Comparative Effectiveness of COVID-19 Vaccines in Preventing Infections and Disease Progression from SARS-CoV-2 Omicron BA.5 and BA.2, Portugal

Population Behavior Changes Underlying Phasic Shifts of SARS-CoV-2 Exposure Settings Across 3 Omicron Epidemic Waves in Hong Kong: Prospective Cohort Study

BACKGROUND

Exposure risk was shown to have affected individual susceptibility and the epidemic spread of COVID-19. The dynamics of risk by and across exposure settings alongside the variations following the implementation of social distancing interventions are understudied.

OBJECTIVE

This study aims to examine the population's trajectory of exposure risk in different settings and its association with SARS-CoV-2 infection across 3 consecutive Omicron epidemic waves in Hong Kong.

METHODS

From March to June 2022, invitation letters were posted to 41,132 randomly selected residential addresses for the recruitment of households into a prospective population cohort. Through web-based monthly surveys coupled with email reminders, a representative from each enrolled household self-reported incidents of SARS-CoV-2 infections, COVID-19 vaccination uptake, their activity pattern in the workplace, and daily and social settings in the preceding month. As a proxy of their exposure risk, the reported activity trend in each setting was differentiated into trajectories based on latent class growth analyses. The associations of different trajectories of SARS-CoV-2 infection overall and by Omicron wave (wave 1: February-April; wave 2: May-September; wave 3: October-December) in 2022 were evaluated by using Cox proportional hazards models and Kaplan-Meier analysis.

RESULTS

In total, 33,501 monthly responses in the observation period of February-December 2022 were collected from 5321 individuals, with 41.7% (2221/5321) being male and a median age of 46 (IQR 34-57) years. Against an expanding COVID-19 vaccination coverage from 81.9% to 95.9% for 2 doses and 20% to 77.7% for 3 doses, the cumulative incidence of SARS-CoV-2 infection escalated from <0.2% to 25.3%, 32.4%, and 43.8% by the end of waves 1, 2, and 3, respectively. Throughout February-December 2022, 52.2% (647/1240) of participants had worked regularly on-site, 28.7% (356/1240) worked remotely, and 19.1% (237/1240) showed an assorted pattern. For daily and social settings, 4 and 5 trajectories were identified, respectively, with 11.5% (142/1240) and 14.6% (181/1240) of the participants gauged to have a high exposure risk. Compared to remote working, working regularly on-site (adjusted hazard ratio [aHR] 1.47, 95% CI 1.19-1.80) and living in a larger household (aHR 1.12, 95% CI 1.06-1.18) were associated with a higher risk of SARS-CoV-2 infection in wave 1. Those from the highest daily exposure risk trajectory (aHR 1.46, 95% CI 1.07-2.00) and the second highest social exposure risk trajectory (aHR 1.52, 95% CI 1.18-1.97) were also at an increased risk of infection in waves 2 and 3, respectively, relative to the lowest risk trajectory.

CONCLUSIONS

In an infection-naive population, SARS-CoV-2 transmission was predominantly initiated at the workplace, accelerated in the household, and perpetuated in the daily and social environments, as stringent restrictions were scaled down. These patterns highlight the phasic shift of exposure settings, which is important for informing the effective calibration of targeted social distancing measures as an alternative to lockdown.

A DFTB study on the electronic response of encapsulated DNA nucleobases onto chiral CNTs as a sequencer

Sequencing the DNA nucleobases is essential in the diagnosis and treatment of many diseases related to human genes. In this article, the encapsulation of DNA nucleobases with some of the important synthesized chiral (7, 6), (8, 6), and (10, 8) carbon nanotubes were investigated. The structures were modeled by applying density functional theory based on tight binding method (DFTB) by considering semi-empirical basis sets. Encapsulating DNA nucleobases on the inside of CNTs caused changes in the electronic properties of the selected chiral CNTs. The results confirmed that van der Waals (vdW) interactions, π-orbitals interactions, non-bonded electron pairs, and the presence of high electronegative atoms are the key factors for these changes. The result of electronic parameters showed that among the CNTs, CNT (8, 6) is a suitable choice in sequencing guanine (G) and cytosine (C) DNA nucleobases. However, they are not able to sequence adenine (A) and thymine (T). According to the band gap energy engineering approach and absorption energy, the presence of G and C DNA nucleobases decreased the band gap energy of CNTs. Hence selected CNTs suggested as biosensor substrates for sequencing G and C DNA nucleobases.

Understanding spatiotemporal patterns of COVID-19 incidence in Portugal: A functional data analysis from August 2020 to March 2022

During the SARS-CoV-2 pandemic, governments and public health authorities collected massive amounts of data on daily confirmed positive cases and incidence rates. These data sets provide relevant information to develop a scientific understanding of the pandemic's spatiotemporal dynamics. At the same time, there is a lack of comprehensive approaches to describe and classify patterns underlying the dynamics of COVID-19 incidence across regions over time. This seriously constrains the potential benefits for public health authorities to understand spatiotemporal patterns of disease incidence that would allow for better risk communication strategies and improved assessment of mitigation policies efficacy. Within this context, we propose an exploratory statistical tool that combines functional data analysis with unsupervised learning algorithms to extract meaningful information about the main spatiotemporal patterns underlying COVID-19 incidence on mainland Portugal. We focus on the timeframe spanning from August 2020 to March 2022, considering data at the municipality level. First, we describe the temporal evolution of confirmed daily COVID-19 cases by municipality as a function of time, and outline the main temporal patterns of variability using a functional principal component analysis. Then, municipalities are classified according to their spatiotemporal similarities through hierarchical clustering adapted to spatially correlated functional data. Our findings reveal disparities in disease dynamics between northern and coastal municipalities versus those in the southern and hinterland. We also distinguish effects occurring during the 2020-2021 period from those in the 2021-2022 autumn-winter seasons. The results provide proof-of-concept that the proposed approach can be used to detect the main spatiotemporal patterns of disease incidence. The novel approach expands and enhances existing exploratory tools for spatiotemporal analysis of public health data.

Effectiveness of primary series, first, and second booster vaccination of monovalent mRNA COVID-19 vaccines against symptomatic SARS-CoV-2 infections and severe diseases during the SARS-CoV-2 omicron BA.5 epidemic in Japan: vaccine effectiveness real-time surveillance for SARS-CoV-2 (VERSUS)

BACKGROUND

This study aimed to evaluate VE of primary, first, and second booster ancestral-strain monovalent mRNA COVID-19 vaccination against symptomatic infections and severe diseases in Japan.

METHODS

We conducted a test-negative case-control study. We included medically attended episodes and hospitalizations involving individuals aged ≥ 16 with signs and symptoms from July to November 2022, when Omicron BA.5 was dominant nationwide. To evaluate VE, we calculated adjusted ORs of vaccination among test-positive versus test-negative individuals using a mixed-effects logistic regression.

RESULTS

For VE against symptomatic infections among individuals aged 16 to 59, VE of primary vaccination at > 180 days was 26.1% (95% CI: 10.6-38.8%); VE of the first booster was 58.5% (48.4-66.7%) at ≤ 90 days, decreasing to 41.1% (29.5-50.8%) at 91 to 180 days. For individuals aged ≥ 60, VE of the first booster was 42.8% (1.7-66.7%) at ≤ 90 days, dropping to 15.4% (-25.9-43.2%) at 91 to 180 days, and then increasing to 44.0% (16.4-62.5%) after the second booster. For VE against severe diseases, VE of the first and second booster was 77.3% (61.2-86.7%) at ≤ 90 days and 55.9% (23.4-74.6%) afterward.

CONCLUSION

mRNA booster vaccination provided moderate protection against symptomatic infections and high-level protection against severe diseases during the BA.5 epidemic in Japan.

Effectiveness of the Original COVID-19 Vaccine against COVID-19 Exacerbations during the Omicron Wave: A Population-based Study in Okayama, Japan

Introduction

In Japan, approximately 97 million individuals have received their primary two doses of coronavirus disease 2019 (COVID-19) vaccine at the end of 2022. In this study, we aim to examine the effectiveness of the primary vaccines and compare its efficacy to booster vaccine shots in terms of preventing COVID-19 exacerbations during the Omicron-predominant period in Japan.

Methods

For this analysis, we have collected all the confirmed COVID-19-positive cases from different medical institutions in Okayama City and have also utilized the information from the public Vaccination Record System. Taking the number of vaccinations into consideration, we then conducted a population-based study to assess the effectiveness of the two primary vaccine doses in preventing COVID-19 exacerbations during the Omicron waves. Our primary and secondary outcomes were COVID-19 exacerbations with respiratory failure (i.e., oxygen saturation on room air ≤ 93%, requiring supplemental oxygen), intensive care unit admission and/or mechanical ventilator requirement, or death, in accordance with the Japanese COVID-19 guidelines, and pneumonia during the course of COVID-19 infection, respectively.

Results

In total, 95,329 COVID-19-positive individuals, aged 5 years and above, were included in this analysis (study period from January 1 to September 10, 2022). As per our findings, the effectiveness of the primary two doses against COVID-19 exacerbations compared with those who had never been vaccinated was 55.5% (95% confidential interval [CI]: 32.6-71.7), whereas it was higher after the third dose (76.9%; 95% CI: 66.7-84.0) and the fourth dose (75.7%; 95% CI: 58.8-85.7). Effectiveness was sustained for ≥ 5 months after the third vaccination, and preventive effectiveness was observed in individuals aged ≥ 65 years.

Conclusions

As per the results of this study, we can conclude that the efficacy of the primary two doses of SARS-CoV-2 vaccine can be further strengthened in terms of preventing COVID-19 exacerbations by administering third and fourth booster vaccine shots. The additional bivalent vaccine is anticipated to further increase its efficacy against the Omicron strain, suggesting that individuals who have not received their booster shots yet should consider getting them to prevent COVID-19 exacerbations.

Vaccine breakthrough and rebound infections modeling: Analysis for the United States and the ten U.S. HHS regions

A vaccine breakthrough infection and a rebound infection cases of COVID-19 are studied and analyzed for the ten U.S. Department of Health and Human Services (HHS) regions and the United States as a nation in this work. An innovative multi-strain susceptible-vaccinated-exposed-asymptomatic-symptomatic-recovered (SVEAIR) epidemic model is developed for this purpose for a population assumed to be susceptible to n-different variants of the disease, and those who are vaccinated and recovered from a specific strain k(k ≤ n) of the disease are immune to present strain and its predecessors j = 1, 2, …, k, but can still be infected by newer emerging strains j = k + 1, k + 2, …, n. The model is used to estimate epidemiological parameters, namely, the latent and infectious periods, the transmission rates, vaccination rates, recovery rates for each of the Delta B.1.617.2, Omicron B.1.1.529, and lineages BA.2, BA.2.12.1, BA.4, BA.5, BA.1.1, BA.4.6, and BA.5.2.6 for the United States and for each of the ten HHS regions. The transmission rate is estimated for both the asymptomatic and symptomatic cases. The effect of vaccines on each strain is analyzed. Condition that guarantees existence of an endemic with certain number of strains is derived and used to describe the endemic state of the population.

SARS-CoV-2 Neutralizing Antibodies to B.1 and to BA.5 Variant after Booster Dose of BNT162b2 Vaccine in HIV Patients COVID-Naïve and on Successful Antiretroviral Therapy

Live virus neutralization is the gold standard to investigate immunity. This prospective observational study aimed to determine the magnitude of response against the original B.1 lineage and against the BA.5 lineage six months after the third BNT162b2 mRNA vaccine dose in patients with HIV infection on successful antiretroviral treatment and no previous SARS-CoV-2 infection. A total of 100 subjects (M/F 83/17, median age 54 years) were included in the analysis: 95 had plasma HIV RNA <40 copies/mL, the median CD4+ T cell count at the administration of the third dose was 580 cells/mm³, and the median nadir CD4+ T cell count was 258 cells/mm³. Neutralizing antibodies (NtAb) against B.1 were detectable in all the subjects, but those to BA.5 were only detected in 88 (p < 0.001). The median NtAb titer to B.1 was significantly higher than that to BA.5 (393 vs. 60, p < 0.0001), and there was a strong positive correlation between the paired measurements (p < 0.0001). Linear regression on a subset of 87 patients excluding outlier NtAb titers showed that 48% of the changes in NtAb titers to BA.5 are related to the changes in value titers to B.1. SARS-CoV-2 variants evolve rapidly, challenging the efficacy of vaccines, and data on comparative NtAb responses may help in tailoring intervals between vaccine doses and in predicting vaccine efficacy.