Omicron's molecular structure could help explain its global takeover

Estimating cumulative infection rate of COVID-19 after adjusting the dynamic zero-COVID policy in China

Background

At the end of 2022, China adjusted its coronavirus disease 2019 (COVID-19) prevention and control strategy. How this adjustment affected the cumulative infection rate is debated, and how second booster dose vaccination affected the pandemic remains unclear.

Methods

We collected COVID-19 case data for China's mainland from December 7, 2022, to January 7, 2023, reported by the World Health Organization. We also collected cumulative infection rate data from five large-scale population-based surveys. Next, we developed a dynamic transmission compartment model to characterize the COVID-19 pandemic and to estimate the cumulative infection rate. In addition, we estimated the impact of second booster vaccination on the pandemic by examining nine scenarios with different vaccination coverages (0%, 20%, and 40%) and vaccine effectiveness (30%, 50%, and 70%).

Results

By January 7, 2023, when COVID-19 was classified as a Class B infectious disease, the cumulative infection rate of the Omicron variant nationwide had reached 84.11% (95% confidence interval [CI]: 78.13%-90.08%). We estimated that the cumulative infection rates reached 50.50% (95% CI: 39.58%-61.43%), 56.15% (95% CI: 49.05%-67.22%), 73.82% (95% CI: 64.63%-83.02%), 75.76% (95% CI: 67.02%-84.50%), and 84.99% (95% CI: 79.45%-90.53%) on December 19, 20, 25, and 26, 2022, and on January 15, 2023, respectively. These results are similar to those of the population survey conducted on the corresponding dates, that is 46.93%, 61%, 63.52%, 74%, and 84.7%, respectively. In addition, we estimated that by January 7, 2023, the cumulative infection rate decreased to 29.55% (64.25%) if vaccination coverage and the effectiveness of second booster vaccination were 40% (20%) and 70% (30%), respectively.

Conclusion

We estimate that, in late 2022, the cumulative infection rate was approximately 84% and that second booster vaccination before the policy adjustment was effective in reducing this rate.

Evaluation of Vaccine Strategies among Healthcare Workers during COVID-19 Omicron Outbreak in Taiwan

BACKGROUND/OBJECTIVES

This study aimed to assess the reactogenicity and immunogenicity of various SARS-CoV-2 vaccines and compare their protective effects against COVID-19 among healthcare workers (HCWs) during the Omicron outbreak in Taiwan.

METHODS

Conducted from March 2021 to July 2023, this prospective observational study included healthy HCWs without prior COVID-19 immunization. Participants chose between adenovirus-vectored (AstraZeneca), mRNA (Moderna, BioNTech-Pfizer), and protein-based (Medigen, Novavax) vaccines. Blood samples were taken at multiple points to measure neutralizing antibody (nAb) titers, and adverse events (AEs) were recorded via questionnaires.

RESULTS

Of 710 HCWs, 668 (94.1%) completed three doses, and 290 (40.8%) received a fourth dose during the Omicron outbreak. AEs were more common with AstraZeneca and Moderna vaccines, while Medigen caused fewer AEs. Initial nAb titers were highest with Moderna but waned over time regardless of the vaccine. Booster doses significantly increased nAb titers, with the highest levels observed in Moderna BA1 recipients. The fourth dose significantly reduced COVID-19 incidence, with Moderna BA1 being the most effective.

CONCLUSIONS

Regular booster doses, especially with mRNA and adjuvant-protein vaccines, effectively enhance nAb levels and reduce infection rates, providing critical protection for frontline HCWs during variant outbreaks.

Detection of SARS-CoV-2 Variants Imported Through Land Borders at the Height of the COVID-19 Pandemic in Ghana, 2022

Background The World Health Organization recommends surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at points of entry to systematically collect and analyze data to inform decisions about the effective and appropriate use of resources needed for interventions. This study sought to determine the prevalence of SARS-CoV-2 and its variants imported into Ghana by travelers entering the country via land borders from February to July 2022. Methods A cross-sectional approach was employed, where recruited participants consented to the collection of oropharyngeal and nasopharyngeal samples. Specimens were analyzed for the presence of SARS-CoV-2 ribonucleic acid (RNA) using a commercially available VeriQ nCoV-OM COVID-19 Multiplex Detection kit. Amplicon sequencing protocols (ARTIC network, Oxford Nanopore Technologies (ONT), New England Biolabs, British Columbia Centre for Disease Control (BCCDC), COVID-19 Genomics UK (COG-UK), Canadian COVID-19 Genomics Network (CanCOGen), and ONT MinION) were used for SARS-CoV-2 sequencing. Logistic regression and phylogenetic analyses were conducted on the generated data. Results We detected a SARS-CoV-2 prevalence of 3.6% (170/4,621) among a total of 4,621 travelers screened. The average age of travelers was 32.11 ± 11.77, with the majority being male (68%, 3,132/4,621). After adjusting for educational status, household size, vaccination status, and study site, those with primary and tertiary education levels had 1.74 (95% CI: 1.16-2.62, P = 0.007) and 2.27 (95% CI: 1.27-4.05, P = 0.006) higher odds of testing positive for SARS-CoV-2 compared to those with no education. Vaccinated travelers had 0.65 odds (95% CI: 0.48-0.89, P = 0.007) of testing positive for SARS-CoV-2. The Omicron variant (B.1.1.529) emerged as the predominant lineage, constituting 77% (27/35) of isolates, compared to Alpha, Delta, and Recombinant variants. Phylogenetic analysis corroborated this finding, highlighting Delta and Omicron as the dominant circulating SARS-CoV-2 variants. Notably, Ghanaian strains from this study clustered with global variants, suggesting multiple introductions, likely through land borders. Conclusion A low prevalence of SARS-CoV-2 was recorded in this study, prompting the decision to reopen land borders and ease pandemic-related travel restrictions. Omicron was identified as the dominant variant. These findings emphasize the crucial role of routine surveillance at port health and advocate for a collaborative approach to addressing public health crises, preventing unnecessary travel and trade restrictions through data-based decision-making.

Second Boost of Omicron SARS-CoV-2 S1 Subunit Vaccine Induced Broad Humoral Immune Responses in Elderly Mice

Currently approved COVID-19 vaccines prevent symptomatic infection, hospitalization, and death from the disease. However, repeated homologous boosters, while considered a solution for severe forms of the disease caused by new SARS-CoV-2 variants in elderly individuals and immunocompromised patients, cannot provide complete protection against breakthrough infections. This highlights the need for alternative platforms for booster vaccines. In our previous study, we assessed the boost effect of the SARS-CoV-2 Beta S1 recombinant protein subunit vaccine (rS1Beta) in aged mice primed with an adenovirus-based vaccine expressing SARS-CoV-2-S1 (Ad5.S1) via subcutaneous injection or intranasal delivery, which induced robust humoral immune responses (1). In this follow-up study, we demonstrated that a second booster dose of a non-adjuvanted recombinant Omicron (BA.1) S1 subunit vaccine with Toll-like receptor 4 (TLR4) agonist RS09 (rS1RS09OM) was effective in stimulating strong S1-specific immune responses and inducing significantly high neutralizing antibodies against the Wuhan, Delta, and Omicron variants in 100-week-old mice. Importantly, the second booster dose elicits cross-reactive antibody responses, resulting in ACE2 binding inhibition against the spike protein of SARS-CoV-2 variants, including Omicron (BA.1) and its subvariants. Interestingly, the levels of IgG and neutralizing antibodies correlated with the level of ACE2 inhibition in the booster serum samples, although Omicron S1-specific IgG level showed a weaker correlation compared to Wuhan S1-specific IgG level. Furthermore, we compared the immunogenic properties of the rS1 subunit vaccine in young, middle-aged, and elderly mice, resulting in reduced immunogenicity with age, especially an impaired Th1-biased immune response in aged mice. Our findings demonstrate that the new variant of concern (VOC) rS1 subunit vaccine as a second booster has the potential to offer cross-neutralization against a broad range of variants and to improve vaccine effectiveness against newly emerging breakthrough SARS-CoV-2 variants in elderly individuals who were previously primed with the authorized vaccines.

Rational prediction of immunogenicity clustering through cross-reactivity analysis of thirteen SARS-CoV-2 variants

SARS-CoV-2 breakthrough infections in vaccinated individuals underscore the threat posed by continuous mutating variants, such as Omicron, to vaccine-induced immunity. This necessitates the search for broad-spectrum immunogens capable of countering infections from such variants. This study evaluates the immunogenicity relationship among SARS-CoV-2 variants, from D614G to XBB, through Guinea pig vaccination, covering D614G, Alpha, Beta, Gamma, Delta, BA.1, BA.2, BA.2.75, BA.2.75.2, BA.5, BF.7, BQ.1.1, and XBB, employing three immunization strategies: three-dose monovalent immunogens, three-dose bivalent immunogens, and a two-dose vaccination with D614G followed by a booster immunization with a variant strain immunogen. Three distinct immunogenicity clusters were identified: D614G, Alpha, Beta, Gamma, and Delta as cluster 1, BA.1, BA.2, and BA.2.75 as cluster 2, BA.2.75.2, BA.5, BF.7, BQ.1.1, and XBB as cluster 3. Broad-spectrum protection could be achieved through a combined immunization strategy using bivalent immunogens or D614G and XBB, or two initial D614G vaccinations followed by two XBB boosters. A comparison of neutralizing antibody levels induced by XBB boosting and equivalent dosing of D614G and XBB revealed that the XBB booster produced higher antibody levels. The study suggests that vaccine antigen selection should focus on the antigenic alterations among variants, eliminating the need for updating vaccine components for each variant.

Nanotechnology in the COVID-19 era: Carbon-based nanomaterials as a promising solution

The Coronavirus Disease 2019 (COVID-19) pandemic has led to collaboration between nanotechnology scientists, industry stakeholders, and clinicians to develop solutions for diagnostics, prevention, and treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections. Nanomaterials, including carbon-based materials (CBM) such as graphene and carbon nanotubes, have been studied for their potential in viral research. CBM unique effects on microorganisms, immune interaction, and sensitivity in diagnostics have made them a promising subject of SARS-CoV-2 research. This review discusses the interaction of CBM with SARS-CoV-2 and their applicability, including CBM physical and chemical properties, the known interactions between CBM and viral components, and the proposed prevention, treatment, and diagnostics uses.

Global Distribution, Dispersal Patterns, and Trend of Several Omicron Subvariants of SARS-CoV-2 across the Globe

Our study aims to describe the global distribution and dispersal patterns of the SARS-CoV-2 Omicron subvariants. Genomic surveillance data were extracted from the CoV-Spectrum platform, searching for BA.1*, BA.2*, BA.3*, BA.4*, and BA.5* variants by geographic region. BA.1* increased in November 2021 in South Africa, with a similar increase across all continents in early December 2021. BA.1* did not reach 100% dominance in all continents. The spread of BA.2*, first described in South Africa, differed greatly by geographic region, in contrast to BA.1*, which followed a similar global expansion, firstly occurring in Asia and subsequently in Africa, Europe, Oceania, and North and South America. BA.4* and BA.5* followed a different pattern, where BA.4* reached high proportions (maximum 60%) only in Africa. BA.5* is currently, by Mid-August 2022, the dominant strain, reaching almost 100% across Europe, which is the first continent aside from Africa to show increasing proportions, and Asia, the Americas, and Oceania are following. The emergence of new variants depends mostly on their selective advantage, translated as enhanced transmissibility and ability to invade people with existing immunity. Describing these patterns is useful for a better understanding of the epidemiology of the VOCs' transmission and for generating hypotheses about the future of emerging variants.

High-Throughput Molecular Dynamics-Based Alchemical Free Energy Calculations for Predicting the Binding Free Energy Change Associated with the Selected Omicron Mutations in the Spike Receptor-Binding Domain of SARS-CoV-2

The ongoing pandemic caused by SARS-CoV-2 has gone through various phases. Since the initial outbreak, the virus has mutated several times, with some lineages showing even stronger infectivity and faster spread than the original virus. Among all the variants, omicron is currently classified as a variant of concern (VOC) by the World Health Organization, as the previously circulating variants have been replaced by it. In this work, we have focused on the mutations observed in omicron sub lineages BA.1, BA.2, BA.4 and BA.5, particularly at the receptor-binding domain (RBD) of the spike protein that is responsible for the interactions with the host ACE2 receptor and binding of antibodies. Studying such mutations is particularly important for understanding the viral infectivity, spread of the disease and for tracking the escape routes of this virus from antibodies. Molecular dynamics (MD) based alchemical free energy calculations have been shown to be very accurate in predicting the free energy change, due to a mutation that could have a deleterious or a stabilizing effect on either the protein itself or its binding affinity to another protein. Here, we investigated the significance of five spike RBD mutations on the stability of the spike protein binding to ACE2 by free energy calculations using high throughput MD simulations. For comparison, we also used conventional MD simulations combined with a Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) based approach, and compared our results with the available experimental data. Overall, the alchemical free energy calculations performed far better than the MM-GBSA approach in predicting the individual impact of the mutations. When considering the experimental variation, the alchemical free energy method was able to produce a relatively accurate prediction for N501Y, the mutant that has previously been reported to increase the binding affinity to hACE2. On the other hand, the other individual mutations seem not to have a significant effect on the spike RBD binding affinity towards hACE2.

COVID-19 vaccine update: vaccine effectiveness, SARS-CoV-2 variants, boosters, adverse effects, and immune correlates of protection

Coronavirus Disease 2019 (COVID-19) has been the most severe public health challenge in this century. Two years after its emergence, the rapid development and deployment of effective COVID-19 vaccines have successfully controlled this pandemic and greatly reduced the risk of severe illness and death associated with COVID-19. However, due to its ability to rapidly evolve, the SARS-CoV-2 virus may never be eradicated, and there are many important new topics to work on if we need to live with this virus for a long time. To this end, we hope to provide essential knowledge for researchers who work on the improvement of future COVID-19 vaccines. In this review, we provided an up-to-date summary for current COVID-19 vaccines, discussed the biological basis and clinical impact of SARS-CoV-2 variants and subvariants, and analyzed the effectiveness of various vaccine booster regimens against different SARS-CoV-2 strains. Additionally, we reviewed potential mechanisms of vaccine-induced severe adverse events, summarized current studies regarding immune correlates of protection, and finally, discussed the development of next-generation vaccines.

A comprehensive analysis of the mutational landscape of the newly emerging Omicron (B.1.1.529) variant and comparison of mutations with VOCs and VOIs

The Omicron variant is spreading rapidly throughout several countries. Thus, we comprehensively analyzed Omicron's mutational landscape and compared mutations with VOC/VOI. We analyzed SNVs throughout the genome, and AA variants (NSP and SP) in VOC/VOI, including Omicron. We generated heat maps to illustrate the AA variants with high mutation prevalence (> 75% frequency) of Omicron, which demonstrated eight mutations with > 90% prevalence in ORF1a and 29 mutations with > 75% prevalence in S-glycoprotein. A scatter plot for Omicron and VOC/VOI's cluster evaluation was computed. We performed a risk analysis of the antibody-binding risk among four mutations (L452, F490, P681, D614) and observed three mutations (L452R, F490S, D614G) destabilized antibody interactions. Our comparative study evaluated the properties of 28 emerging mutations of the S-glycoprotein of Omicron, and the ΔΔG values. Our results showed K417N with minimum and Q954H with maximum ΔΔG value. Furthermore, six important RBD mutations (G339D, S371L, N440K, G446S, T478K, Q498R) were chosen for comprehensive analysis for stabilizing/destabilizing properties and molecular flexibility. The G339D, S371L, N440K, and T478K were noted as stable mutations with 0.019 kcal/mol, 0.127 kcal/mol, 0.064 kcal/mol, and 1.009 kcal/mol. While, G446S and Q498R mutations showed destabilizing results. Simultaneously, among six RBD mutations, G339D, G446S, and Q498R mutations increased the molecular flexibility of S-glycoprotein. This study depicts the comparative mutational pattern of Omicron and other VOC/VOI, which will help researchers to design and deploy novel vaccines and therapeutic antibodies to fight against VOC/VOI, including Omicron.

Wastewater-based epidemiology: A Brazilian SARS-COV-2 surveillance experience

Since 2020, developed countries have rapidly shared both publicly and academically relevant wastewater surveillance information. Data on SARS-CoV-2 circulation is pivotal for guiding public health policies and improving the COVID-19 pandemic response. Conversely, low- and middle-income countries, such as Latin America and the Caribbean, showed timid activities in the Wastewater-Based Epidemiology (WBE) context. In these countries, isolated groups perform viral wastewater monitoring, and the data are unevenly shared or accessible to health agencies and the scientific community. This manuscript aims to highlight the relevance of a multiparty effort involving research, public health, and governmental agencies to support usage of WBE methodology to its full potential during the COVID-19 pandemic as part of a joint One Health surveillance approach. Thus, in this study, we explored the results obtained from wastewater surveillance in different regions of Brazil as a part of the COVID-19 Wastewater Monitoring Network ANA (National Water Agency), MCTI (Ministry of Science, Technology, and Innovations) and MS (Ministry of Health). Over the epidemiological weeks of 2021 and early 2022, viral RNA concentrations in wastewater followed epidemiological trends and variations. The highest viral loads in wastewater samples were detected during the second Brazilian wave of COVID-19. Corroborating international reports, our experience demonstrated usefulness of the WBE approach in viral surveillance. Wastewater surveillance allows hotspot identification, and therefore, early public health interventions. In addition, this methodology allows tracking of asymptomatic and oligosymptomatic individuals, who are generally underreported, especially in emerging countries with limited clinical testing capacity. Therefore, WBE undoubtedly contributes to improving public health responses in the context of this pandemic, as well as other sanitary emergencies.

Perspective Chapter: SARS-CoV-2 Variants - Two Years Post-Onset of the Pandemic

Since the pandemic began in China in December 2019, thousands of variants of SARS-CoV-2 have emerged globally since late 2020. The World Health Organization (WHO) defined the SARS-CoV-2 variant of concern (VOC) as a variant with increased transmissibility, virulence, and decreased response to available diagnostics, vaccines, and therapeutics. Areas of the emerging variant of concern arise from countries like the United Kingdom, South Africa, Brazil, and India. These mutations carry a lineage from N501Y, D614G, N439K, Y453F, and others, which are globally dominated by clades 20A, 20B, and 20C. SARS-CoV-2 VOC emerged after 11 months of evolution since the onset through massive human-to-human transmission with five major VOCs recognized by the WHO, namely Alpha, Beta, Gamma, Delta, and Omicron. Their emergence could be attributed to changing immunological dynamics in the human population, which has resulted in resistance or escape from neutralizing antibodies, or to mutations and/or recombinations that increase transmission or pathogenicity. This literature review intends to identify and report on SARS-CoV-2 variants that have evolved two years post-onset of the pandemic and their disease implications.

Does pre-existing immunity determine the course of SARS-CoV-2 infection in health-care workers? Single-center experience

OBJECTIVES

To assess the severity of symptoms, duration of infection and viral loads of health-care workers (HCWs) who tested positive for Coronavirus disease 2019 (COVID-19) during Omicron's prevalence, in regard to vaccination and previous infection.

METHODS

During 2 weeks of highest rate of COVID-19 cases in Bosnia and Herzegovina, the positive nasopharyngeal swabs were analysed in 141 HCWs by reverse transcription quantitative PCR, targeting four different genes: RdRp, E, N and nsp14. Uniformed questionnaire was used to collect relevant sociodemographic and epidemiological data from HCWs divided into four groups: unvaccinated/not previously infected (group 1); unvaccinated/previously infected (group 2); vaccinated/not previously infected (group 3); and vaccinated/previously infected (group 4).

RESULTS

We observed that occurrence of fever and smell or taste loss were more frequent in group 1 (86.4% and 25%) and group 3 (76.9% and 19.2%), in comparison to group 2 (64.4% and 6.7%) and group 4 (69.2% and 3.8%), (p = 0.023 and p = 0.003). Although statistically not significant, group 2 (61.9%), group 3 (65.4%), and group 4 (70.8%) experienced negativization within 7 days of positive RT-qPCR test, whereas 51.2% of HCWs from group 1 tested negative later on. There is no significant difference between all four groups regarding Ct values of analysed genes.

CONCLUSION

During Omicron's prevalence, the vaccination had less substantial effect on symptomatic disease among HCWs, while fever and loss of smell or taste were considerably less likely to occur upon reinfection. Since viral loads and negativization periods do not seem to significantly vary, irrespective of pre-existing immunity, systemic vaccination and mask-wearing should still be considered among HCWs.