a main or secondary diagnosis, in a population of 23 million individuals in Denmark, Finland, Norway, and Sweden.

Main outcome measures

Heart failure, or death from any cause within 90 days of admission to hospital for new onset myocarditis, and hospital readmission within 90 days of discharge to hospital for new onset myocarditis. Clinical outcomes of myocarditis associated with SARS-CoV-2 mRNA vaccination, covid-19 disease, and conventional myocarditis were compared.

Results

In 2018-22, 7292 patients were admitted to hospital with new onset myocarditis, with 530 (7.3%) categorised as having myocarditis associated with SARS-CoV-2 mRNA vaccination, 109 (1.5%) with myocarditis associated with covid-19 disease, and 6653 (91.2%) with conventional myocarditis. At the 90 day follow-up, 62, nine, and 988 patients had been readmitted to hospital in each group (vaccination, covid-19, and conventional myocarditis groups, respectively), corresponding to a relative risk of readmission of 0.79 (95% confidence interval 0.62 to 1.00) and 0.55 (0.30 to 1.04) for the vaccination type and covid-19 type myocarditis groups, respectively, compared with the conventional myocarditis group. At the 90 day follow-up, 27, 18, and 616 patients had a diagnosis of heart failure or died in the vaccination type, covid-19 type, and conventional myocarditis groups, respectively. The relative risk of heart failure within 90 days was 0.56 (95% confidence interval 0.37 to 0.85) and 1.48 (0.86 to 2.54) for myocarditis associated with vaccination and covid-19 disease, respectively, compared with conventional myocarditis; the relative risk of death was 0.48 (0.21 to 1.09) and 2.35 (1.06 to 5.19), respectively. Among patients aged 12-39 years with no predisposing comorbidities, the relative risk of heart failure or death was markedly higher for myocarditis associated with covid-19 disease than for myocarditis associated with vaccination (relative risk 5.78, 1.84 to 18.20).

Conclusions

Compared with myocarditis associated with covid-19 disease and conventional myocarditis, myocarditis after vaccination with SARS-CoV-2 mRNA vaccines was associated with better clinical outcomes within 90 days of admission to hospital.

Age-stratified infection fatality rate of COVID-19 in the non-elderly population

The largest burden of COVID-19 is carried by the elderly, and persons living in nursing homes are particularly vulnerable. However, 94% of the global population is younger than 70 years and 86% is younger than 60 years. The objective of this study was to accurately estimate the infection fatality rate (IFR) of COVID-19 among non-elderly people in the absence of vaccination or prior infection. In systematic searches in SeroTracker and PubMed (protocol: https://osf.io/xvupr), we identified 40 eligible national seroprevalence studies covering 38 countries with pre-vaccination seroprevalence data. For 29 countries (24 high-income, 5 others), publicly available age-stratified COVID-19 death data and age-stratified seroprevalence information were available and were included in the primary analysis. The IFRs had a median of 0.034% (interquartile range (IQR) 0.013-0.056%) for the 0-59 years old population, and 0.095% (IQR 0.036-0.119%) for the 0-69 years old. The median IFR was 0.0003% at 0-19 years, 0.002% at 20-29 years, 0.011% at 30-39 years, 0.035% at 40-49 years, 0.123% at 50-59 years, and 0.506% at 60-69 years. IFR increases approximately 4 times every 10 years. Including data from another 9 countries with imputed age distribution of COVID-19 deaths yielded median IFR of 0.025-0.032% for 0-59 years and 0.063-0.082% for 0-69 years. Meta-regression analyses also suggested global IFR of 0.03% and 0.07%, respectively in these age groups. The current analysis suggests a much lower pre-vaccination IFR in non-elderly populations than previously suggested. Large differences did exist between countries and may reflect differences in comorbidities and other factors. These estimates provide a baseline from which to fathom further IFR declines with the widespread use of vaccination, prior infections, and evolution of new variants.

The rapid and efficient strategy for SARS-CoV-2 Omicron transmission control: analysis of outbreaks at the city level

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron (B.1.1.529) variant is highly transmissible with potential immune escape. Hence, control measures are continuously being optimized to guard against large-scale coronavirus disease 2019 (COVID-19) outbreaks. This study aimed to explore the relationship between the intensity of control measures in response to different SARS-CoV-2 variants and the degree of outbreak control at city level.

METHODS

A retrospective study was conducted in 49 cities with COVID-19 outbreaks between January 2020 and June 2022. Epidemiological data on COVID-19 were extracted from the National Health Commission, People's Republic of China, and the population flow data were sourced from the Baidu migration data provided by the Baidu platform. Outbreak control was quantified by calculating the degree of infection growth and the time-varying reproduction number ([Formula: see text]). The intensity of the outbreak response was quantified by calculating the reduction in population mobility during the outbreak period. Correlation and regression analyses of the intensity of the control measures and the degree of outbreak control for the Omicron variant and non-Omicron mutants were conducted, respectively.

RESULTS

Overall, 65 outbreaks occurred in 49 cities in China from January 2020 to June 2022. Of them, 66.2% were Omicron outbreaks and 33.8% were non-Omicron outbreaks. The intensity of the control measures was positively correlated with the degree of outbreak control (r = 0.351, P = 0.03). The degree of reduction in population mobility was negatively correlated with the Rt value (r = - 0.612, P < 0.01). Therefore, under the same control measure intensity, the number of new daily Omicron infections was 6.04 times higher than those attributed to non-Omicron variants, and the Rt value of Omicron outbreaks was 2.6 times higher than that of non-Omicron variants. In addition, the duration of non-Omicron variant outbreaks was shorter than that of the outbreaks caused by the Omicron variant (23.0 ± 10.7, 32.9 ± 16.3, t = 2.243, P = 0.031).

CONCLUSIONS

Greater intensity of control measures was associated with more effective outbreak control. Thus, in response to the Omicron variant, the management to restrict population movement should be used to control its spread quickly, especially in the case of community transmission occurs widely. Faster than is needed for non-Omicron variants, and decisive control measures should be imposed and dynamically adjusted in accordance with the evolving epidemic situation.

SARS-CoV-2 Seroprevalence among Canadian Blood Donors: The Advance of Omicron

With the emergence of the SARS-CoV-2 Omicron variant in late 2021, Canadian public health case/contact testing was scaled back due to high infection rates with milder symptoms in a highly vaccinated population. We monitored the seroprevalence of SARS-CoV-2 nucleocapsid (anti-N) and spike protein (anti-S) antibodies in blood donors across Canada from September 2021 to June 2022 in 202,123 randomly selected samples. Multivariable logistic regression of anti-N positivity with month, age, sex, racialization, region, material and social deprivation (based on postal code) identified as independent predictors. Piece-wise logistic regression analysed the association between anti-S concentration and month, and anti-N/anti-S positivity. Infection-related seroprevalence (anti-N positive) was 4.38% (95% CI: 3.96, 4.81) in September reaching 50.70% (50.15, 52.16) in June; nearly 100% were anti-S positive throughout. Anti-N positivity was associated with younger age, male sex, the Alberta and Prairies regions, greater material deprivation and less social deprivation (p < 0.001). Anti-S concentration was high initially (3306 U/mL, IQR 4280 U/mL), increased to (13,659 U/mL, IQR 28,224 U/mL) by June (p < 0.001), following the pattern of deployment of the third and fourth vaccine doses and was higher in those that were anti-N positive (p < 0.001). Despite already high vaccination-related seroprevalence, infection-related seroprevalence increased dramatically with the emergence of the Omicron SARS-CoV-2 variant.