Transmission of Omicron (B.1.1.529) - SARS-CoV-2 Variant of Concern in a designated quarantine hotel for travelers: a challenge of elimination strategy of COVID-19

Targeting mutation sites in the omicron variant of SARS-CoV-2 as potential therapeutic strategy against COVID-19 by antiretroviral drugs

The multiple mutation of the spike (S) protein of the Omicron SARS-CoV-2 variant is a major concern, as it has been implicated in the severity of COVID-19 and its complications. These mutations have been attributed to COVID-19-infected immune-compromised individuals, with HIV patients being suspected to top the list. The present study investigated the mutation of the S protein of the omicron variant in comparison to the Delta and Wuhan variants. It also investigated the molecular interactions of antiretroviral drugs (ARVd) vis-à-vis dolutegravir, lamivudine, tenofovir-disoproxilfumarate and lenacapavir with the initiation and termination codons of the mRNAs of the mutated proteins of the omicron variant using computational tools. The complete genome sequences of the respective S proteins for omicron (OM066778.1), Delta (OK091006.1) and Wuhan (NC 045512.2) SARS-CoV-2 variants were retrieved from the National Center for Biotechnology Information (NCBI) database. Evolutionary analysis revealed high trends of mutations in the S protein of the omicron SARS-CoV-2 variant compared to the delta and Wuhan variants coupled with 68 % homology. The sequences of the translation initiation sites (TISs), translation termination sites (TTSs), high mutation region-1 (HMR1) and high region mutation-2 (HMR2) mRNAs were retrieved from the full genome of the omicron variant S protein. Molecular docking analysis revealed strong molecular interactions of ARVd with TISs, TTSs, HMR1 and HMR2 of the S protein mRNA. These results indicate mutations in the S protein of the Omicron SARS-CoV-2 variant compared to the Delta and Wuhan variants. These mutation points may present new therapeutic targets for COVID-19.

Is SARS-CoV-2 elimination or mitigation best? Regional and disease characteristics determine the recommended strategy

Public health responses to the COVID-19 pandemic varied across the world. Some countries (e.g. mainland China, New Zealand and Taiwan) implemented elimination strategies involving strict travel measures and periods of rigorous non-pharmaceutical interventions (NPIs) in the community, aiming to achieve periods with no disease spread; while others (e.g. many European countries and the USA) implemented mitigation strategies involving less strict NPIs for prolonged periods, aiming to limit community spread. Travel measures and community NPIs have high economic and social costs, and there is a need for guidelines that evaluate the appropriateness of an elimination or mitigation strategy in regional contexts. To guide decisions, we identify key criteria and provide indicators and visualizations to help answer each question. Considerations include determining whether disease elimination is: (1) necessary to ensure healthcare provision; (2) feasible from an epidemiological point of view and (3) cost-effective when considering, in particular, the economic costs of travel measures and treating infections. We discuss our recommendations by considering the regional and economic variability of Canadian provinces and territories, and the epidemiological characteristics of different SARS-CoV-2 variants. While elimination may be a preferable strategy for regions with limited healthcare capacity, low travel volumes, and few ports of entry, mitigation may be more feasible in large urban areas with dense infrastructure, strong economies, and with high connectivity to other regions.

Time trends and modifiable factors of COVID-19 contact tracing coverage, Geneva, Switzerland, June 2020 to February 2022

BackgroundContact tracing was one of the central non-pharmaceutical interventions implemented worldwide to control the spread of SARS-CoV-2, but its effectiveness depends on its ability to detect contacts.AimEvaluate the proportion of secondary infections captured by the contact tracing system in Geneva.MethodsWe analysed 166,892 concomitant infections occurring at the same given address from June 2020 until February 2022 using an extensive operational database of SARS-CoV-2 tests in Geneva. We used permutation to compare the total number of secondary infections occurring at the same address with that reported through manual contact tracing.ResultsContact tracing captured on average 41% of secondary infections, varying from 23% during epidemic peaks to 60% during low epidemic activity. People living in wealthy neighbourhoods were less likely to report contacts (odds ratio (OR): 1.6). People living in apartment buildings were also less likely to report contacts than those living in a house (OR: 1.1-3.1) depending on the SARS-CoV-2 variant, the building size and the presence of shops. This under-reporting of contacts in apartment buildings decreased during periods of mandatory wearing of face masks and restrictions on private gatherings.ConclusionContact tracing alone did not detect sufficient secondary infections to reduce the spread of SARS-CoV-2. Campaigns targeting specific populations, such as those in wealthy areas or apartment buildings, could enhance coverage. Additionally, measures like wearing face masks, improving ventilation and implementing restrictions on gatherings should also be considered to reduce infections resulting from interactions that may not be perceived as high risk.

Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2

ABSTRACTIncreasing spread by SARS-CoV-2 Omicron variants challenges existing vaccines and broadly reactive neutralizing antibodies (bNAbs) against COVID-19. Here we determine the diversity, potency, breadth and structural insights of bNAbs derived from memory B cells of BNT162b2-vaccinee after homogeneous Omicron BA.1 breakthrough infection. The infection activates diverse memory B cell clonotypes for generating potent class I/II and III bNAbs with new epitopes mapped to the receptor-binding domain (RBD). The top eight bNAbs neutralize wildtype and BA.1 potently but display divergent IgH/IgL sequences and neuralization profiles against other variants of concern (VOCs). Two of them (P2D9 and P3E6) belonging to class III NAbs display comparable potency against BA.4/BA.5, although structural analysis reveals distinct modes of action. P3E6 neutralizes all variants tested through a unique bivalent interaction with two RBDs. Our findings provide new insights into hybrid immunity on BNT162b2-induced diverse memory B cells in response to Omicron breakthrough infection for generating diverse bNAbs with distinct structural basis.

Water-blocking Asphyxia of N95 Medical Respirator During Hot Environment Work Tasks With Whole-body Enclosed Anti-bioaerosol Suit

Background

During hot environment work tasks with whole-body enclosed anti-bioaerosol suit, the combined effect of heavy sweating and exhaled hot humid air may cause the N95 medical respirator to saturate with water/sweat (i.e., water-blocking).

Methods

32 young male subjects with different body mass indexes (BMI) in whole-body protection (N95 medical respirator + one-piece protective suit + head covering + protective face screen + gloves + shoe covers) were asked to simulate waste collecting from each isolated room in a seven-story building at 27-28°C, and the weight, inhalation resistance (Rf), and aerosol penetration of the respirator before worn and after water-blocking were analyzed.

Results

All subjects reported water-blocking asphyxia of the N95 respirators within 36-67 min of the task. When water-blocking occurred, the Rf and 10-200 nm total aerosol penetration (Pt) of the respirators reached up to 1270-1810 Pa and 17.3-23.3%, respectively, which were 10 and 8 times of that before wearing. The most penetration particle size of the respirators increased from 49-65 nm before worn to 115-154 nm under water-blocking condition, and the corresponding maximum size-dependent aerosol penetration increased from 2.5-3.5% to 20-27%. With the increase of BMI, the water-blocking occurrence time firstly increased then reduced, while the Rf, Pt, and absorbed water all increased significantly.

Conclusions

This study reveals respirator water-blocking and its serious negative impacts on respiratory protection. When performing moderate-to-high-load tasks with whole-body protection in a hot environment, it is recommended that respirator be replaced with a new one at least every hour to avoid water-blocking asphyxia.

Dynamic variations in and prediction of COVID-19 with omicron in the four first-tier cities of mainland China, Hong Kong, and Singapore

Background

The COVID-19 pandemic, which began in late 2019, has resulted in the devastating collapse of the social economy and more than 10 million deaths worldwide. A recent study suggests that the pattern of COVID-19 cases will resemble a mini-wave rather than a seasonal surge. In general, COVID-19 has more severe impacts on cities than on rural areas, especially in cities with high population density.

Methods

In this study, the background situation of COVID-19 transmission is discussed, including the population number and population density. Moreover, a widely used time series autoregressive integrated moving average (ARIMA) model is applied to simulate and forecast the COVID-19 variations in the six cities. We comprehensively analyze the dynamic variations in COVID-19 in the four first-tier cities of mainland China (BJ: Beijing, SH: Shanghai, GZ: Guangzhou and SZ: Shenzhen), Hong Kong (HK), China and Singapore (SG) from 2020 to 2022.

Results

The major results show that the six cities have their own temporal characteristics, which are determined by the different control and prevention measures. The four first-tier cities of mainland China (i.e., BJ, SH, GZ, and SZ) have similar variations with one wave because of their identical "Dynamic COVID-19 Zero" strategy and strict Non-Pharmaceutical Interventions (NPIs). HK and SG have multiple waves primarily caused by the input cases. The ARIMA model has the ability to provide an accurate forecast of the COVID-19 pandemic trend for the six cities, which could provide a useful approach for predicting the short-term variations in infectious diseases.Accurate forecasting has significant value for implementing reasonable control and prevention measures.

Conclusions

Our main conclusions show that control and prevention measures should be dynamically adjusted and organically integrated for the COVID-19 pandemic. Moreover, the mathematical models are proven again to provide an important scientific basis for disease control.

Detection and isolation of infectious SARS-CoV-2 omicron subvariants collected from residential settings

Airborne transmission of infectious (viable) SARS-CoV-2 is increasingly accepted as the primary manner by which the virus is spread from person to person. Risk of exposure to airborne virus is higher in enclosed and poorly ventilated spaces. We present a study focused on air sampling within residences occupied by individuals with COVID-19. Air samplers (BioSpot-VIVAS, VIVAS, and BC-251) were positioned in primary- and secondary-occupancy regions in seven homes. Swab samples were collected from high-touch surfaces. Isolation of SARS-CoV-2 was attempted for samples with virus detectable by RT-qPCR. Viable virus was quantified by plaque assay, and complete virus genome sequences were obtained for selected samples from each sampling day. SARS-CoV-2 was detected in 24 of 125 samples (19.2%) by RT-qPCR and isolated from 14 (11.2%) in cell cultures. It was detected in 80.9% (17/21) and cultured from 61.9% (13/21) of air samples collected using water condensation samplers, compared to swab samples which had a RT-qPCR detection rate of 10.5% (4/38) and virus isolation rate of 2.63% (1/38). No statistically significant differences existed in the likelihood of virus detection by RT-qPCR or amount of infectious virus in the air between areas of primary and secondary occupancy within residences. Our work provides information about the presence of SARS-CoV-2 in the air within homes of individuals with COVID-19. Information herein can help individuals make informed decisions about personal exposure risks when sharing indoor spaces with infected individuals isolating at home and further inform health departments and the public about SARS-CoV-2 exposure risks within residences.

Dynamic variations in COVID-19 with the SARS-CoV-2 Omicron variant in Kazakhstan and Pakistan

BACKGROUND

The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) and the Omicron variant presents a formidable challenge for control and prevention worldwide, especially for low- and middle-income countries (LMICs). Hence, taking Kazakhstan and Pakistan as examples, this study aims to explore COVID-19 transmission with the Omicron variant at different contact, quarantine and test rates.

METHODS

A disease dynamic model was applied, the population was segmented, and three time stages for Omicron transmission were established: the initial outbreak, a period of stabilization, and a second outbreak. The impact of population contact, quarantine and testing on the disease are analyzed in five scenarios to analysis their impacts on the disease. Four statistical metrics are employed to quantify the model's performance, including the correlation coefficient (CC), normalized absolute error, normalized root mean square error and distance between indices of simulation and observation (DISO).

RESULTS

Our model has high performance in simulating COVID-19 transmission in Kazakhstan and Pakistan with high CC values greater than 0.9 and DISO values less than 0.5. Compared with the present measures (baseline), decreasing (increasing) the contact rates or increasing (decreasing) the quarantined rates can reduce (increase) the peak values of daily new cases and forward (delay) the peak value times (decreasing 842 and forward 2 days for Kazakhstan). The impact of the test rates on the disease are weak. When the start time of stage II is 6 days, the daily new cases are more than 8 and 5 times the rate for Kazakhstan and Pakistan, respectively (29,573 vs. 3259; 7398 vs. 1108). The impact of the start times of stage III on the disease are contradictory to those of stage II.

CONCLUSIONS

For the two LMICs, Kazakhstan and Pakistan, stronger control and prevention measures can be more effective in combating COVID-19. Therefore, to reduce Omicron transmission, strict management of population movement should be employed. Moreover, the timely application of these strategies also plays a key role in disease control.

Infection of healthcare workers despite a high vaccination rate during the fifth wave of COVID-19 due to Omicron variant in Hong Kong

Background

No nosocomial infection was recorded in our healthcare workers (HCWs) during the early phase of the coronavirus disease 2019 (COVID-19) pandemic. With the emergence of the Omicron variant of increased transmissibility, infection in HCWs occurred as expected. We aimed to study the epidemiology of infection in HCWs and to describe the infection control measures during the outbreak of the Omicron variant.

Methods

With daily rapid antigen testing and molecular confirmation test for COVID-19, infected HCWs were interviewed by infection control nurses (ICNs) to investigate the potential source of infection. The epidemiology of COVID-19 in Hong Kong served as reference.

Results

During the fifth wave of COVID-19 (31 December 2021 to 31 May 2022), 1,200,068 cases were reported (incidence 95 times higher than in preceding waves in Hong Kong; 162,103 vs 1,707 per million population respectively, P<0.001). The proportion of infected HCWs was significantly higher than that of the general population (24.9%, 1,607/6,452 vs 16.2%, 1,200,068/7,403,100 respectively; P<0.01). The proportion of infected non-clinical staff was significantly higher than that of clinical staff (31.8%, 536/1,687 vs 22.5%, 1,071/4,765 respectively; P<0.001). Of 82.8% (1,330/1,607) infected HCWs interviewed by ICNs, 99.5% (1,324/1,330) had been fully vaccinated; 49.5% (659/1,330) had no identifiable source; 40.7% (541/1,330) were probably infected from household members; 9.8% (130/1,330) had possible exposure to confirmed patients or HCWs, but no lapse in infection control measures or inappropriate use of personal protective equipment was recalled.

Conclusion

Omicron variant is highly transmissible such that breakthrough infection occurred despite high level of vaccination.

Recent trends in carbon nanotube (CNT)-based biosensors for the fast and sensitive detection of human viruses: a critical review

The current COVID-19 pandemic, with its numerous variants including Omicron which is 50-70% more transmissible than the previously dominant Delta variant, demands a fast, robust, cheap, and easily deployed identification strategy to reduce the chain of transmission, for which biosensors have been shown as a feasible solution at the laboratory scale. The use of nanomaterials has significantly enhanced the performance of biosensors, and the addition of CNTs has increased detection capabilities to an unrivaled level. Among the various CNT-based detection systems, CNT-based field-effect transistors possess ultra-sensitivity and low-noise detection capacity, allowing for immediate analyte determination even in the presence of limited analyte concentrations, which would be typical of early infection stages. Recently, CNT field-effect transistor-type biosensors have been successfully used in the fast diagnosis of COVID-19, which has increased research and commercial interest in exploiting current developments of CNT field-effect transistors. Recent progress in the design and deployment of CNT-based biosensors for viral monitoring are covered in this paper, as are the remaining obstacles and prospects. This work also highlights the enormous potential for synergistic effects of CNTs used in combination with other nanomaterials for viral detection.

Optimal control of the coronavirus pandemic with both pharmaceutical and non-pharmaceutical interventions

Coronaviruses are types of viruses that are widely spread in humans, birds, and other mammals, leading to hepatic, respiratory, neurologic, and enteric diseases. The disease is presently a pandemic with great medical, economical, and political impacts, and it is mostly spread through physical contact. To extinct the virus, keeping physical distance and taking vaccine are key. In this study, a dynamical transmission compartment model for coronavirus (COVID-19) is designed and rigorously analyzed using Routh-Hurwitz condition for the stability analysis. A global dynamics of mathematical formulation was investigated with the help of a constructed Lyapunov function. We further examined parameter sensitivities (local and global) to identify terms with greater impact or influence on the dynamics of the disease. Our approach is data driven to test the efficacy of the proposed model. The formulation was incorporated with available confirmed cases from January 22, 2020, to December 20, 2021, and parameterized using real-time series data that were collected on a daily basis for the first 705 days for fourteen countries, out of which the model was simulated using four selected countries: USA, Italy, South Africa, and Nigeria. A least square technique was adopted for the estimation of parameters. The simulated solutions of the model were analyzed using MAPLE-18 with Runge-Kutta-Felberg method (RKF45 solver). The model entrenched parameters analysis revealed that there are both disease-free and endemic equilibrium points. The solutions depicted that the free equilibrium point for COVID-19 is asymptotic locally stable, when the epidemiological reproduction number condition ( R 0 < 1 ) . The simulation results unveiled that the pandemic can be controlled if other control measures, such as face mask wearing in public areas and washing of hands, are combined with high level of compliance to physical distancing. Furthermore, an autonomous derivative equation for the five-dimensional deterministic was done with two control terms and constant rates for the pharmaceutical and non-pharmaceutical strategies. The Lagrangian and Hamilton were formulated to study the model optimal control existence, using Pontryagin's Maximum Principle describing the optimal control terms. The designed objective functional reduced the intervention costs and infections. We concluded that the COVID-19 curve can be flattened through strict compliance to both pharmaceutical and non-pharmaceutical strategies. The more the compliance level to physical distance and taking of vaccine, the earlier the curve is flattened and the earlier the economy will be bounce-back.

Detection of hospital environmental contamination during SARS-CoV-2 Omicron predominance using a highly sensitive air sampling device

Background and objectives

The high transmissibility of SARS-CoV-2 has exposed weaknesses in our infection control and detection measures, particularly in healthcare settings. Aerial sampling has evolved from passive impact filters to active sampling using negative pressure to expose culture substrate for virus detection. We evaluated the effectiveness of an active air sampling device as a potential surveillance system in detecting hospital pathogens, for augmenting containment measures to prevent nosocomial transmission, using SARS-CoV-2 as a surrogate.

Methods

We conducted air sampling in a hospital environment using the AerosolSense^TM air sampling device and compared it with surface swabs for their capacity to detect SARS-CoV-2.

Results

When combined with RT-qPCR detection, we found the device provided consistent SARS-CoV-2 detection, compared to surface sampling, in as little as 2 h of sampling time. The device also showed that it can identify minute quantities of SARS-CoV-2 in designated "clean areas" and through a N95 mask, indicating good surveillance capacity and sensitivity of the device in hospital settings.

Conclusion

Active air sampling was shown to be a sensitive surveillance system in healthcare settings. Findings from this study can also be applied in an organism agnostic manner for surveillance in the hospital, improving our ability to contain and prevent nosocomial outbreaks.

SARS-CoV-2 Omicron variant shows less efficient replication and fusion activity when compared with Delta variant in TMPRSS2-expressed cells

The novel SARS-CoV-2 Omicron variant (B.1.1.529), first found in early November 2021, has sparked considerable global concern and it has >50 mutations, many of which are known to affect transmissibility or cause immune escape. In this study, we sought to investigate the virological characteristics of the Omicron variant and compared it with the Delta variant which has dominated the world since mid-2021. Omicron variant replicated more slowly than the Delta variant in transmembrane serine protease 2 (TMPRSS2)-overexpressing VeroE6 (VeroE6/TMPRSS2) cells. Notably, the Delta variant replicated well in Calu3 cell line which has robust TMPRSS2 expression, while the Omicron variant replicated poorly in this cell line. Competition assay showed that Delta variant outcompeted Omicron variant in VeroE6/TMPRSS2 and Calu3 cells. To confirm the difference in entry pathway between the Omicron and Delta variants, we assessed the antiviral effect of bafilomycin A1, chloroquine (inhibiting endocytic pathway), and camostat (inhibiting TMPRSS2 pathway). Camostat potently inhibited the Delta variant but not the Omicron variant, while bafilomycin A1 and chloroquine could inhibit both Omicron and Delta variants. Moreover, the Omicron variant also showed weaker cell-cell fusion activity when compared with Delta variant in VeroE6/TMPRSS2 cells. Collectively, our results suggest that Omicron variant infection is not enhanced by TMPRSS2 but is largely mediated via the endocytic pathway. The difference in entry pathway between Omicron and Delta variants may have an implication on the clinical manifestations or disease severity.

Understanding the impact of rapid antigen tests on SARS-CoV-2 transmission in the fifth wave of COVID-19 in Hong Kong in early 2022

The fast-spreading Omicron variant of SARS-CoV-2 overwhelmed Hong Kong, causing the fifth wave of COVID-19. It remains to be determined what mitigation measures might have played a role in reversing the rising trend of confirmed cases in this major outbreak. The government of Hong Kong has launched the mass rapid antigen tests (RAT) in the population and the StayHomeSafe scheme since February 2022. In this study, we examined the impact of the mass RAT on disease transmission and the case fatality ratio. It was suggested that the implementation of RAT plausibly played a role in the steady decrease of the effective reproduction number, leading to diminished SARS-CoV-2 transmission. In addition, we projected the disease burden of the outbreak in a scenario analysis to highlight the necessity of the StayHomeSafe scheme in Hong Kong. The Omicron outbreak experience in Hong Kong may provide actionable insights for navigating the challenges of COVID-19 surges in other regions and countries.

Outbreak of SARS-CoV-2 Omicron Infection in a Centralized Quarantine Location in Hangzhou, China

This cohort study assesses whether transmission of COVID-19 occurred among individuals staying on different floors at a hotel used as a centralized quarantine location in Hangzhou, China.

Probable Aerosol Transmission of SARS-CoV-2 through Floors and Walls of Quarantine Hotel, Taiwan, 2021

We investigated a cluster of SARS-CoV-2 infections in a quarantine hotel in Taiwan in December 2021. The cluster involved 3 case patients who lived in nonadjacent rooms on different floors. They had no direct contact during their stay. By direct exploration of the space above the room ceilings, we found residual tunnels, wall defects, and truncated pipes between their rooms. We conducted a simplified tracer-gas experiment to assess the interconnection between rooms. Aerosol transmission through structural defects in floors and walls in this poorly ventilated hotel was the most likely route of virus transmission. This event demonstrates the high transmissibility of Omicron variants, even across rooms and floors, through structural defects. Our findings emphasize the importance of ventilation and integrity of building structure in quarantine facilities.

Vaccination with SARS-CoV-2 inactivated vaccines reduced the risk of anxiety and depression in a population majored by health care workers during the recent omicron variant outbreak

Background

The mental health status of the population majored by health care workers in China during the omicron variant outbreak remains unknown. Furthermore, the effect of COVID-19-inactivated vaccines on mental health is yet to be investigated.

Methods

A cross-sectional, online survey study was conducted from 12-20 April, 2022. The prevalence of symptoms of depression and anxiety were evaluated using the Hospital Anxiety and Depression Scale.

Results

Responses from a total of 1,387 participants were analyzed, 39.7% of which reported symptoms of mental health illness. The incidence of anxiety (30.4% vs. 48.4%, p < 0.001) and depression (27.1% vs. 46.3%, p < 0.001) decreased with COVID-19 inactivated vaccination. From multivariate analysis, living in Shanghai (anxiety: Odds ratio [OR]: 1.58, 95% confidence interval [CI]: 1.14-2.19, p = 0.006; depression: OR: 1.61, 95% CI: 1.16-2.25, p = 0.005), with a mental illness (anxiety: OR: 8.97, 95% CI: 1.01-79.56, p = 0.049; depression: OR: 9.32, 95% CI: 1.06-82.30, p = 0.045) increased the incidence of anxiety and depression. Elderly participants (anxiety: OR: 0.986, 95% CI: 0.975-0.997, p = 0.012; depression: OR: 0.976, 95% CI: 0.965-0.987, p < 0.001) who had been vaccinated against COVID-19 (anxiety: OR: 0.49, 95% CI: 0.32-0.75, p = 0.001; depression: OR: 0.45, 95% CI: 0.29-0.69, p < 0.001) had decreased incidences of anxiety and depression.

Conclusion

Our findings increase the awareness of the high incidence of mental health illness symptoms during the omicron variant outbreak despite previous experiences with the COVID-19 pandemic, and vaccination is suggested to reduce the risk of anxiety and depression.

Pathogenesis and Preventive Tactics of Immune-Mediated Non-Pulmonary COVID-19 in Children and Beyond

The COVID-19 pandemic has evolved to immune escape and threatened small children and the elderly with a higher severity and fatality of non-pulmonary diseases. These life-threatening non-pulmonary COVID-19 diseases such as acute necrotizing encephalopathies (ANE) and multisystem inflammatory syndrome in children (MIS-C) are more prevalent in children. However, the mortality of multisystem inflammatory syndrome in adults (MIS-A) is much higher than that of MIS-C although the incidence of MIS-A is lower. Clarification of immunopathogenesis and genetic susceptibility of inflammatory non-pulmonary COVID-19 diseases would provide an appropriate guide for the crisis management and prevention of morbidity and fatality in the ongoing pandemic. This review article described three inflammatory non-pulmonary COVID-19 diseases including (1) meningoencephalitis (ME), (2) acute necrotizing encephalopathies (ANE), and (3) post-infectious multisystem inflammatory syndrome in children (MIS-C) and in adults (MIS-A). To prevent these life-threatening non-pulmonary COVID-19 diseases, hosts carrying susceptible genetic variants should receive prophylactic vaccines, avoid febrile respiratory tract infection, and institute immunomodulators and mitochondrial cocktails as early as possible.

Evolution and Control of COVID-19 Epidemic in Hong Kong

Hong Kong SAR has adopted universal masking, social distancing, testing of all symptomatic and high-risk groups for isolation of confirmed cases in healthcare facilities, and quarantine of contacts as epidemiological control measures without city lockdown or border closure. These measures successfully suppressed the community transmission of pre-Omicron SARS-CoV-2 variants or lineages during the first to the fourth wave. No nosocomial SARS-CoV-2 infection was documented among healthcare workers in the first 300 days. The strategy of COVID-19 containment was adopted to provide additional time to achieve population immunity by vaccination. The near-zero COVID-19 situation for about 8 months in 2021 did not enable adequate immunization of the eligible population. A combination of factors was identified, especially population complacency associated with the low local COVID-19 activity, together with vaccine hesitancy. The importation of the highly transmissible Omicron variant kickstarted the fifth wave of COVID-19, which could no longer be controlled by our initial measures. The explosive fifth wave, which was partially contributed by vertical airborne transmission in high-rise residential buildings, resulted in over one million cases of infection. In this review, we summarize the epidemiology of COVID-19 and the infection control and public health measures against the importation and dissemination of SARS-CoV-2 until day 1000.

Transmission of SARS-CoV-2 in a primary school setting with and without public health measures using real-world contact data: A modelling study

Background

Stringent public health measures have been shown to influence the transmission of SARS-CoV-2 within school environments. We investigated the potential transmission of SARS-CoV-2 in a primary school setting with and without public health measures, using fine-grained physical positioning traces captured before the COVID-19 pandemic.

Methods

Approximately 172.63 million position data from 98 students and six teachers from an open-plan primary school were used to predict a potential transmission of SARS-CoV-2 in primary school settings. We first estimated the daily average number of contacts of students and teachers with an infected individual during the incubation period. We then used the Reed-Frost model to estimate the probability of transmission per contact for the SARS-CoV-2 Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron variant (B.1.1.529). Finally, we built a binomial distribution model to estimate the probability of onward transmission in schools with and without public health measures, including face masks and physical distancing.

Results

An infectious student would have 49.1 (95% confidence interval (CI) = 46.1-52.1) contacts with their peers and 2.00 (95% CI = 1.82-2.18) contacts with teachers per day. An infectious teacher would have 47.6 (95% CI = 45.1-50.0) contacts with students and 1.70 (95% CI = 1.48-1.92) contacts with their colleague teachers per day. While the probability of onward SARS-CoV-2 transmission was relatively low for the Alpha and Delta variants, the risk increased for the Omicron variant, especially in the absence of public health measures. Onward teacher-to-student transmission (88.9%, 95% CI = 88.6%-89.1%) and teacher-to-teacher SARS-CoV-2 transmission (98.4%, 95% CI = 98.5%-98.6%) were significantly higher for the Omicron variant without public health measures in place.

Conclusions

Our findings illustrate that, despite a lower frequency of close contacts, teacher-to-teacher close contacts demonstrated a higher risk of transmission per contact of SARS-CoV-2 compared to student-to-student close contacts. This was especially significant with the Omicron variant, with onward transmission more likely occurring from teacher index cases than student index cases. Public health measures (eg, face masks and physical distance) seem essential in reducing the risk of onward transmission within school environments.

Impact of ventilation and avoidance measures on SARS-CoV-2 risk of infection in public indoor environments

BACKGROUND

The literature includes many studies which individually assess the efficacy of protective measures against the spread of the SARS-CoV-2 virus. This study considers the high infection risk in public buildings and models the quality of the indoor environment, related safety measures, and their efficacy in preventing the spread of the SARS-CoV-2 virus.

METHODS

Simulations are created that consider protective factors such as hand hygiene, face covering and engagement with Covid-19 vaccination programs in reducing the risk of infection in a university foyer. Furthermore, a computational fluid dynamics model is developed to simulate and analyse the university foyer under three ventilation regimes. The probability of transmission was measured across different scenarios.

FINDINGS

Estimates suggest that the Delta variant requires the air change rate to be increased >1000 times compared to the original strain, which is practically not feasible. Consequently, appropriate hygiene practices, such as wearing masks, are essential to reducing secondary infections. A comparison of different protective factors in simulations found the overall burden of infections resulting from indoor contact depends on (i) face mask adherence, (ii) quality of the ventilation system, and (iii) other hygiene practices.

INTERPRETATION

Relying on ventilation, whether natural, mechanical, or mixed, is not sufficient alone to mitigate the risk of aerosol infections. This is due to the internal configuration of the indoor space in terms of (i) size and number of windows, their location and opening frequency, as well as the position of the air extraction and supply inlets, which often induce hotspots with stagnating air, (ii) the excessive required air change rate. Hence, strict reliance on proper hygiene practices, namely adherence to face coverings and hand sanitising, are essential. Consequently, face mask adherence should be emphasized and promoted by policymakers for public health applications. Similar research may need to be conducted using a similar approach on the Omicron (B.1.1.529) variant.

A comprehensive review on Covid-19 Omicron (B.1.1.529) variant

The world has been combating different variants of SARS-COV-19 since its first outbreak in Wuhan city. SARS-COV-19 is caused by the coronavirus. The corona virus mutates and becomes more transmissible than earlier variants as the day passes. Till 24 November 2021, SARS-COV-19 has four variants Alpha, Beta, Gamma, and Delta, respectively. Among them, the delta variant caused severe havoc across the world. South Africa registered a new variant with the World Health Organization (WHO) on 24 November 2021, which is much more transmissible than previous variants. The WHO classified it as a variant of concern (VOC) on 26 November 2021 and called it the Greek letter Omicron (B.1.1.529), the fifteenth letter in the alphabet. Here a serious attempt was made to comprehend the omicron variant's origin, nomenclature, characteristics, mutations, the difference between delta and omicron variant, epidemiology, transmission, clinical features, impact on immunity, immune evasion, vaccines efficacy, etc.

Explosive outbreak of SARS-CoV-2 Omicron variant is associated with vertical transmission in high-rise residential buildings in Hong Kong

The phenomenon of vertical transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in high-rise residential buildings (HRRBs) is unique in our densely populated cosmopolitan city. The compulsory testing of a whole building under the scheme of restriction-testing declaration (RTD) during the fourth wave (non-Omicron variant) and fifth wave (mostly Omicron variant) of COVID-19 outbreak in Hong Kong allowed us to study the prevalence of this phenomenon, which may represent a form of airborne transmission. From 23 January 2021 to 24 March 2022, 25,450 (5.8%) of 436,397 residents from 223 (63.0%) of 354 HRRBs under RTD were test-positive for SARS-CoV-2. Using the clustering of cases among vertically aligned flats with shared drainage stack and lightwell as a surrogate marker of vertical transmission, the number of vertically aligned flats with positive COVID-19 cases was significantly higher in the fifth wave compared with the fourth wave (14.2%, 6471/45,531 vs 0.24%, 3/1272; p < 0.001; or 2212 vs 1 per-million-flats; p < 0.001). Excluding 22,801 residents from 38 HRRBs who were tested negative outside the 12-week periods selected in fourth and fifth waves, the positive rate among residents was significantly higher among residents during the fifth wave than the fourth wave (6.5%, 25,434/389,700 vs 0.07%, 16/23,896; p < 0.001). Within the flats with COVID-19 cases, the proportion of vertically aligned flats was also significantly higher in the fifth wave than in the fourth wave (95.6%, 6471/6766 vs 30.0%, 3/10, p < 0.001). The proportion of HRRBs with COVID-19 cases was significantly higher during the corresponding 12-week period chosen for comparison (78.2%, 219/280 vs 11.1%, 4/36; p < 0.001). Whole-genome phylogenetic analysis of 332 viral genomes showed that Omicron BA.2 was the predominant strain, supporting the high transmissibility of BA.2 by airborne excreta-aerosol route in HRRBs of Hong Kong.

What were the historical reasons for the resistance to recognizing airborne transmission during the COVID-19 pandemic?

The question of whether SARS-CoV-2 is mainly transmitted by droplets or aerosols has been highly controversial. We sought to explain this controversy through a historical analysis of transmission research in other diseases. For most of human history, the dominant paradigm was that many diseases were carried by the air, often over long distances and in a phantasmagorical way. This miasmatic paradigm was challenged in the mid to late 19th century with the rise of germ theory, and as diseases such as cholera, puerperal fever, and malaria were found to actually transmit in other ways. Motivated by his views on the importance of contact/droplet infection, and the resistance he encountered from the remaining influence of miasma theory, prominent public health official Charles Chapin in 1910 helped initiate a successful paradigm shift, deeming airborne transmission most unlikely. This new paradigm became dominant. However, the lack of understanding of aerosols led to systematic errors in the interpretation of research evidence on transmission pathways. For the next five decades, airborne transmission was considered of negligible or minor importance for all major respiratory diseases, until a demonstration of airborne transmission of tuberculosis (which had been mistakenly thought to be transmitted by droplets) in 1962. The contact/droplet paradigm remained dominant, and only a few diseases were widely accepted as airborne before COVID-19: those that were clearly transmitted to people not in the same room. The acceleration of interdisciplinary research inspired by the COVID-19 pandemic has shown that airborne transmission is a major mode of transmission for this disease, and is likely to be significant for many respiratory infectious diseases.

Cross-variant protection against SARS-CoV-2 infection in hamsters immunized with monovalent and bivalent inactivated vaccines

Rapid development and successful use of vaccines against SARS-CoV-2 might hold the key to curb the ongoing pandemic of COVID-19. Emergence of vaccine-evasive SARS-CoV-2 variants of concern (VOCs) has posed a new challenge to vaccine design and development. One urgent need is to determine what types of variant-specific and bivalent vaccines should be developed. Here, we compared homotypic and heterotypic protection against SARS-CoV-2 infection of hamsters with monovalent and bivalent whole-virion inactivated vaccines derived from representative VOCs. In addition to the ancestral SARS-CoV-2 Wuhan strain, Delta (B.1.617.2; δ) and Theta (P.3; θ) variants were used in vaccine preparation. Additional VOCs including Omicron (B.1.1.529) and Alpha (B.1.1.7) variants were employed in the challenge experiment. Consistent with previous findings, Omicron variant exhibited the highest degree of immune evasion, rendering all different forms of inactivated vaccines substantially less efficacious. Notably, monovalent and bivalent Delta variant-specific inactivated vaccines provided optimal protection against challenge with Delta variant. Yet, some cross-variant protection against Omicron and Alpha variants was seen with all monovalent and bivalent inactivated vaccines tested. Taken together, our findings support the notion that an optimal next-generation inactivated vaccine against SARS-CoV-2 should contain the predominant VOC in circulation. Further investigations are underway to test whether a bivalent vaccine for Delta and Omicron variants can serve this purpose.

SARS-CoV-2 IgG seropositivity after the severe Omicron wave of COVID-19 in Hong Kong

The Omicron variant has led to a major fifth wave of COVID-19 in Hong Kong between January and May 2022. Here, we used seroprevalence to estimate the combined incidence of vaccination and SARS-CoV-2 infection, including subclinical infection which were not diagnosed at the acute stage. The overall seropositive rate of IgG against receptor binding domain (anti-RBD IgG) increased from 52.2% in December 2021 to 89.3% in May 2022. The level of anti-RBD IgG was lowest in the 0-9 and ≥80 year-old age groups in May 2022. The seropositive rate of antibody against ORF8, which reflects the rate of prior infection, was 23.4% in May 2022. Our data suggest that although most individuals were either vaccinated or infected after the fifth wave, children and older adults remain most vulnerable. Public health measures should target these vulnerable age groups in order to ameliorate the healthcare consequences of upcoming waves.

The Advantages of the Zero-COVID-19 Strategy

Introduction: To curb the COVID-19 pandemic, countries across the globe have adopted either a mitigation or anelimination policy, such as the zero-COVID-19 strategy. However, further research is needed to systematically investigate the advantages of the zero-COVID-19 strategy in the literature. To bridge the research gap, this study examines the zero-COVID-19 strategy in terms of its advantages as a global anti-pandemic framework. Methods: A literature review was conducted in PubMed, PsycINFO, and Scopus to locate academic articles that discussed the advantages of the zero-COVID-19 strategy. Braun and Clarke’s thematic analysis approach was adopted to guide the data analysis process. Results: The findings of our study show that the advantages of the zero-COVID-19 strategy range from short-term (e.g., limited virus infections, hospitalizations, and deaths), to medium-term (e.g., reduced presence of other infectious diseases), and long-term (e.g., low incidence of long COVID-19). While local residents mainly leverage these advantages, they also impact the global community (e.g., stable global supply of essentials, such as COVID-19 vaccines). Conclusions: COVID-19 is catastrophic, yet controllable. Our study examined the advantages of the zero-COVID-19 strategy from a nuanced perspective and discussed how these advantages benefit both the local and the global community in pandemic control and management. Future studies could investigate the shortcomings of the zero-COVID-19 strategy, especially its unintended consequences, such as adverse impacts on vulnerable populations’ mental health, so that society could more efficiently, economically, and empathetically capitalize on the potential of the zero-COVID-19 strategy for the betterment of personal and public health.

Air dispersal of respiratory viruses other than severe acute respiratory coronavirus virus 2 (SARS-CoV-2) and the implication on hospital infection control

Background:

Air dispersal of respiratory viruses other than SARS-CoV-2 has not been systematically reported. The incidence and factors associated with air dispersal of respiratory viruses are largely unknown.

Methods:

We performed air sampling by collecting 72,000 L of air over 6 hours for pediatric and adolescent patients infected with parainfluenza virus 3 (PIF3), respiratory syncytial virus (RSV), rhinovirus, and adenovirus. The patients were singly or 2-patient cohort isolated in airborne infection isolation rooms (AIIRs) from December 3, 2021, to January 26, 2022. The viral load in nasopharyngeal aspirates (NPA) and air samples were measured. Factors associated with air dispersal were investigated and analyzed.

Results:

Of 20 singly isolated patients with median age of 30 months (range, 3 months–15 years), 7 (35%) had air dispersal of the viruses compatible with their NPA results. These included 4 (40%) of 10 PIF3-infected patients, 2 (66%) of 3 RSV-infected patients, and 1 (50%) of 2 adenovirus-infected patients. The mean viral load in their room air sample was 1.58×10³ copies/mL. Compared with 13 patients (65%) without air dispersal, these 7 patients had a significantly higher mean viral load in their NPA specimens (6.15×10⁷ copies/mL vs 1.61×10⁵ copies/mL; P < .001). Another 14 patients were placed in cohorts as 7 pairs infected with the same virus (PIF3, 2 pairs; RSV, 3 pairs; rhinovirus, 1 pair; and adenovirus, 1 pair) in double-bed AIIRs, all of which had air dispersal. The mean room air viral load in 2-patient cohorts was significantly higher than in rooms of singly isolated patients (1.02×10⁴ copies/mL vs 1.58×10³ copies/mL; P = .020).

Conclusion:

Air dispersal of common respiratory viruses may have infection prevention and public health implications.

mRNA-based COVID-19 Vaccines Booster Dose: Benefits, Risks and Coverage

The number of COVID-19 vaccine-rich countries that have started COVID-19 third-dose booster programs is growing dramatically despite the lack of robust evidence on the effectiveness, safety, and frequency of the required booster doses that makes the individuals/populations immune to COVID -19 infection. Beyond the ethical dilemma, the scarcity of studies on the optimal timing for offering booster doses, eligibility criteria, and if there is any association between premature or delayed administration and the degree of protection against infection. The aim of this mini- review was to collect and analyze published data on this topic in a trial to answer some questions related to the benefits versus the risks of offering frequent boosters of mRNA vaccines for increasing the population immunity against COVID-19 infection considering the current policy of providing SARS-CoV-2 vaccine booster doses in rich countries versus those in relatively poor countries with limited access to vaccination. (www.actabiomedica.it).

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Associated With an Indoor Music Event That Required Proof of Full Vaccination Against Coronavirus Disease 2019 (COVID-19) Prior to Entry-Seattle, July 2021

In July 2021, Public Health-Seattle & King County investigated a coronavirus disease 2019 (COVID-19) outbreak at an indoor event intended for fully vaccinated individuals, revealing unvaccinated staff, limited masking, poor ventilation, and overcrowding. Supporting businesses to develop and implement comprehensive COVID-19 prevention plans is essential for reducing spread in these settings.

Decreased Antibiotic Consumption Coincided with Reduction in Bacteremia Caused by Bacterial Species with Respiratory Transmission Potential during the COVID-19 Pandemic

Nonpharmaceutical interventions implemented during the COVID-19 pandemic (2020−2021) have provided a unique opportunity to understand their impact on the wholesale supply of antibiotics and incidences of infections represented by bacteremia due to common bacterial species in Hong Kong. The wholesale antibiotic supply data (surrogate indicator of antibiotic consumption) and notifications of scarlet fever, chickenpox, and tuberculosis collected by the Centre for Health Protection, and the data of blood cultures of patients admitted to public hospitals in Hong Kong collected by the Hospital Authority for the last 10 years, were tabulated and analyzed. A reduction in the wholesale supply of antibiotics was observed. This decrease coincided with a significant reduction in the incidence of community-onset bacteremia due to Streptococcus pyogenes, Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, which are encapsulated bacteria with respiratory transmission potential. This reduction was sustained during two pandemic years (period 2: 2020−2021), compared with eight pre-pandemic years (period 1: 2012−2019). Although the mean number of patient admissions per year (1,704,079 vs. 1,702,484, p = 0.985) and blood culture requests per 1000 patient admissions (149.0 vs. 158.3, p = 0.132) were not significantly different between periods 1 and 2, a significant reduction in community-onset bacteremia due to encapsulated bacteria was observed in terms of the mean number of episodes per year (257 vs. 58, p < 0.001), episodes per 100,000 admissions (15.1 vs. 3.4, p < 0.001), and per 10,000 blood culture requests (10.1 vs. 2.1, p < 0.001), out of 17,037,598 episodes of patient admissions with 2,570,164 blood culture requests. Consistent with the findings of bacteremia, a reduction in case notification of scarlet fever and airborne infections, including tuberculosis and chickenpox, was also observed; however, there was no reduction in the incidence of hospital-onset bacteremia due to Staphylococcus aureus or Escherichia coli. Sustained implementation of non-pharmaceutical interventions against respiratory microbes may reduce the overall consumption of antibiotics, which may have a consequential impact on antimicrobial resistance. Rebound of conventional respiratory microbial infections is likely with the relaxation of these interventions.

Human Identical Sequences, hyaluronan, and hymecromone ─ the new mechanism and management of COVID-19

COVID-19 caused by SARS-CoV-2 has created formidable damage to public health and market economy. Currently, SARS-CoV-2 variants has exacerbated the transmission from person-to-person. Even after a great deal of investigation on COVID-19, SARS-CoV-2 is still rampaging globally, emphasizing the urgent need to reformulate effective prevention and treatment strategies. Here, we review the latest research progress of COVID-19 and provide distinct perspectives on the mechanism and management of COVID-19. Specially, we highlight the significance of Human Identical Sequences (HIS), hyaluronan, and hymecromone ("Three-H") for the understanding and intervention of COVID-19. Firstly, HIS activate inflammation-related genes to influence COVID-19 progress through NamiRNA-Enhancer network. Accumulation of hyaluronan induced by HIS-mediated HAS2 upregulation is a substantial basis for clinical manifestations of COVID-19, especially in lymphocytopenia and pulmonary ground-glass opacity. Secondly, detection of plasma hyaluronan can be effective for evaluating the progression and severity of COVID-19. Thirdly, spike glycoprotein of SARS-CoV-2 may bind to hyaluronan and further serve as an allergen to stimulate allergic reaction, causing sudden adverse effects after vaccination or the aggravation of COVID-19. Finally, antisense oligonucleotides of HIS or inhibitors of hyaluronan synthesis (hymecromone) or antiallergic agents could be promising therapeutic agents for COVID-19. Collectively, Three-H could hold the key to understand the pathogenic mechanism and create effective therapeutic strategies for COVID-19.

Outbreak investigation of airborne transmission of Omicron (B.1.1.529) - SARS-CoV-2 variant of concern in a restaurant: Implication for enhancement of indoor air dilution

Airborne transmission of SARS-CoV-2 has been increasingly recognized in the outbreak of COVID-19, especially with the Omicron variant. We investigated an outbreak due to Omicron variant in a restaurant. Besides epidemiological and phylogenetic analyses, the secondary attack rates of customers of restaurant-related COVID-19 outbreak before (Outbreak R1) and after enhancement of indoor air dilution (Outbreak R2) were compared. On 27th December 2021, an index case stayed in restaurant R2 for 98 min. Except for 1 sitting in the same table, six other secondary cases sat in 3 corners at 3 different zones, which were served by different staff. The median exposure time was 34 min (range: 19-98 min). All 7 secondary cases were phylogenetically related to the index. Smoke test demonstrated that the airflow direction may explain the distribution of secondary cases. Compared with an earlier COVID-19 outbreak in another restaurant R1 (19th February 2021), which occurred prior to the mandatory enhancement of indoor air dilution, the secondary attack rate among customers in R2 was significantly lower than that in R1 (3.4%, 7/207 vs 28.9%, 22/76, p<0.001). Enhancement of indoor air dilution through ventilation and installation of air purifier could minimize the risk of SARS-CoV-2 transmission in the restaurants.

Estimated Mask Use and Temporal Relationship to COVID-19 Epidemiology of Black Lives Matter Protests in 12 Cities

There is an increased risk of SARS-CoV-2 transmission during mass gatherings and a risk of asymptomatic infection. We aimed to estimate the use of masks during Black Lives Matter (BLM) protests and whether these protests increased the risk of COVID-19. Two reviewers screened 496 protest images for mask use, with high inter-rater reliability. Protest intensity, use of tear gas, government control measures, and testing rates were estimated in 12 cities. A correlation analysis was conducted to assess the potential effect of mask use and other measures, adjusting for testing rates, on COVID-19 epidemiology 4 weeks (two incubation periods) post-protests. Mask use ranged from 69 to 96% across protests. There was no increase in the incidence of COVID-19 post-protest in 11 cities. After adjusting for testing rates, only Miami, which involved use of tear gas and had high protest intensity, showed a clear increase in COVID-19 after one incubation period post-protest. No significant correlation was found between incidence and protest factors. Our study showed that protests in most cities studied did not increase COVID-19 incidence in 2020, and a high level of mask use was seen. The absence of an epidemic surge within two incubation periods of a protest is indicative that the protests did not have a major influence on epidemic activity, except in Miami. With the globally circulating highly transmissible Alpha, Delta, and Omicron variants, layered interventions such as mandated mask use, physical distancing, testing, and vaccination should be applied for mass gatherings in the future.

Comparison of Omicron and Delta Variant Infection COVID-19 Cases - Guangdong Province, China, 2022

What is already known about this topic?

The Omicron variant has been listed as a variant of concern, but the characteristics still remain unclear.

What is added by this report?

The vaccinated proportion of 65 imported coronavirus disease 2019 cases that were infected with Omicron variant in this study was 89.23%, which was higher than Delta cases. Most imported cases infected with Omicron were tested positive using polymerase chain reaction after entering Guangdong within 3 days, a shorter period than Delta.

What are the implications for public health practice?

Under this observation, the international travelers infected with Omicron variant were detected positive earlier after entry than those infected with Delta variant. Breakthrough infections occurred in most Omicron cases in this study, but vaccination was still effective to reduce the incidence of severe illness. Omicron surveillance should be strengthened.

Revisiting SARS-CoV-2 environmental contamination by patients with COVID-19: The Omicron variant does not differ from previous strains

SARS-CoV-2 Omicron strain emergence raised concerns that its enhanced infectivity is partly due to altered spread/contamination modalities. We therefore sampled high-contact surfaces and air in close proximity to patients who were verified as infected with the Omicron strain, using identical protocols applied to sample patients positive to the original or Alpha strains. Cumulatively, for all 3 strains, viral RNA was detected in 90 of 168 surfaces and 6 of 49 air samples (mean cycle threshold [Ct]=35.2±2.5). No infective virus was identified. No significant differences in prevalence were found between strains.

Rapid spread of SARS-CoV-2 Omicron subvariant BA.2 in a single-source community outbreak

Background

The SARS-CoV-2 Omicron variant BA.2 sublineage has increased rapidly in Europe and Asia since January 2022. Here, we report the epidemiological and genomic analysis of a large single source BA.2 outbreak in a housing estate.

Methods

We analyzed the epidemiological information of a community outbreak of BA.2 (STY outbreak). We performed whole viral genome sequencing using the Oxford Nanopore MinION device. We calculated the doubling time of the outbreak within a housing estate.

Results

The STY outbreak involved a total of 768 individuals as of 5 ^th February 2022, including 432 residents, visitors or staff (56.3%) from a single housing estate (KC Estate). The outbreak at the KC Estate has a short doubling time of 1.28 days (95% confidence interval: 0.560-1.935). The outbreak was promptly controlled with the lockdown of 3 buildings within the housing estate. Whole genome sequencing was performed for 133 patients in the STY outbreak, including 106 residents of the KC Estate. All 133 sequences from the STY outbreak belonged to the BA.2 sublineage, and phylogenetic analysis showed that these sequences cluster together. All individuals in the STY cluster had the unique mutation C12525T.

Conclusions

Our study highlights the exceptionally high transmissibility of the Omicron variant BA.2 sublineage in Hong Kong where stringent measures are implemented as part of the elimination strategy. Continual genomic surveillance is crucial in monitoring the emergence of epidemiologically important Omicron sub-variants.

Virucidal Activity of Different Mouthwashes against the Salivary Load of SARS-CoV-2: A Narrative Review

The saliva of COVID-19-confirmed patients presents a high viral load of the virus. Aerosols generated during medical and dental procedures can transport the virus and are a possible causative agent of cross-infection. Since the onset of the pandemic, numerous investigations have been attempting to mitigate the risk of transmission by reducing the viral load in saliva using preprocedural mouthwashes. This study aims to review the most up-to-date in vitro and in vivo studies investigating the efficacy of different mouthwashes on reducing the salivary viral load of SARS-CoV-2, giving particular attention to the most recent randomized control trials published.

Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron

The SARS-CoV-2 Omicron variant with increased fitness is spreading rapidly worldwide. Analysis of cryo-EM structures of the spike (S) from Omicron reveals amino acid substitutions forging interactions that stably maintain an active conformation for receptor recognition. The relatively more compact domain organization confers improved stability and enhances attachment but compromises the efficiency of the viral fusion step. Alterations in local conformation, charge, and hydrophobic microenvironments underpin the modulation of the epitopes such that they are not recognized by most NTD- and RBD-antibodies, facilitating viral immune escape. Structure of the Omicron S bound with human ACE2, together with the analysis of sequence conservation in ACE2 binding region of 25 sarbecovirus members, as well as heatmaps of the immunogenic sites and their corresponding mutational frequencies, sheds light on conserved and structurally restrained regions that can be used for the development of broad-spectrum vaccines and therapeutics.

Omicron Genetic and Clinical Peculiarities That May Overturn SARS-CoV-2 Pandemic: A Literature Review

The Coronavirus disease 2019 (COVID-19) pandemic poses a great threat to global public health. The original wild-type strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has genetically evolved, and several variants of concern (VOC) have emerged. On 26 November 2021, a new variant named Omicron (B.1.1.529) was designated as the fifth VOC, revealing that SARS-CoV-2 has the potential to go beyond the available therapies. The high number of mutations harboured on the spike protein make Omicron highly transmissible, less responsive to several of the currently used drugs, as well as potentially able to escape immune protection elicited by both vaccines and previous infection. We reviewed the latest publication and the most recent available literature on the Omicron variant, enlightening both reasons for concern and high hopes for new therapeutic strategies.

Neutralization of Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variant by Sera From BNT162b2 or CoronaVac Vaccine Recipients

BACKGROUND

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) omicron variant, designated as a variant of concern by the World Health Organization, carries numerous spike mutations that are known to evade neutralizing antibodies elicited by coronavirus disease 2019 (COVID-19) vaccines. A deeper understanding of the susceptibility of omicron variant to vaccine-induced neutralizing antibodies is urgently needed for risk assessment.

METHODS

Omicron variant strains HKU691 and HKU344-R346K were isolated from patients using TMPRSS2-overexpressing VeroE6 cells. Whole genome sequence was determined using nanopore sequencing. Neutralization susceptibility of ancestral lineage A virus and the omicron, delta and beta variants to sera from 25 BNT162b2 and 25 CoronaVac vaccine recipients was determined using a live virus microneutralization assay.

RESULTS

The omicron variant strain HKU344-R346K has an additional spike R346K mutation, which is present in 8.5% of strains deposited in the GISAID database. Only 20% and 24% of BNT162b2 recipients had detectable neutralizing antibody against the omicron variant HKU691 and HKU344-R346K, respectively, whereas none of the CoronaVac recipients had detectable neutralizing antibody titer against either omicron isolate. For BNT162b2 recipients, the geometric mean neutralization antibody titers (GMTs) of the omicron variant isolates (5.43 and 6.42) were 35.7-39.9-fold lower than that of the ancestral virus (229.4), and the GMTs of both omicron variant isolates were significantly lower than those of the beta and delta variants. There was no significant difference in the GMTs between HKU691 and HKU344-R346K.

CONCLUSIONS

Omicron variant escapes neutralizing antibodies elicited by BNT162b2 or CoronaVac. The additional R346K mutation did not affect the neutralization susceptibility. Our data suggest that the omicron variant may be associated with lower COVID-19 vaccine effectiveness.