The End or a New Era of Development of SARS-CoV-2 Virus: Genetic Variants Responsible for Severe COVID-19 and Clinical Efficacy of the Most Commonly Used Vaccines in Clinical Practice

Booster vaccines dose reduced mortality in hospitalized COVID-19 patients requiring oxygen supplementation: Evidence from the Beijing Omicron outbreak

To assess the impact of vaccines on clinical outcomes among hospitalized COVID-19-infected patients requiring oxygen supplementation during the Beijing Omicron outbreak. We conducted a retrospective cohort study at Beijing Chaoyang Hospital, Capital Medical University, from November 15, 2022, to March 31, 2023. Vaccination statuses were categorized into 3 doses, 2 doses, and unvaccinated (0 dose). The primary outcome was 28-day all-cause mortality. Secondary outcomes included poor outcomes, intensive care unit admission, cardiovascular thromboembolism events, and hospital readmission. Among the included patients, 117 were 2 doses, 285 received booster doses, and 503 were unvaccinated. After propensity score inverse probability weighting, the 3 doses group showed a significantly lower 28-day all-cause mortality compared to the unvaccinated group (inverse probability of treatment weighting-adjusted HR: 0.64, 95% CI: 0.50-0.81). No significant difference was observed in all-cause mortality between the 2 doses and unvaccinated groups. No significant differences were observed in secondary outcome analyses when comparing the 3 doses or 2 doses group to the unvaccinated group. Subgroup analysis revealed significant benefits of booster vaccination in patients with shorter symptom duration, lower Charlson Comorbidity Index, and without immunosuppression status. Our study highlights the significant reduction in all-cause mortality among hospitalized Omicron-infected patients who received a third dose vaccine. These findings underscore the importance of prioritizing booster vaccinations, especially among the elderly. Further research is warranted to confirm and extend these observations.

COVID-19 Vaccination Reporting and Adverse Event Analysis in Taiwan

The COVID-19 pandemic necessitated an urgent global response in vaccine deployment, achieving over 70.6% global vaccination coverage with at least one dose. This study focuses on Taiwan's vaccine administration and adverse event reporting, set against a global backdrop. Using data from Taiwan's Vaccine Adverse Event Reporting System (VAERS) and global vaccination data, this study investigates vaccine safety and the public health implications of vaccination strategies from local and global perspectives. Taiwan's proactive approach, resulting in high vaccination rates, provides a case study for the monitoring and management of vaccine-related adverse events. This study offers insights into the safety profiles of various COVID-19 vaccines and further explores the implications of adverse event reporting rates for vaccine policy and public health strategies. The comparative analysis reveals that, while vaccination has been effective in controlling the virus's spread, safety monitoring remains critical for maintaining public trust. It underscores the necessity of enhanced surveillance and the importance of transparent and tailored risk communication to support informed public health decisions. The findings aim to contribute to the global dialogue on vaccine safety, equitable distribution, evidence-based policy-making, and development of mitigation measures with consideration of local demographics in the ongoing fight against COVID-19.

Evolution of a Distinct SARS-CoV-2 Lineage Identified during an Investigation of a Hospital Outbreak

The SARS-CoV-2 virus steadily evolves, and numerous antigenically distinct variants have emerged over the past three years. Tracking the evolution of the virus would help us understand the process that generates the diverse variants and predict the future evolutionary trajectory of SARS-CoV-2. Here, we report the evolutionary trajectory of a unique Omicron lineage identified during an outbreak investigation that occurred in a residence unit in the healthcare system. The new lineage had four distinct non-synonymous and two distinct synonymous mutations apart from its parental lineage. Since this lineage of virus was exclusively found during the outbreak, we were able to track the detailed evolutionary history of the entire lineage along the transmission path. Furthermore, we estimated the evolutionary rate of the SARS-CoV-2 Omicron variant from the analysis of the evolution of the lineage. This new Omicron sub-lineage acquired 3 mutations in a 12-day period, and the evolutionary rate was estimated as 3.05 × 10-3 subs/site/year. This study provides more insight into an ever-evolving virus.

Evaluation of the reasons for the non‑COVID‑19 status: A socio‑demographic analysis

The present study aimed to evaluate the reasons behind the fact that some individuals did not contract coronavirus disease 2019 (COVID-19), considering certain socio-demographic data. The present cross-sectional study was conducted at a state hospital between February 1, 2022 and March 1, 2022. The study group consisted of individuals who never had COVID-19, and the control group consisted of individuals who did not know at the time of the study whether they had COVID-19. A data collection form consisting of 29 questions created based on a literature review was used. A total of 2,958 subjects (study group, 669; control group, 2,289) were included; of these, 53.1% were females and 46.9% were males. It was found that housewives (P<0.001), individuals with secondary school and lower education levels (P=0.02), those residing in rural areas (P=0.003), those who received a combination vaccine (P<0.001), those with chronic diseases (P=0.016), those who consumed more fruits (P=0.001), those who used N95 masks (P=0.002), those with pets (P<0.001) and those who did not follow the news regarding COVID-19 (P=0.016) had a higher probability of not contracting COVID-19. On the whole, the present study observed that socio-demographic factors affected the non-COVID-19 status.

Neutralization of Different Variants of SARS-CoV-2 by a F(ab')2 Preparation from Sera of Horses Immunized with the Viral Receptor Binding Domain

The Receptor Binding Domain (RBD) of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is the functional region of the viral Spike protein (S), which is involved in cell attachment to target cells. The virus has accumulated progressively mutations in its genome, particularly in the RBD region, many of them associated with immune evasion of the host neutralizing antibodies. Some of the viral lineages derived from this evolution have been classified as Variant of Interest (VOI) or Concern (VOC). The neutralizing capacity of a F(ab')2 preparation from sera of horses immunized with viral RBD was evaluated by lytic plaque reduction assay against different SARS-CoV-2 variants. A F(ab')2 preparation of a hyperimmune serum after nine immunizations with RBD exhibited a high titer of neutralizing antibodies against the ancestral-like strain (1/18,528). A reduction in the titer of the F(ab')2 preparation was observed against the different variants tested compared to the neutralizing activity against the ancestral-like strain. The highest reduction in the neutralization titer was observed for the Omicron VOC (4.7-fold), followed by the Mu VOI (2.6), Delta VOC (1.8-fold), and Gamma VOC (1.5). Even if a progressive reduction in the neutralizing antibodies titer against the different variants evaluated was observed, the serum still exhibited a neutralizing titer against the Mu VOI and the Omicron VOC (1/7113 and 1/3918, respectively), the evaluated strains most resistant to neutralization. Therefore, the preparation retained neutralizing activity against all the strains tested.

Molecular Mechanisms of Pathogenesis, Prevention, and Therapy of COVID-19: Summarizing the Results of 2022

The aim of this Special Issue is to analyze the key patterns of the 2019 coronavirus disease pandemic (COVID-19), the biology of SARS-CoV-2 (severe-acute-respiratory-syndrome-related coronavirus 2, formerly 2019-nCoV), and the characteristics of the human body's response to the invasion of this virus [...].

Applications of time series analysis in epidemiology: Literature review and our experience during COVID-19 pandemic

Time series analysis is a valuable tool in epidemiology that complements the classical epidemiological models in two different ways: Prediction and forecast. Prediction is related to explaining past and current data based on various internal and external influences that may or may not have a causative role. Forecasting is an exploration of the possible future values based on the predictive ability of the model and hypothesized future values of the external and/or internal influences. The time series analysis approach has the advantage of being easier to use (in the cases of more straightforward and linear models such as Auto-Regressive Integrated Moving Average). Still, it is limited in forecasting time, unlike the classical models such as Susceptible-Exposed-Infectious-Removed. Its applicability in forecasting comes from its better accuracy for short-term prediction. In its basic form, it does not assume much theoretical knowledge of the mechanisms of spreading and mutating pathogens or the reaction of people and regulatory structures (governments, companies, etc.). Instead, it estimates from the data directly. Its predictive ability allows testing hypotheses for different factors that positively or negatively contribute to the pandemic spread; be it school closures, emerging variants, etc. It can be used in mortality or hospital risk estimation from new cases, seroprevalence studies, assessing properties of emerging variants, and estimating excess mortality and its relationship with a pandemic.

In Vitro Efficacy of Antivirals and Monoclonal Antibodies against SARS-CoV-2 Omicron Lineages XBB.1.9.1, XBB.1.9.3, XBB.1.5, XBB.1.16, XBB.2.4, BQ.1.1.45, CH.1.1, and CL.1

The spread of COVID-19 continues, expressed by periodic wave-like increases in morbidity and mortality. The reason for the periodic increases in morbidity is the emergence and spread of novel genetic variants of SARS-CoV-2. A decrease in the efficacy of monoclonal antibodies (mAbs) has been reported, especially against Omicron subvariants. There have been reports of a decrease in the efficacy of specific antiviral drugs as a result of mutations in the genes of non-structural proteins. This indicates the urgent need for practical healthcare to constantly monitor pathogen variability and its effect on the efficacy of preventive and therapeutic drugs. As part of this study, we report the results of the continuous monitoring of COVID-19 in Moscow using genetic and virological methods. As a result of this monitoring, we determined the dominant genetic variants and identified the variants that are most widespread, not only in Moscow, but also in other countries. A collection of viruses from more than 500 SARS-CoV-2 isolates has been obtained and characterized. The genetic lines XBB.1.9.1, XBB.1.9.3, XBB.1.5, XBB.1.16, XBB.2.4, BQ.1.1.45, CH.1.1, and CL.1, representing the greatest concern, were identified among the dominant variants. We studied the in vitro efficacy of mAbs Tixagevimab + Cilgavimab (Evusheld), Sotrovimab, Regdanvimab, Casirivimab + Imdevimab (Ronapreve), and Bebtelovimab, as well as the specific antiviral drugs Remdesivir, Molnupiravir, and Nirmatrelvir, against these genetic lines. At the current stage of the COVID-19 pandemic, the use of mAbs developed against early SARS-CoV-2 variants has little prospect. Specific antiviral drugs retain their activity, but further monitoring is needed to assess the risk of their efficacy being reduced and adjust recommendations for their use.

Effectiveness and safety of COVID-19 vaccines in patients with oncological diseases: State-of-the-art

Although the coronavirus disease 2019 (COVID-19) pandemic was declared to be no longer “a public health emergency of international concern” with its wide range of clinical manifestations and late complications, severe acute respiratory syndrome coronavirus 2 infection proved to be a serious threat, especially to the elderly and patients with comorbidities. Patients with oncologic diseases are vulnerable to severe infection and death. Indeed, patients with oncohematological diseases have a higher risk of severe COVID-19 and impaired post-vaccination immunity. Unfortunately, cancer patients are usually excluded from vaccine trials and investigations of post-vaccinal immune responses and the effectiveness of the vaccines. We aimed to elucidate to what extent patients with cancer are at increased risk of developing severe COVID-19 and what is their overall case fatality rate. We also present the current concept and evidence on the effectiveness and safety of COVID-19 vaccines, including boosters, in oncology patients. In conclusion, despite the considerably higher mortality in the cancer patient group than the general population, countries with high vaccination rates have demonstrated trends toward improved survival of cancer patients early and late in the pandemic.