Reproduction Number of the Omicron Variant Triples That of the Delta Variant

Transmissibility of the variant of concern for SARS-CoV-2 in six regions

Introduction

Differences in transmissibility of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) in different districts are hard to assess. To address this, our study focused on calculating the Real-time reproduction number (R t ) for these variants in different regions.

Methods

According to the criteria defined by the World Health Organization (WHO), the global landscape was categorized into six distinct regions. In each region, the predominant SARS-CoV-2 variant was first identified based on the proportion of variant sequencing analysis results. Then, using serial interval (SI) parameters, we calculated R t for the relevant Variant of Concern (VOC) in each region. This approach enabled us to compare the R t values of the same variant across different regions and analyze the transmissibility of each region's variant in relation to the overall situation in that region.

Results

The progression of VOC for SARS-CoV-2 shows regional variations. However, a common sequence of evolution is observed: Wild-type → Alpha → Beta → Delta → Omicron. Moreover, an increasing trend is discerned within diverse regions where the shift in R t of distinct VOC corresponds with the overarching R t route of SARS-CoV-2 in specific regions.

Conclusion

As the COVID-19 pandemic advances, regional epidemiological trends are aligning, likely due to similar virus mutations and shared public health strategies, suggesting opportunities for standardized global responses.

Relative efficacy of masks and respirators as source control for viral aerosol shedding from people infected with SARS-CoV-2: a controlled human exhaled breath aerosol experimental study

BACKGROUND

Tight-fitting masks and respirators, in manikin studies, improved aerosol source control compared to loose-fitting masks. Whether this translates to humans is not known.

METHODS

We compared efficacy of masks (cloth and surgical) and respirators (KN95 and N95) as source control for SARS-CoV-2 viral load in exhaled breath of volunteers with COVID-19 using a controlled human experimental study. Volunteers (N = 44, 43% female) provided paired unmasked and masked breath samples allowing computation of source-control factors.

FINDINGS

All masks and respirators significantly reduced exhaled viral load, without fit tests or training. A duckbill N95 reduced exhaled viral load by 98% (95% CI: 97%-99%), and significantly outperformed a KN95 (p < 0.001) as well as cloth and surgical masks. Cloth masks outperformed a surgical mask (p = 0.027) and the tested KN95 (p = 0.014).

INTERPRETATION

These results suggest that N95 respirators could be the standard of care in nursing homes and healthcare settings when respiratory viral infections are prevalent in the community and healthcare-associated transmission risk is elevated.

FUNDING

Defense Advanced Research Projects Agency, National Institute of Allergy and Infectious Diseases, Centers for Disease Control and Prevention, the Bill & Melinda Gates Foundation, and The Flu Lab.

The Omicron XBB.1 Variant and Its Descendants: Genomic Mutations, Rapid Dissemination and Notable Characteristics

The SARS-CoV-2 virus, which is a major threat to human health, has undergone many mutations during the replication process due to errors in the replication steps and modifications in the structure of viral proteins. The XBB variant was identified for the first time in Singapore in the fall of 2022. It was then detected in other countries, including the United States, Canada, and the United Kingdom. We study the impact of sequence changes on spike protein structure on the subvariants of XBB, with particular attention to the velocity of variant diffusion and virus activity with respect to its diffusion. We examine the structural and functional distinctions of the variants in three different conformations: (i) spike glycoprotein in complex with ACE2 (1-up state), (ii) spike glycoprotein (closed-1 state), and (iii) S protein (open-1 state). We also estimate the affinity binding between the spike protein and ACE2. The market binding affinity observed in specific variants raises questions about the efficacy of current vaccines in preparing the immune system for virus variant recognition. This work may be useful in devising strategies to manage the ongoing COVID-19 pandemic. To stay ahead of the virus evolution, further research and surveillance should be carried out to adjust public health measures accordingly.

Impact of public health policy and mobility change on transmission potential of severe acute respiratory syndrome coronavirus 2 in Rhode Island, March 2020 - November 2021

To study the SARS-CoV-2 transmission potential in Rhode Island (RI) and its association with policy changes and mobility changes, the time-varying reproduction number, Rt, was estimated. The daily incident case counts (16 March 2020, through 30 November 2021) were bootstrapped within a 15-day sliding window and multiplied by Poisson-distributed multipliers (λ = 4, sensitivity analysis: 11) to generate 1000 estimated infection counts, to which EpiEstim was applied to generate Rt time series. The median Rt percentage change when policies changed was estimated. The time lag correlations were assessed between the 7-day moving average of the relative changes in Google mobility data in the first 90 days, and Rt and estimated infection count, respectively. There were three major pandemic waves in RI in 2020-2021: spring 2020, winter 2020-2021 and fall-winter 2021. The median Rt fluctuated within the range of 0.5-2 from April 2020 to November 2021. Mask mandate (18 April 2020) was associated with a decrease in Rt (-25.99%, 95% CrI: -37.42%, -14.30%). Termination of mask mandates on 6 July 2021 was associated with an increase in Rt (36.74%, 95% CrI: 27.20%, 49.13%). Positive correlations were found between changes in grocery and pharmacy, Rt retail and recreation, transit, and workplace visits, for both Rt and estimated infection count, respectively. Negative correlations were found between changes in residential area visits for both Rt and estimated infection count, respectively. Public health policies enacted in RI were associated with changes in the pandemic trajectory. This ecological study provides further evidence of how non-pharmaceutical interventions and vaccination slowed COVID-19 transmission in RI.

Level and factors of support for the Living with the Virus policy in a Chinese adult general population: a mediation analysis via positive and negative attitudes toward the policy

Background

This study investigated the public's support for the Living with the Virus (LWV) policy, its associated factors, and related mediations at a time when more countries were considering adopting the LWV policy amid the COVID-19 pandemic.

Methods

A random, population-based telephone survey was conducted among 500 Chinese adults in Hong Kong during March/April 2022.

Results

39.6% of the participants were supportive/strongly supportive of the LWV policy. Perceived efficacy of the control measures was negatively associated with the support and was partially mediated via the perception that the policy would greatly improve the economy/daily life of the policy. Perceived physical harms of the Omicron variant was negatively associated with the support and was fully mediated via perceived negative impacts of the policy. 26.2%/54.6% believed that the policy would improve the economy/daily life greatly; about 40% perceived negative impacts on deaths and the medical system due to the policy. COVID-19 ever infection did not significantly moderate the studied associations.

Conclusion

The public was split regarding the support for the LWV policy and whether it would cause better economy/daily life, unnecessary deaths, and the collapse of the medical system. Health communication is needed in shifting toward the LWV policy.

Evolution of the SARS-CoV-2 Omicron Variants: Genetic Impact on Viral Fitness

Over the last three years, the pandemic of COVID-19 has had a significant impact on people's lives and the global economy. The incessant emergence of variant strains has compounded the challenges associated with the management of COVID-19. As the predominant variant from late 2021 to the present, Omicron and its sublineages, through continuous evolution, have demonstrated iterative viral fitness. The comprehensive elucidation of the biological implications that catalyzed this evolution remains incomplete. In accordance with extant research evidence, we provide a comprehensive review of subvariants of Omicron, delineating alterations in immune evasion, cellular infectivity, and the cross-species transmission potential. This review seeks to clarify the underpinnings of biology within the evolution of SARS-CoV-2, thereby providing a foundation for strategic considerations in the post-pandemic era of COVID-19.

Model-based analysis of the incidence trends and transmission dynamics of COVID-19 associated with the Omicron variant in representative cities in China

BACKGROUND

In 2022, Omicron outbreaks occurred at multiple sites in China. It is of great importance to track the incidence trends and transmission dynamics of coronavirus disease 2019 (COVID-19) to guide further interventions.

METHODS

Given the population size, economic level and transport level similarities, two groups of outbreaks (Shanghai vs. Chengdu and Sanya vs. Beihai) were selected for analysis. We developed the SEAIQRD, ARIMA, and LSTM models to seek optimal modeling techniques for waves associated with the Omicron variant regarding data predictive performance and mechanism transmission dynamics, respectively. In addition, we quantitatively modeled the impacts of different combinations of more stringent interventions on the course of the epidemic through scenario analyses.

RESULTS

The best-performing LSTM model showed better prediction accuracy than the best-performing SEAIQRD and ARIMA models in most cases studied. The SEAIQRD model had an absolute advantage in exploring the transmission dynamics of the outbreaks. Regardless of the time to inflection point or the time to Rt curve below 1.0, Shanghai was later than Chengdu (day 46 vs. day 12/day 54 vs. day 14), and Sanya was later than Beihai (day 16 vs. day 12/day 20 vs. day 16). Regardless of the number of peak cases or the cumulative number of infections, Shanghai was higher than Chengdu (34,350 vs. 188/623,870 vs. 2,181), and Sanya was higher than Beihai (1,105 vs. 203/16,289 vs. 3,184). Scenario analyses suggested that upgrading control level in advance, while increasing the index decline rate and quarantine rate, were of great significance for shortening the time to peak and Rt below 1.0, as well as reducing the number of peak cases and final affected population.

CONCLUSIONS

The LSTM model has great potential for predicting the prevalence of Omicron outbreaks, whereas the SEAIQRD model is highly effective in revealing their internal transmission mechanisms. We recommended the use of joint interventions to contain the spread of the virus.

Analysis of the effect of PCR testing and antigen testing on controlling the transmission for Omicron based on different scenarios

After the policy adjustment, China no longer carries out COVID-19 PCR testing for all people, and antigen testing has become the main way to detect and manage infectious sources. We developed a dynamic model to evaluate and compare the effects between PCR and antigen testing for controlling the pandemic. Due to the increase of contact degree, the peak reduction effect of PCR testing in population is lower than that of antigen testing. Even if it was only 20% of people isolated at home after antigen testing, the peak of the epidemic could be reduced by 9.46%. If the proportion of antigen testing is further increased to 80%, the peak of the pandemic can be reduced by 31.41%. Antigen testing performed better effects in school (reduction proportion 29.27%) and community (29.34%) than in workplace (27.75%). Therefore, we recommend that antigen testing in the population should be encouraged during the pandemic, and home isolation of infected persons should be advocated, especially in crowded places. To improve the availability of antigen, the testing proportion should be further enhanced.

Security or severity? A research of COVID-19 pandemic control policy based on nonlinear programming approach

The COVID-19 pandemic has caused huge impacts to human health and world's econ-omy. Finding out the balance between social productions and pandemic control becomes crucial. In this paper, we first extend the SIR model by introducing two new status. We calibrate the model by 2022 Shanghai COVID-19 outbreak. The results shows compared to zero-constraint policy, under our control policy, 50 % more life can be saved at the cost of 2.13 % loss of consumptions. Our results also emphasize the importance of the dynamic nature and the timing of control policy, either a static pandemic control or a lagged pandemic control damages badly to people's livelihood and social productions. Counter factual experiments show that compared to the baseline, when a persistent high-strength control is applied, aggregate productions decreases by 57 %; when pandemic control ends too early, the death would rise by 15 %, when pandemic control starts too late, the death rises by 23 % and aggregate productions decreases by 13 %.

Quarantine experience of healthcare workers in close contact with COVID-19 patients in China: a qualitative study

BACKGROUND

This study investigated the experiences of front-line healthcare workers who had been in close contact with COVID-19 patients and had been quarantined in order to provide guidance on quarantine measures with more humanistic care when dealing with future public health emergencies.

METHODS

We conducted a qualitative study using semistructured, qualitative, in-depth interviews between April and June 2022. The interviews were recorded and transcribed, followed by a thematic analysis. The study followed the Standards for Reporting Qualitative Research.

RESULTS

This study identified the following four themes: (1) personal psychological changes, (2) increased reflection on life and work during quarantine, (3) the important role of others' support and (4) different types of demands during quarantine and isolation. Each theme is supported by several subthemes that further illustrate the participants' experiences.

CONCLUSIONS

Quarantine of close contacts is necessary to prevent outbreaks. Front-line doctors and nurses are at a greater risk of COVID-19 infection than others. The results showed the psychological reactions of ordinary close contacts, and the unique feelings and experiences of doctors and nurses during the epidemic. Therefore, future research should cooperate with multiple departments to assess their needs, provide them with individualised care and love and give them incentives in order to reduce their psychological burden, improve their quality of life and allow them to engage in healthcare with a healthy mind.

Antibody escape, the risk of serotype formation, and rapid immune waning: Modeling the implications of SARS-CoV-2 immune evasion

As the COVID-19 pandemic progresses, widespread community transmission of SARS-CoV-2 has ushered in a volatile era of viral immune evasion rather than the much-heralded stability of "endemicity" or "herd immunity." At this point, an array of viral strains has rendered essentially all monoclonal antibody therapeutics obsolete and strongly undermined the impact of vaccinal immunity on SARS-CoV-2 transmission. In this work, we demonstrate that antibody escape resulting in evasion of pre-existing immunity is highly evolutionarily favored and likely to cause waves of short-term transmission. In the long-term, invading strains that induce weak cross-immunity against pre-existing strains may co-circulate with those pre-existing strains. This would result in the formation of serotypes that increase disease burden, complicate SARS-CoV-2 control, and raise the potential for increases in viral virulence. Less durable immunity does not drive positive selection as a trait, but such strains may transmit at high levels if they establish. Overall, our results draw attention to the importance of inter-strain cross-immunity as a driver of transmission trends and the importance of early immune evasion data to predict the trajectory of the pandemic.

Data-driven models for the risk of infection and hospitalization during a pandemic: Case study on COVID-19 in Nepal

The newly emerging pandemic disease often poses unexpected troubles and hazards to the global health system, particularly in low and middle-income countries like Nepal. In this study, we developed mathematical models to estimate the risk of infection and the risk of hospitalization during a pandemic which are critical for allocating resources and planning health policies. We used our models in Nepal's unique data set to explore national and provincial-level risks of infection and risk of hospitalization during the Delta and Omicron surges. Furthermore, we used our model to identify the effectiveness of non-pharmaceutical interventions (NPIs) to mitigate COVID-19 in various groups of people in Nepal. Our analysis shows no significant difference in reproduction numbers in provinces between the Delta and Omicron surge periods, but noticeable inter-provincial disparities in the risk of infection (for example, during Delta (Omicron) surges, the risk of infection of Bagmati province is: ∼ 98.94 (89.62); Madhesh province: ∼ 12.16 (5.1); Karnali province ∼31.16 (3) per hundred thousands). Our estimates show a significantly low level of hospitalization risk during the Omicron surge compared to the Delta surge (hospitalization risk is: ∼10% in Delta and ∼2.5% in Omicron). We also found significant inter-provincial disparities in the hospitalization rate (for example, ∼ 6% in Madhesh province and ∼ 21% in Sudur Paschim) during the Delta surge. Moreover, our results show that closing only schools, colleges, and workplaces reduces the risk of infection by one-third, while a complete lockdown reduces the infections by two-thirds. Our study provides a framework for the computation of the risk of infection and the risk of hospitalization and offers helpful information for controlling the pandemic.

Reproduction number of SARS-CoV-2 Omicron variants, China, December 2022-January 2023

China adjusted the zero-COVID strategy in late 2022, triggering an unprecedented Omicron wave. We estimated the time-varying reproduction numbers of 32 provincial-level administrative divisions from December 2022 to January 2023. We found that the pooled estimate of initial reproduction numbers is 4.74 (95% confidence interval: 4.41, 5.07).

Illness representation of COVID-19 affected public's support and anticipated panic regarding the living with the virus policy: a cross-sectional study in a Chinese general population

Background

There is a global trend for countries to adopt the Living with the Virus (LWV) policy regarding COVID-19. Little is known about the public's supportiveness and emotional responses (e.g., anticipated panic) related to this policy. Such responses may be associated with illness representations of COVID-19 (i.e., how people think and feel about COVID-19). This novel topic was investigated in this study to facilitate policy-making and health communication.

Methods

A random, population-based telephone survey interviewed 500 adults aged ≥18 of the Hong Kong general adult population from March to April 2022.

Results

The prevalence of the public's support and anticipated panic regarding the LWV policy, which were negatively correlated with each other, was 39.6 and 24.2%, respectively. The illness representation constructs of consequences, timeline, identity, illness concern, and emotional representations were negatively associated with supportiveness and positively associated with anticipated panic regarding the LWV policy. Illness coherence was significantly associated with policy support but not with anticipated panic. The associations between personal control/treatment control and supportiveness/anticipated panic were statistically non-significant. Moderation analyses showed that the above significant associations were invariant between those with and without previous COVID-19 infection.

Conclusion

Policymakers need to be sensitized about the public's supportive/unsupportive attitude and potential worry (panic) when adopting the LWV policy. Such attitudes/emotional responses may be affected by people's illness representations of COVID-19. In general, those who found COVID-19 involving a milder nature and less negative emotions would be more supportive and anticipated less panic under the LWV policy.

The Impact of SARS-CoV-2 Immune Status and Societal Restrictions in Controlling COVID-19 across the World

To control the COVID-19 pandemic, many countries implemented vaccination and imposed societal restrictions both at the national level and for international travel. As a check of corona status, COVID passes have been issued. A COVID pass could be obtained when either fully vaccinated against COVID-19, or after recovering from a documented COVID-19 episode, or after a recent (24-48 h) negative SARS-CoV-2 antigen test. A global analysis of SARS-CoV-2 immune status determined by past infection and/or vaccination, vaccination rates, as well as societal restrictions in controlling the COVID-19 pandemic is presented. The data show that across the world, vaccination was more effective in reducing SARS-CoV-2 infections with the delta variant than the omicron variant. Strict societal restrictions could control spread of the virus, but relief of the restrictions was associated with an increase in omicron infections. No significant difference in SARS-CoV-2 infections were found when comparing countries or territories which did or did not implement a COVID pass.

Age-specific transmission dynamics under suppression control measures during SARS-CoV-2 Omicron BA.2 epidemic

BACKGROUND

From March to June 2022, an Omicron BA.2 epidemic occurred in Shanghai. We aimed to better understand the transmission dynamics and identify age-specific transmission characteristics for the epidemic.

METHODS

Data on COVID-19 cases were collected from the Shanghai Municipal Health Commission during the period from 20th February to 1st June. The effective reproductive number (R_t) and transmission distance between cases were calculated. An age-structured SEIR model with social contact patterns was developed to reconstruct the transmission dynamics and evaluate age-specific transmission characteristics. Least square method was used to calibrate the model. Basic reproduction number (R₀) was estimated with next generation matrix.

RESULTS

R₀ of Omicron variant was 7.9 (95% CI: 7.4 to 8.4). With strict interventions, R_t had dropped quickly from 3.6 (95% CI: 2.7 to 4.7) on 4th March to below 1 on 18th April. The mean transmission distance of the Omicron epidemic in Shanghai was 13.4 km (95% CI: 11.1 to 15.8 km), which was threefold longer compared with that of epidemic caused by the wild-type virus in Wuhan, China. The model estimated that there would have been a total 870,845 (95% CI: 815,400 to 926,289) cases for the epidemic from 20th February to 15th June, and 27.7% (95% CI: 24.4% to 30.9%) cases would have been unascertained. People aged 50-59 years had the highest transmission risk 0.216 (95% CI: 0.210 to 0.222), and the highest secondary attack rate (47.62%, 95% CI: 38.71% to 56.53%).

CONCLUSIONS

The Omicron variant spread more quickly and widely than other variants and resulted in about one third cases unascertained for the recent outbreak in Shanghai. Prioritizing isolation and screening of people aged 40-59 might suppress the epidemic more effectively. Routine surveillance among people aged 40-59 years could also provide insight into the stage of the epidemic and the timely detection of new variants.

TRIAL REGISTRATION

We did not involve clinical trial.

Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas

The SARS-CoV-2 variants of concern (VOCs) Delta and Omicron spread globally during mid and late 2021, respectively. In this study, we compare the dissemination dynamics of these VOCs in the Amazonas state, one of Brazil's most heavily affected regions. We sequenced the virus genome from 4128 patients collected in Amazonas between July 1st, 2021, and January 31st, 2022, and investigated the viral dynamics using a phylodynamic approach. The VOCs Delta and Omicron BA.1 displayed similar patterns of phylogeographic spread but different epidemic dynamics. The replacement of Gamma by Delta was gradual and occurred without an upsurge of COVID-19 cases, while the rise of Omicron BA.1 was extremely fast and fueled a sharp increase in cases. Thus, the dissemination dynamics and population-level impact of new SARS-CoV-2 variants introduced in the Amazonian population after mid-2021, a setting with high levels of acquired immunity, greatly vary according to their viral phenotype.

Association between the overall burden of comorbidity and Ct values among the older patients with Omicron infection: Mediated by inflammation

Objectives

To investigate the associations between the overall burden of comorbidity, inflammatory indicators in plasma and Ct values among the elderly with COVID-19.

Methods

We conducted a retrospective observational study. The results of each nucleic acid test of during hospitalization were obtained. Linear regression models assessed the associations between the overall burden of comorbidity, inflammatory indicators in plasma and Ct values among the elderly. A causal mediation analysis was performed to assess the mediation effects of inflammatory indicators on the association between the overall burden of comorbidity and Ct values.

Results

A total of 767 COVID-19 patients aged ≥ 60 years were included between April 2022 and May 2022. Patients with a high burden of comorbidity had significantly lower Ct values of the ORF gene than subjects with a low burden of comorbidity (median, 24.81 VS 26.58, P &lt; 0.05). Linear regression models showed that a high burden of comorbidity was significantly associated with higher inflammatory responses, including white blood cell count, neutrophil count and C-reactive protein. Also, white blood cell count, neutrophil count, C-reactive protein and the overall burden of comorbidity assessed by age-adjusted Charlson comorbidity index were independent risk factors for the Ct values. A mediation analysis detected the mediation effect of white blood cells on the association between the burden of comorbidity and Ct values, with the indirect effect estimates of 0.381 (95% CI: 0.166, 0.632, P &lt; 0.001). Similarly, the indirect effect of C-reactive protein was -0.307 (95% CI: -0.645, -0.064, P = 0.034). White blood cells and C-reactive protein significantly mediated the relationship between the burden of comorbidity and Ct values by 29.56% and 18.13% of the total effect size, respectively.

Conclusions

Inflammation mediated the association between the overall burden of comorbidity and Ct values among elderly with COVID-19, which suggests that combined immunomodulatory therapies could reduce the Ct values for such patients with a high burden of comorbidity.

Editorial: Infectious Disease Epidemiology and Transmission Dynamics

Infectious diseases, such as COVID-19 [...].

Lancemaside A from Codonopsis lanceolata: Studies on Antiviral Activity and Mechanism of Action against SARS-CoV-2 and Its Variants of Concern

Several plant-derived natural products with anti-SARS-CoV-2 activity have been evaluated for the potential to serve as chemotherapeutic agents for the treatment of COVID-19. Codonopsis lanceolata (CL) has long been used as a medicinal herb in East Asian countries to treat inflammatory diseases of the respiratory system but its antiviral activity has not been investigated so far. Here, we showed that CL extract and its active compound lancemaside A (LA) displayed potent inhibitory activity against SARS-CoV-2 infection using a pseudotyped SARS-CoV-2 entry assay system. We demonstrated that this inhibitory effect of LA was due to the alteration of membrane cholesterol and blockade of the membrane fusion between SARS-CoV-2 and host cells by filipin staining and cell-based membrane fusion assays. Our findings also showed that LA, as a membrane fusion blocker, could impede the endosomal entry pathway of SARS-CoV-2 and its variants of concern (VOCs), including Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529), in Vero cells with similar of IC₅₀ values ranging from 2.23 to 3.37 μM as well as the TMPRSS2-mediated viral entry pathway in A549 cells overexpressing ACE2 and TMPRSS2 with IC₅₀ value of 3.92 μM. We further demonstrated that LA could prevent the formation of multinucleated syncytia arising from SARS-CoV-2 spike protein-mediated membrane fusion. Altogether, the findings reported here suggested that LA could be a broad-spectrum anti-SARS-CoV-2 therapeutic agent by targeting the fusion of viral envelope with the host cell membrane.

Assessment of indoor air quality and risk of COVID-19 infection in Spanish secondary school and university classrooms

Despite the risk of transmission of SARS-CoV-2, Spanish educational centers were reopened after six months of lockdown. Ventilation was mostly adopted as a preventive measure to reduce the transmission risk of the virus. However, it could also affect indoor air quality (IAQ). Therefore, here we evaluate the ventilation conditions, COVID-19 risk, and IAQ in secondary school and university classrooms in Toledo (central Spain) from November 2020 to June 2021. Ventilation was examined by monitoring outdoor and indoor CO₂ levels. CO₂, occupancy and hygrothermal parameters, allowed estimating the relative transmission risk of SARS-CoV-2 (Alpha and Omicron BA.1), H _r, under different scenarios, using the web app COVID Risk ^airborne . Additionally, the effect of ventilation on IAQ was evaluated by measuring indoor/outdoor (I/O) concentration ratios of O₃, NO₂, and suspended particulate matter (PM). University classrooms, particularly the mechanically ventilated one, presented better ventilation conditions than the secondary school classrooms, as well as better thermal comfort conditions. The estimated H _r for COVID-19 ranged from intermediate (with surgical masks) to high (no masks, teacher infected). IAQ was generally good in all classrooms, particularly at the university ones, with I/O below unity, implying an outdoor origin of gaseous pollutants, while the source of PM was heterogeneous. Consequently, controlled mechanical ventilation systems are essential in educational spaces, as well as wearing well-fitting FFP2-N95 masks indoors is also highly recommended to minimize the transmission risk of COVID-19 and other airborne infectious diseases.

The Omicron-transformer: Rise of the subvariants in the age of vaccines

Introduction: Omicron is the latest SARS-CoV-2 variant of concern, the pathogen that causes COVID-19. Since its emergence in late 2021, Omicron has displaced other circulating variants and caused successive waves of infection worldwide throughout 2022. Omicron is characterised by the rapid emergence of many subvariants and high rates of infection in people with vaccine- and/or infection-induced immunity. This review article will consolidate current knowledge regarding Omicron subvariants, the role of boosters, and future vaccine development. Method: This narrative review is based on a literature search using PubMed. Search terms related to Omicron were used and priority was given to published peer-reviewed articles over pre-prints. Results: Studies indicate that vaccinations and boosters are important to reduce disease severity, hospitalisation and death from Omicron. A variety of factors, such as differing host factors, circulating variants, and forces of infection, can influence the benefit of repeated booster administration. Next-generation bivalent vaccines have now been approved in some countries including Singapore and have demonstrated the ability to induce broad variant protection. Future third-generation vaccines involving mucosal vaccines and/or pan-sarbecovirus vaccines may provide broader and longer-lasting protection. Conclusion: Due to current high levels of vaccine- and infection-induced immunity, it is likely that rates of severe illness, hospitalisation, and death due to Omicron will continue to moderate. Nevertheless, the virus is ever-changing, and public health policies, especially those related to vaccinations, will also have to continually evolve and adapt as COVID-19 transitions to endemicity. Keywords: Booster, COVID-19, infectious diseases, Omicron, vaccine

Emergence of SARS-CoV-2 Omicron variant and strategies for tackling the infection

INTRODUCTION

Nowadays, emerging SARS-CoV-2 Omicron, the novel highly mutated VOC, has quickly spread as the dominant variant in over 190 countries worldwide through the first part of 2022, which is influencing the infectivity, transmissibility, pathogenicity, and severity of COVID-19 pandemic. Additionally, clinical cases and experimental studies have reported that Omicron variant likely leads to weakened immune protection elicited by infection, antibody therapies, and vaccines. The new wave, from late February, 2022, was escalated abruptly by higher levels of transmission of Omicron BA.2 sublineage in China.

METHODS AND RESULTS

Following a systematic database search, this review summarizes the salient features of Omicron sublineages, and their impact on transmissibility, disease severity as well as the efficacy of the available vaccines and treatment against the Omicron.

CONCLUSION

We hope this study will provide a scientific reference for alleviating the burden of COVID-19.

COVID-19 variants' cross-reactivity on the paper microfluidic particle counting immunoassay

SARS-CoV-2 has mutated many times since the onset of the COVID-19 pandemic, and the omicron is currently the most dominant variant. Determining the specific strain of the virus is beneficial in providing proper care and containment of the disease. We have previously reported a novel method of counting the number of particle immunoagglutination on a paper microfluidic chip using a smartphone-based fluorescence microscope. A single-copy-level detection was demonstrated from clinical saline gargle samples. In this work, we further evaluated two different SARS-CoV-2 monoclonal antibodies to spike vs. nucleocapsid antigens for detecting omicron vs. delta and spike vs. nucleocapsid proteins. The SARS-CoV-2 monoclonal antibody to nucleocapsid proteins could distinguish omicron from delta variants and nucleocapsid from spike proteins. However, such distinction could not be found with the monoclonal antibody to spike proteins, despite the numerous mutations found in spike proteins among variants. This result may suggest a clue to the role of nucleocapsid proteins in recognizing different variants.

Risk assessment of imported COVID-19 in China: A modelling study in Sichuan Province

The importation of COVID-19 cases in China is due to the returning of Chinese citizens abroad, where the majority of cases stand. This study aimed to evaluate the risk of importing COVID-19 into the Sichuan Province of China and conduct a short-term risk prediction assessment and analysis. Data on COVID-19 cases in each country and Sichuan were collected, as well as visitors to Sichuan, population, area, and medical resources in each city in Sichuan province. According to different control strategies of entry aviation and quarantine control, we built models of epidemic transmission to estimate the risk for imported COVID-19 cases in 21 cities of Sichuan. Within 140 days of the policy change's implementation, the number of susceptible, infected, and recovered people in all cities followed the same pattern over time: (1) the number of susceptible people declined slowly at first, then accelerated to reach a stable value; (2) the number of infections gradually increased to a peak, then decreased; and (3) the number of recovered patients gradually increased to a stable value. Under the four different scenarios, there were no significant differences between the risk peaks because the social distance did not change. However, the peak time would be delayed due to the implementation of flight control and nucleic acid detection measures. The improvement of foreign epidemics (reduction of attenuation factors) all delayed the arrival of the peak risk value in Chengdu by about 20 days; however, the size of the peak value did not change significantly. The improvement of nucleic acid detection accuracy delayed the arrival of the peak risk value in Chengdu, but the size of the peak value did not change significantly. Therefore, flight control and the improvement of nucleic acid detection accuracy and overseas epidemic situations have positively affected the prevention and control of the epidemic in Sichuan.

High mortality and morbidity among vaccinated residents infected with the SARS-CoV-2 Omicron variant during an outbreak in a nursing home in Kyoto City, Japan

Background

Outbreaks of coronavirus disease 2019 (COVID-19) in long-term care facilities are associated with mortality, although vaccination have contributed to improvements. This study reports clinical impacts of a COVID-19 outbreak in a nursing home for elderly individuals in Kyoto City, Japan.

Methods

We performed epidemiologic and molecular investigations of the outbreak and characterized outcomes of the nursing home residents.

Results

During the outbreak period, a total of 31 residents (39.2%) and 26 staff members (49.1%) were infected with COVID-19. All residents and staff received two doses of a vaccine approximately 7 months prior. Ten residents with severe hypoxemia could not be transferred to a hospital due to a shortage of beds for COVID-19 patients. Within 90 days of the onset of the outbreak, 8 residents with COVID-19 (25.8%) died. A total of 48.4% of residents with COVID-19 developed 1 or more comorbidities. Viral genome analysis showed that the outbreak was caused by the Omicron BA.1.1.2 variant.

Conclusions

Despite vaccination, high mortality and morbidity were observed in the COVID-19 outbreak due to the Omicron variant. Limiting medical care for residents with COVID-19 in facilities that experience ongoing outbreaks may be needed to reduce the risk of mortality among nursing home residents.

Risk Factors Associated with Mortality in Hospitalized Patients with Laboratory Confirmed SARS-CoV-2 Infection During the Period of Omicron (B.1.1.529) Variant Predominance

Background

SARS-CoV-2 Omicron variant has a high transmission rate. In December 2021, Omicron became the dominant variant and quickly accounted for majority of infections in the United States. Drug shortages have led to prioritization of patients for COVID-19 treatment based on risk factors for severe disease.

Methods

A retrospective analysis of hospitalized patients with COVID-19 infection at Veteran Affairs Healthcare System across the United States. The primary outcome was 14-day all-cause mortality after the first documented positive SARS-CoV-2 laboratory test. Odds ratios were generated from a multivariate logistic regression of significant factors.

Results

This study included 12,936 COVID-19 inpatients during a period of Omicron predominance. Age ≥ 65 years is a predictor of 14-day mortality among the vaccinated and unvaccinated population (OR 4.05, CI 3.06-5.45, P ≤ .0001). Triple vaccinated patients demonstrated a 52% decreased risk of death with COVID-19 infection (OR 0.48, CI 0.37-0.61, P ≤ .0001). Patients who were double vaccinated had a 39% decreased risk of death with COVID-19 infection (OR 0.61, CI 0.46-0.80, P = .003).

Conclusion

Advanced age ≥ 65 is the greatest risk factor for mortality in hospitalized COVID-19 patients. COVID-19 vaccination, especially booster doses, was associated with a decreased risk of 14-day mortality compared to double vaccinated or non-vaccinated patients. Results of this study suggest that advanced age should be considered first for prioritization of COVID-19 treatments for Omicron.

Effectiveness of COVID-19 Vaccine Booster Shot Compared with Non-Booster: A Meta-Analysis

The analysis of the effectiveness of booster shots compared with primary vaccination is extremely vital. This paper aimed to summarize the results of all available evidence studies on the effectiveness of booster vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Articles published up to 21 June 2022 were systematically searched through PubMed and EMBASE databases. The searched studies were independently assessed for quality using the Newcastle–Ottawa Scale. Results: Seven studies (nine datasets) met the criteria and were included in this study. The pooled results demonstrated a 71% (OR = 0.29, 95% CI = 0.17–0.48) reduction in SARS-CoV-2 infection rates among subjects who received a booster shot compared with those who did not receive a booster shot of coronavirus disease (COVID-19) vaccine. In addition, this analysis emphasized that during the period when the Delta variant was predominant, subjects who received the booster shot showed an 82% (OR = 0.18, 95% CI = 0.13–0.25) reduction in infection rates. Moreover, during the period of dominance of the Omicron variant, subjects who received the booster vaccination displayed a 47% (OR = 0.53, 95% CI = 0.35–0.81) reduction in infection rates. This finding confirmed that booster vaccination against the Omicron variant is significantly less effective than that against the Delta variant. In pandemic periods, correlations between the dominant variant and the efficacy of the COVID-19 vaccine booster should be considered when making vaccine booster plans.

Systematic review and meta-analyses of superspreading of SARS-CoV-2 infections

Superspreading, or overdispersion in transmission, is a feature of SARS-CoV-2 transmission which results in surging epidemics and large clusters of infection. The dispersion parameter is a statistical parameter used to characterize and quantify heterogeneity. In the context of measuring transmissibility, it is analogous to measures of superspreading potential among populations by assuming that collective offspring distribution follows a negative-binomial distribution. We conducted a systematic review and meta-analysis on globally reported dispersion parameters of SARS-CoV-2 infection. All searches were carried out on 10 September 2021 in PubMed for articles published from 1 January 2020 to 10 September 2021. Multiple estimates of the dispersion parameter have been published for 17 studies, which could be related to where and when the data was obtained, in 8 countries (e.g., China, USA, India, Indonesia, Israel, Japan, New Zealand, and Singapore). High heterogeneity was reported among the included studies. The mean estimates of dispersion parameters range from 0.06 to 2.97 over eight countries, the pooled estimate was 0.55 (95% CI: 0.30, 0.79), with changing means over countries and decreasing slightly with the increasing reproduction number. The expected proportion of cases accounting for 80% of all transmissions is 19% (95% CrI: 7, 34) globally. The study location and method were found to be important drivers for diversity in estimates of dispersion parameters. While under high potential of superspreading, larger outbreaks could still occur with the import of the COVID-19 virus by traveling even when an epidemic seems to be under control. This article is protected by copyright. All rights reserved.