Tracking and controlling the spatiotemporal spread of SARS-CoV-2 Omicron variant in South Africa

Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia: A Retrospective Genomic Surveillance Study

Mutations have driven the evolution and development of new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with potential implications for increased transmissibility, disease severity and vaccine escape among others. Genome sequencing is a technique that allows scientists to read the genetic code of an organism and has become a powerful tool for studying emerging infectious diseases. Here, we conducted a cross-sectional study in selected districts of the Eastern Province of Zambia, from November 2021 to February 2022. We analyzed SARS-CoV-2 samples (n = 76) using high-throughput sequencing. A total of 4097 mutations were identified in 69 SARS-CoV-2 genomes with 47% (1925/4097) of the mutations occurring in the spike protein. We identified 83 unique amino acid mutations in the spike protein of the seven Omicron sublineages (BA.1, BA.1.1, BA.1.14, BA.1.18, BA.1.21, BA.2, BA.2.23 and XT). Of these, 43.4% (36/83) were present in the receptor binding domain, while 14.5% (12/83) were in the receptor binding motif. While we identified a potential recombinant XT strain, the highly transmissible BA.2 sublineage was more predominant (40.8%). We observed the substitution of other variants with the Omicron strain in the Eastern Province. This work shows the importance of pandemic preparedness and the need to monitor disease in the general population.

Spatiotemporal Patterns of the Omicron Wave of COVID-19 in the United States

COVID-19 has undergone multiple mutations, with the Omicron variant proving to be highly contagious and rapidly spreading across many countries. The United States was severely hit by the Omicron variant. However, it was still unclear how Omicron transferred across the United States. Here, we collected daily COVID-19 cases and deaths in each county from 1 December 2021 to 28 February 2022 as the Omicron wave. We adopted space-time scan statistics, the Hoover index, and trajectories of the epicenter to quantify spatiotemporal patterns of the Omicron wave of COVID-19. The results showed that the highest and earliest cluster was located in the Northeast. The Hoover index for both cases and deaths exhibited phases of rapid decline, slow decline, and relative stability, indicating a rapid spread of the Omicron wave across the country. The Hoover index for deaths was consistently higher than that for cases. The epicenter of cases and deaths shifted from the west to the east, then southwest. Nevertheless, cases were more widespread than deaths, with a lag in mortality data. This study uncovers the spatiotemporal patterns of Omicron transmission in the United States, and its underlying mechanisms deserve further exploration.

Reduced SARS-CoV-2 infection risk is associated with the use of Seven-Flavor Herb Tea: A multi-center observational study in Shanghai, China

OBJECTIVE

Omicron, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, is responsible for numerous infections in China. This study investigates the association between the use of Seven-Flavor Herb Tea (SFHT) and the risk of SARS-CoV-2 infection to develop precise and differentiated strategies for control of the coronavirus disease 2019 (COVID-19).

METHODS

This case-control study was conducted at shelter hospitals and quarantine hotels in China. A total of 5348 laboratory-confirmed COVID-19 patients were enrolled between April 1 and May 31, 2022, while 2190 uninfected individuals served as healthy controls. Structured questionnaires were used to collect data on demographics, underlying diseases, vaccination status, and use of SFHT. Patients were propensity-score-matched using 1:1 nearest-neighbor matching of the logit of the propensity score. Subsequently, a conditional logistic regression model was used for data analysis.

RESULTS

Overall, 7538 eligible subjects were recruited, with an average age of [45.54 ± 16.94] years. The age of COVID-19 patients was significantly higher than that of uninfected individuals ([48.25 ± 17.48] years vs [38.92 ± 13.41] years; t = 22.437, P < 0.001). A total of 2190 COVID-19 cases were matched with uninfected individuals at a 1:1 ratio. The use of SFHT (odds ratio = 0.753, 95% confidence interval: 0.692, 0.820) was associated with a lower risk of SARS-CoV-2 infection compared to untreated individuals.

CONCLUSION

Our findings suggest that taking SFHT reduces the risk of SARS-CoV-2 infection. This is a useful study in the larger picture of COVID-19 management, but data from large-sample multi-center, randomized clinical trial are warranted to confirm the finding. Please cite this article as: Zhang SX, Chen XX, Zheng Y, Cai BH, Shi W, Ru M, Li H, Zhang DD, Tian Y, Chen YL. Reduced SARS-CoV-2 infection risk is associated with the use of Seven-Flavor Herb Tea: a multi-center observational study in Shanghai, China. J Integr Med. 2023; Epub ahead of print.

Predicting onset risk of COVID-19 symptom to support healthy travel route planning in the new normal of long-term coexistence with SARS-CoV-2

Due to the increased outdoor transmission risk of new SARS-COV-2 variants, the health of urban residents in daily travel is being threatened. In the new normal of long-term coexistence with SARS-CoV-2, how to avoid being infected by SARS-CoV-2 in daily travel has become a key issue. Hence, a spatiotemporal solution has been proposed to assist healthy travel route planning. Firstly, an enhanced urban-community-scale geographic model was proposed to predict daily COVID-19 symptom onset risk by incorporating the real-time effective reproduction numbers, and daily population variation of fully vaccinated. On-road onset risk predictions in the next following days were then extracted for searching healthy routes with the least onset risk values. The healthy route planning was further implemented in a mobile application. Hong Kong, one of the representative highly populated cities, has been chosen as an example to apply the spatiotemporal solution. The application results in the four epidemic waves of Hong Kong show that based on the high accurate prediction of COVID-19 symptom onset risk, the healthy route planning could reduce people's exposure to the COVID-19 symptoms onset risk. To sum, the proposed solution can be applied to support the healthy travel of residents in more cities in the new normalcy.

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

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

The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub

Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this work how lineages BA.1 and BA.2 entered and spread in the country by sequencing 2173 new SARS-CoV-2 genomes collected between October 2021 and April 2022 and analyzing them in addition to more than 18,000 publicly available sequences with phylodynamic methods. We registered that Omicron was present in Brazil as early as 16 November 2021 and by January 2022 was already more than 99% of samples. More importantly, we detected that Omicron has been mostly imported through the state of São Paulo, which in turn dispersed the lineages to other states and regions of Brazil. This knowledge can be used to implement more efficient non-pharmaceutical interventions against the introduction of new SARS-CoV variants focused on surveillance of airports and ground transportation.

The Role of Functional Urban Areas in the Spread of COVID-19 Omicron (Northern Spain)

This study focuses on the space-time patterns of the COVID-19 Omicron wave at a regional scale, using municipal data. We analyze the Basque Country and Cantabria, two adjacent regions in the north of Spain, which between them numbered 491,816 confirmed cases in their 358 municipalities from 15th November 2021 to 31st March 2022. The study seeks to determine the role of functional urban areas (FUAs) in the spread of the Omicron variant of the virus, using ESRI Technology (ArcGIS Pro) and applying intelligence location methods such as 3D-bins and emerging hot spots. Those methods help identify trends and types of problem area, such as hot spots, at municipal level. The results demonstrate that FUAs do not contain an over-concentration of COVID-19 cases, as their location coefficient is under 1.0 in relation to population. Nevertheless, FUAs do have an important role as drivers of spread in the upward curve of the Omicron wave. Significant hot spot patterns are found in 85.0% of FUA area, where 98.9% of FUA cases occur. The distribution of cases shows a spatially stationary linear correlation linked to demographically progressive areas (densely populated, young profile, and with more children per woman) which are well connected by highways and railroads. Based on this research, the proposed GIS methodology can be adapted to other case studies. Considering geo-prevention and WHO Health in All Policies approaches, the research findings reveal spatial patterns that can help policymakers in tackling the pandemic in future waves as society learns to live with the virus.

Omicron-BA.1 Dispersion Rates in Mexico Varied According to the Regional Epidemic Patterns and the Diversity of Local Delta Subvariants

PURPOSE

The Omicron subvariant BA.1 of SARS-CoV-2 was first detected in November 2021 and quickly spread worldwide, displacing the Delta variant. In this work, a characterization of the spread of this variant in Mexico is presented.

METHODS

The time to fixation of BA.1, the diversity of Delta sublineages, the population density, and the level of virus circulation during the inter-wave interval were determined to analyze differences in BA.1 spread.

RESULTS

BA.1 began spreading during the first week of December 2021 and became dominant in the next three weeks, causing the fourth COVID-19 epidemiological surge in Mexico. Unlike previous variants, BA.1 did not exhibit a geographically distinct circulation pattern. However, a regional difference in the speed of the replacement of the Delta variant was observed.

CONCLUSIONS

Viral diversity and the relative abundance of the virus in a particular area around the time of the introduction of a new lineage seem to have influenced the spread dynamics, in addition to population density. Nonetheless, if there is a significant difference in the fitness of the variants, or if the time allowed for the competition is sufficiently long, it seems the fitter virus will eventually become dominant, as observed in the eventual dominance of the BA.1.x variant in Mexico.

A Spatiotemporal Solution to Control COVID-19 Transmission at the Community Scale for Returning to Normalcy: COVID-19 Symptom Onset Risk Spatiotemporal Analysis

BACKGROUND

Following the recent COVID-19 pandemic, returning to normalcy has become the primary goal of global cities. The key for returning to normalcy is to avoid affecting social and economic activities while supporting precise epidemic control. Estimation models for the spatiotemporal spread of the epidemic at the refined scale of cities that support precise epidemic control are limited. For most of 2021, Hong Kong has remained at the top of the "global normalcy index" because of its effective responses. The urban-community-scale spatiotemporal onset risk prediction model of COVID-19 symptom has been used to assist in the precise epidemic control of Hong Kong.

OBJECTIVE

Based on the spatiotemporal prediction models of COVID-19 symptom onset risk, the aim of this study was to develop a spatiotemporal solution to assist in precise prevention and control for returning to normalcy.

METHODS

Over the years 2020 and 2021, a spatiotemporal solution was proposed and applied to support the epidemic control in Hong Kong. An enhanced urban-community-scale geographic model was proposed to predict the risk of COVID-19 symptom onset by quantifying the impact of the transmission of SARS-CoV-2 variants, vaccination, and the imported case risk. The generated prediction results could be then applied to establish the onset risk predictions over the following days, the identification of high-onset-risk communities, the effectiveness analysis of response measures implemented, and the effectiveness simulation of upcoming response measures. The applications could be integrated into a web-based platform to assist the antiepidemic work.

RESULTS

Daily predicted onset risk in 291 tertiary planning units (TPUs) of Hong Kong from January 18, 2020, to April 22, 2021, was obtained from the enhanced prediction model. The prediction accuracy in the following 7 days was over 80%. The prediction results were used to effectively assist the epidemic control of Hong Kong in the following application examples: identified communities within high-onset-risk always only accounted for 2%-25% in multiple epidemiological scenarios; effective COVID-19 response measures, such as prohibiting public gatherings of more than 4 people were found to reduce the onset risk by 16%-46%; through the effect simulation of the new compulsory testing measure, the onset risk was found to be reduced by more than 80% in 42 (14.43%) TPUs and by more than 60% in 96 (32.99%) TPUs.

CONCLUSIONS

In summary, this solution can support sustainable and targeted pandemic responses for returning to normalcy. Faced with the situation that may coexist with SARS-CoV-2, this study can not only assist global cities in responding to the future epidemics effectively but also help to restore social and economic activities and people's normal lives.

How to control the spatiotemporal spread of Omicron in the region with low vaccination rates

Currently, finding ways to effectively control the spread of Omicron in regions with low vaccination rates is an urgent issue. In this study, we use a district-level model for predicting the COVID-19 symptom onset risk to explore and control the whole process of spread of Omicron in South Africa at a finer spatial scale. We found that in the early stage of the accelerated spread, Omicron spreads rapidly from the districts at the center of human mobility to other important districts of the human mobility network and its peripheral districts. In the subsequent diffusion-contraction stage, Omicron rapidly spreads to districts with low human mobility and then mainly contracts to districts with the highest human mobility. We found that increasing daily vaccination rates 10 times mainly reduced the symptom onset risk in remote areas with low human mobility. Implementing Alert Level 5 in the three districts at the epicenter, and Alert Level 1 in the remaining 49 districts, the spatial spread related to human mobility was effectively restricted, and the daily onset risk in districts with high human mobility also decreased by 20-80%.

Fractal-fractional age-structure study of omicron SARS-CoV-2 variant transmission dynamics

This paper proposes a new fractal-fractional age-structure model for the omicron SARS-CoV-2 variant under the Caputo-Fabrizio fractional order derivative. Caputo-Fabrizio fractal-fractional order is particularly successful in modelling real-world phenomena due to its repeated memory effect and ability to capture the exponentially decreasing impact of disease transmission dynamics. We consider two age groups, the first of which has a population under 50 and the second of a population beyond 50. Our results show that at a population dynamics level, there is a high infection and recovery of omicron SARS-CoV-2 variant infection among the population under 50 (Group-1), while a high infection rate and low recovery of omicron SARS-CoV-2 variant infection among the population beyond 50 (Group-2) when the fractal-fractional order is varied.

The wave of the SARS-CoV-2 Omicron variant resulted in a rapid spike and decline as highlighted by municipal wastewater surveillance

This paper highlights the extraordinarily rapid spread of SARS-CoV-2 loads in wastewater that during the Omicron wave in December 2021-February 2022, compared with the profiles acquired in 2020-21 with 410 samples from two wastewater treatment plants (Trento+suburbs, 132,500 inhabitants). Monitoring of SARS-CoV-2 in wastewater focused on: (i) 3 samplings/week and analysis, (ii) normalization to calculate genomic units (GU) inh-1 d-1; (iii) calculation of a 7-day moving average to smooth daily fluctuations; (iv) comparison with the 'current active cases'/100,000 inh progressively affected by the mass vaccination. The time profiles of SARS-CoV-2 in wastewater matched the waves of active cases. In February-April 2021, a viral load of 1.0E＋07 GU inh-1 d- 1 corresponded to 700 active cases/100,000 inh. In July-September 2021, although the low current active cases, sewage revealed an appreciable SARS-CoV-2 circulation (in this period 2.2E＋07 GU inh-1 d-1 corresponded to 90 active cases/100,000 inh). Omicron was not detected in wastewater until mid-December 2021. The Omicron spread caused a 5-6 fold increase of the viral load in two weeks, reaching the highest peak (2.0-2.2E＋08 GU inh-1 d-1 and 4500 active cases/100,000 inh) during the pandemic. In this period, wastewater surveillance anticipated epidemiological data by about 6 days. In winter 2021-22, despite the 4-7 times higher viral loads in wastewater, hospitalizations were 4 times lower than in winter 2020-21 due to the vaccination coverage >80%. The Omicron wave demonstrated that SARS-CoV-2 monitoring of wastewater anticipated epidemiological data, confirming its importance in long-term surveillance.

Aptamer-Gated Mesoporous Silica Nanoparticles for N Protein Triggered Release of Remdesivir and Treatment of Novel Coronavirus (2019-nCoV)

Since the 2019-nCoV outbreak was first reported, hundreds of millions of people all over the world have been infected. There is no doubt that improving the cure rate of 2019-nCoV is one of the most effective means to deal with the current serious epidemic. At present, Remdesivir (RDV) has been clinically proven to be effective in the treatment of SARS-CoV-2. However, the uncertain side effects make it important to reduce the use of drugs while ensuring the self-healing effect. We report an approach here with targeted therapy for the treatment of SARS-CoV-2 and other coronaviruses illness. In this study, mesoporous silica was used as the carrier of RDV, the nucleocapsid protein (N protein) aptamer was hybridized with the complementary chain, and the double-stranded DNA was combined with gold nanoparticles as the gates of mesoporous silica pores. When the RDV-loaded mesoporous silica is incubated with the N protein, aptamer with gold nanoparticles dissociate from the complementary DNA oligonucleotide on the mesoporous silica surface and bind to the N protein. The releasing of RDV was determined by detecting the UV-vis absorption peak of RDV in the solution. These results show that the RDV delivery system designed in this work has potential clinical application for the treatment of 2019-nCoV.

Spatiotemporal analysis of the morbidity of global Omicron from November 2021 to February 2022

The Omicron variant was first reported to the World Health Organization (WHO) from South Africa on November 24, 2021; this variant is spreading rapidly worldwide. No study has conducted a spatiotemporal analysis of the morbidity of Omicron infection at the country level; hence, to explore the spatial transmission of the Omicron variant among the 220 countries worldwide, we aimed to the analyze its spatial autocorrelation and to conduct a multiple linear regression to investigate the underlying factors associated with the pandemic. This study was an ecological study. Data on the number of confirmed cases were extracted from the WHO website. The spatiotemporal characteristic was described in a thematic map. The Global Moran Index (Moran's I) was used to detect the spatial autocorrelation, while the local indicators of spatial association (LISA) were used to analyze the local spatial correlation characteristics. The joinpoint regression model was used to explore the change in the trend of the Omicron incidence over time. The association between the morbidity of Omicron and influencing factors were analyzed using multiple linear regression. This study was an ecological study. Data on the number of confirmed cases were extracted from the WHO website. The spatiotemporal characteristic was described in a thematic map. The Global Moran Index (Moran's I) was used to detect the spatial autocorrelation, while the LISA were used to analyze the local spatial correlation characteristics. The joinpoint regression model was used to explore the change in the trend of the Omicron incidence over time. The association between the morbidity of Omicron and influencing factors were analyzed using multiple linear regression. The value of Moran's I was positive (Moran's I = 0.061, Z-score = 3.772, p = 0.007), indicating a spatial correlation of the morbidity of Omicron at the country level. From November 26, 2021 to February 26, 2022; the morbidity showed obvious spatial clustering. Hotspot clustering was observed mostly in Europe (locations in High-High category: 24). Coldspot clustering was observed mostly in Africa and Asia (locations in Low-Low category: 32). The result of joinpoint regression showed an increasing trend from December 21, 2021 to January 26, 2022. Results of the multiple linear regression analysis demonstrated that the morbidity of Omicron was strongly positively correlated with income support (coefficient = 1.905, 95% confidence interval [CI]: 1.354-2.456, p < 0.001) and strongly negatively correlated with close public transport (coefficient = -1.591, 95% CI: -2.461 to -0.721, p = 0.001). Omicron outbreaks exhibited spatial clustering at the country level worldwide; the countries with higher disease morbidity could impact the other countries that are surrounded by and close to it. The locations with High-High clustering category, which referred to the countries with higher disease morbidity, were mainly observed in Europe, and its adjoining country also showed high spatial clustering. The morbidity of Omicron increased from December 21, 2021 to January 26, 2022. The higher morbidity of Omicron was associated with the economic and policy interventions implemented; hence, to deal with the epidemic, the prevention and control measures should be strengthened in all aspects.

Assessing the mechanism of citywide test-trace-isolate Zero-COVID policy and exit strategy of COVID-19 pandemic

BACKGROUND

Countries that aimed for eliminating the cases of COVID-19 with test-trace-isolate policy are found to have lower infections, deaths, and better economic performance, compared with those that opted for other mitigation strategies. However, the continuous evolution of new strains has raised the question of whether COVID-19 eradication is still possible given the limited public health response capacity and fatigue of the epidemic. We aim to investigate the mechanism of the Zero-COVID policy on outbreak containment, and to explore the possibility of eradication of Omicron transmission using the citywide test-trace-isolate (CTTI) strategy.

METHODS

We develop a compartmental model incorporating the CTTI Zero-COVID policy to understand how it contributes to the SARS-CoV-2 elimination. We employ our model to mimic the Delta outbreak in Fujian Province, China, from September 10 to October 9, 2021, and the Omicron outbreak in Jilin Province, China for the period from March 1 to April 1, 2022. Projections and sensitivity analyses were conducted using dynamical system and Latin Hypercube Sampling/ Partial Rank Correlation Coefficient (PRCC).

RESULTS

Calibration results of the model estimate the Fujian Delta outbreak can end in 30 (95% confidence interval CI: 28-33) days, after 10 (95% CI: 9-11) rounds of citywide testing. The emerging Jilin Omicron outbreak may achieve zero COVID cases in 50 (95% CI: 41-57) days if supported with sufficient public health resources and population compliance, which shows the effectiveness of the CTTI Zero-COVID policy.

CONCLUSIONS

The CTTI policy shows the capacity for the eradication of the Delta outbreaks and also the Omicron outbreaks. Nonetheless, the implementation of radical CTTI is challenging, which requires routine monitoring for early detection, adequate testing capacity, efficient contact tracing, and high isolation compliance, which constrain its benefits in regions with limited resources. Moreover, these challenges become even more acute in the face of more contagious variants with a high proportion of asymptomatic cases. Hence, in regions where CTTI is not possible, personal protection, public health control measures, and vaccination are indispensable for mitigating and exiting the COVID-19 pandemic.

Understanding spatiotemporal symptom onset risk of Omicron BA.1, BA.2 and hamster-related Delta AY.127

Purpose

Investigation of the community-level symptomatic onset risk regarding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern, is crucial to the pandemic control in the new normal.

Methods

Investigated in this study is the spatiotemporal symptom onset risk with Omicron BA.1, BA.2, and hamster-related Delta AY.127 by a joint analysis of community-based human mobility, virus genomes, and vaccinations in Hong Kong.

Results

The spatial spread of Omicron BA.2 was found to be 2.91 times and 2.56 times faster than that of Omicron BA.1 and Delta AY.127. Identified has been an early spatial invasion process in which spatiotemporal symptom onset risk was associated with intercommunity and cross-community human mobility of a dominant source location, especially regarding enhancement of the effects of the increased intrinsic transmissibility of Omicron BA.2. Further explored is the spread of Omicron BA.1, BA.2, and Delta AY.127 under different full and booster vaccination rate levels. An increase in full vaccination rates has primarily contributed to the reduction in areas within lower onset risk. An increase in the booster vaccination rate can promote a reduction in those areas within higher onset risk.

Conclusions

This study has provided a comprehensive investigation concerning the spatiotemporal symptom onset risk of Omicron BA.1, BA.2, and hamster-related Delta AY.127, and as such can contribute some help to countries and regions regarding the prevention of the emergence of such as these variants, on a strategic basis. Moreover, this study provides scientifically derived findings on the impact of full and booster vaccination campaigns working in the area of the reduction of symptomatic infections.

Sub-lineages of the SARS-CoV-2 Omicron variants: Characteristics and prevention

Since the start of the coronavirus disease 2019 (COVID-19) pandemic, new variants of severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) have emerged, accelerating the spread of the virus. Omicron was defined by the World Health Organization in November 2021 as the fifth "variant of concern" after Alpha, Beta, Gamma, and Delta. In recent months, Omicron has become the main epidemic strain. Studies have shown that Omicron carries more mutations than Alpha, Beta, Gamma, Delta, and wild-type, facilitating immune escape and accelerating its transmission. This review focuses on the Omicron variant's origin, transmission, main biological features, subvariants, mutations, immune escape, vaccination, and detection methods. We also discuss the appropriate preventive and therapeutic measures that should be taken to address the new challenges posed by the Omicron variant. This review is valuable to guide the surveillance, prevention, and development of vaccines and other therapies for Omicron variants. It is desirable to develop a more efficient vaccine against the Omicron variant and take more effective measures to constrain the spread of the epidemic and promote public health.

Delineating the spread and prevalence of SARS-CoV-2 Omicron sub-lineages (BA.1- BA.5) and Deltacron using wastewater in the Western Cape, South Africa

This study was one of the first to detect Omicron sublineages BA.4 and BA.5 in wastewater from South Africa. Spearman rank correlation analysis confirmed a strong positive correlation between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA in wastewater samples and clinical cases (r = 0.7749, P < .0001). SARS-CoV-2 viral load detected in wastewater, resulting from the Delta-driven third wave, was significantly higher than during the Omicron-driven fourth wave. Whole-genome sequencing confirmed presence of Omicron lineage defining mutations in wastewater with the first occurrence reported 23 November 2021 (BA.1 predominant). The variant spread rapidly, with prevalence of Omicron-positive wastewater samples rising to >80% by 10 January 2022 with BA.2 as the predominant sublineage by 10 March 2022, whilst on 18 April 2022 BA.4 and BA.5 were detected in selected wastewater sites. These findings demonstrate the value of wastewater-based epidemiology to monitor the spatiotemporal spread and potential origin of new Omicron sublineages.

Curcumin inhibits spike protein of new SARS-CoV-2 variant of concern (VOC) Omicron, an in silico study

BACKGROUND

Omicron (B.1.1.529), a variant of SARS-CoV-2 is currently spreading globally as a dominant strain. Due to multiple mutations at its Spike protein, including 15 amino acid substitutions at the receptor binding domain (RBD), Omicron is a variant of concern (VOC) and capable of escaping vaccine generated immunity. So far, no specific treatment regime is suggested for this VOC.

METHODS

The three-dimensional structure of the Spike RBD domain of Omicron variant was constructed by incorporating 15 amino acid substitutions to the Native Spike (S) structure and structural changes were compared that of the Native S. Seven phytochemicals namely Allicin, Capsaicin, Cinnamaldehyde, Curcumin, Gingerol, Piperine, and Zingeberene were docked with Omicron S protein and Omicron S-hACE2 complex. Further, molecular dynamic simulation was performed between Crcumin and Omicron S protein to evaluate the structural stability of the complex in the physiological environment and compared with that of the control drug Chloroquine.

RESULTS

Curcumin, among seven phytochemicals, was found to have the most substantial inhibitory potential with Omicron S protein. Further, it was found that curcumin could disrupt the Omicron S-hACE2 complex. The molecular dynamic simulation demonstrated that Curcumin could form a stable structure with Omicron S in the physiological environment.

CONCLUSION

To conclude, Curcumin can be considered as a potential therapeutic agent against the highly infectious Omicron variant of SARS-CoV-2.

SARS-CoV-2: phenotype, genotype, and characterization of different variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19), a major international public health concern. Because of very similar amino acid sequences of the seven domain names, SARS-CoV-2 belongs to the Coronavirinae subfamily of the family Coronaviridae, order Nidovirales, and realm Riboviria, placed in exceptional clusters, but categorized as a SARS-like species. As the RNA virus family with the longest genome, the Coronaviridae genome consists of a single strand of positive RNA (25-32 kb in length). Four major structural proteins of this genome include the spike (S), membrane (M), envelope (E), and the nucleocapsid (N) protein, all of which are encoded within the 3' end of the genome. By engaging with its receptor, angiotensin-converting enzyme 2 (ACE2), SARS-CoV-2 infects host cells. According to the most recent epidemiological data, as the illness spread globally, several genetic variations of SARS-CoV-2 appeared quickly, with the World Health Organization (WHO) naming 11 of them. Among these, seven SARS-CoV-2 subtypes have received the most attention. Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.617.2) are now designated as variations of concern (VOC) (B.1.1.529). Lambda (C.37) and Mu are variations of interest (VOI) (B.1.621). The remaining six are either being monitored or are no longer considered a threat. On the basis of studies done so far, antiviral drugs, antibiotics, glucocorticoids, recombinant intravenous immunoglobulin, plasma therapy, and IFN-α2b have been used to treat patients. Moreover, full vaccination is associated with lower infection and helps prevent transmission, but the risk of infection cannot be eliminated completely in vaccinated people.

Global Health Needs Modernized Containment Strategies to Prepare for the Next Pandemic

COVID-19 continues to be a public health crisis, while severely impacting global financial markets causing significant economic and social hardship. As with any emerging disease, pharmaceutical interventions required time, emphasizing the initial and continuing need for non-pharmaceutical interventions. We highlight the role of anthropological and historical perspectives to inform approaches to non-pharmaceutical interventions for future preparedness. The National Academy of Medicine, a not-for-profit, non-governmental US-based medical watchdog organization, published a key document early in the COVID-19 pandemic which points to inadequate quarantine and containment infrastructure as a significant obstacle to an effective pandemic response. In considering how to implement effective quarantine policies and infrastructure, we argue that it is essential to take a longitudinal approach to assess interventions that have been effective in past pandemics while simultaneously addressing and eliminating the negative socio-historical legacies of ineffective quarantine practices. Our overview reinforces the need for social equity and compassion when implementing containment.

Projections of the transmission of the Omicron variant for Toronto, Ontario, and Canada using surveillance data following recent changes in testing policies

At the end of 2021, with the rapid escalation of COVID19 cases due to the Omicron variant, testing centers in Canada were overwhelmed. To alleviate the pressure on the PCR testing capacity, many provinces implemented new strategies that promote self testing and adjust the eligibility for PCR tests, making the count of new cases underreported. We designed a novel compartmental model which captures the new testing guidelines, social behaviours, booster vaccines campaign and features of the newest variant Omicron. To better describe the testing eligibility, we considered the population divided into high risk and non-high-risk settings. The model is calibrated using data from January 1 to February 9, 2022, on cases and severe outcomes in Canada, the province of Ontario and City of Toronto. We conduct analyses on the impact of PCR testing capacity, self testing, different levels of reopening and vaccination coverage on cases and severe outcomes. Our results show that the total number of cases in Canada, Ontario and Toronto are 2.34 (95%CI: 1.22-3.38), 2.20 (95%CI: 1.15-3.72), and 1.97(95%CI: 1.13-3.41), times larger than reported cases, respectively. The current testing strategy is efficient if partial restrictions, such as limited capacity in public spaces, are implemented. Allowing more people to have access to PCR reduces the daily cases and severe outcomes; however, if PCR test capacity is insufficient, then it is important to promote self testing. Also, we found that reopening to a pre-pandemic level will lead to a resurgence of the infections, peaking in late March or April 2022. Vaccination and adherence to isolation protocols are important supports to the testing policies to mitigate any possible spread of the virus.

COVID-19 Omicron variant - Time for airborne precautions

Genetic mutations in SARS-CoV-2 have resulted in variants with more transmissibility and partial resistance to COVID-19 vaccines, as seen in the recently classified variant of concern (VOC) “Omicron”. The rapid spread has raised concerns about Omicron being airborne, which leads to a high risk of contamination in public premises, particularly among the frontline healthcare workers. Mandatory usage of protective face masks and respirators is highly recommended in order to break the chain of transmission. Furthermore, health authorities need to reassess the modes of transmission of VOCs and provide updated guidelines to the general public for its prevention.

Turning point: A new global COVID-19 wave or a signal of the beginning of the end of the global COVID-19 pandemic?

A new variant named Omicron (B.1.1.529), first identified in South Africa, has become of considerable interest to the World Health Organization. This variant differs from the other known major variants, as it carries a large number of unusual mutations, particularly in the spinous process protein and receptor binding domains. Some specific mutation sites make it vaccine resistant, highly infectious, and highly pathogenic. The world fears that the Omicron variant could be even more harmful than the previous major variant, given that it has emerged amid fierce competition to trigger a new global pandemic peak as infections in South Africa rise. However, some epidemiological evidence has emerged that the Omicron variant may produce milder patient symptoms. We speculate if the virulence of the Omicron variant will diminish as transmissibility increases, thereby signaling the beginning of the end for the global COVID-19 pandemic. Based on this view, we make recommendations for COVID-19 mitigation in the present and future. However, it will take a few weeks to determine the true threat posed by the Omicron variant and we need to be fully prepared for future outbreaks, regardless of their severity.