Increased Transmissibility of the SARS-CoV-2 Alpha Variant in a Japanese Population

An analysis of factors contributing to household transmission of COVID-19-using data from active epidemiological investigations performed in the Setagaya ward of Tokyo, Japan

An active epidemiological investigation of COVID-19 cases in the Setagaya ward of Tokyo revealed that household transmission was the main route of infection spread. This study aimed to identify the factors affecting household transmission in patients diagnosed with COVID-19 and their cohabitants, during the wild type virus (December 2020) and alpha variant epidemic (May 2021). Index case factors significantly associated with household transmission for both wild type (WT) and alpha variant (AV), were at least 3 days from onset to diagnosis (WT: risk ratio [RR] 1.44, 95% confidence interval [CI] 1.16-1.79/AV: RR 1.66, CI 1.32-2.08), and a household size of three or more people (WT: RR 1.37, CI 1.10-1.72/AV: RR 1.29, CI 1.05-1.59). There were also significant differences in age ≥ 65 (RR 2.39, CI 1.26-4.54) and symptomatic at diagnosis (RR 3.05, CI 1.22-7.63) in index cases of WT. Among cohabitants, factors associated with household transmission for both strains were being the spouse/partner of the index case (WT: RR 1.68, CI 1.21-1.82/AV: RR 1.97, CI 1.59-2.43) and at least 3 days from onset to diagnosis of the index case (WT: RR 1.48, CI 1.34-2.10/ AV: RR 1.86, CI1.52-2.28). Early diagnosis and isolation are effective for preventing household transmission.

A COVID-19 cluster analysis in an office: Assessing the long-range aerosol and fomite transmissions with infection control measures

Simulated exposure to severe acute respiratory syndrome coronavirus 2 in the environment was demonstrated based on the actual coronavirus disease 2019 cluster occurrence in an office, with a projected risk considering the likely transmission pathways via aerosols and fomites. A total of 35/85 occupants were infected, with the attack rate in the first stage as 0.30. It was inferred that the aerosol transmission at long-range produced the cluster at virus concentration in the saliva of the infected cases on the basis of the simulation, more than 108 PFU mL-1. Additionally, all wearing masks effectiveness was estimated to be 61%-81% and 88%-95% reduction in risk for long-range aerosol transmission in the normal and fit state of the masks, respectively, and a 99.8% or above decline in risk of fomite transmission. The ventilation effectiveness for long-range aerosol transmission was also calculated to be 12%-29% and 36%-66% reductions with increases from one air change per hour (ACH) to two ACH and six ACH, respectively. Furthermore, the virus concentration reduction in the saliva to 1/3 corresponded to the risk reduction for long-range aerosol transmission by 60%-64% and 40%-51% with and without masks, respectively.

Challenges in Emerging Vaccines and Future Promising Candidates against SARS-CoV-2 Variants

Since the COVID-19 outbreak, the severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) virus has evolved into variants with varied infectivity. Vaccines developed against COVID-19 infection have boosted immunity, but there is still uncertainty on how long the immunity from natural infection or vaccination will last. The present study attempts to outline the present level of information about the contagiousness and spread of SARS-CoV-2 variants of interest and variants of concern (VOCs). The keywords like COVID-19 vaccine types, VOCs, universal vaccines, bivalent, and other relevant terms were searched in NCBI, Science Direct, and WHO databases to review the published literature. The review provides an integrative discussion on the current state of knowledge on the type of vaccines developed against SARS-CoV-2, the safety and efficacy of COVID-19 vaccines concerning the VOCs, and prospects of novel universal, chimeric, and bivalent mRNA vaccines efficacy to fend off existing variants and other emerging coronaviruses. Genomic variation can be quite significant, as seen by the notable differences in impact, transmission rate, morbidity, and death during several human coronavirus outbreaks. Therefore, understanding the amount and characteristics of coronavirus genetic diversity in historical and contemporary strains can help researchers get an edge over upcoming variants.

Development of highly sensitive one-step reverse transcription-quantitative PCR for SARS-CoV-2 detection in wastewater

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is a major public health concern that has highlighted the need to monitor circulating strains to better understand the coronavirus disease 2019 (COVID-19) pandemic. This study was carried out to monitor SARS-CoV-2 RNA and its variant-specific mutations in wastewater using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). One-step RT-qPCR using the SARS-CoV-2 Detection RT-qPCR Kit for Wastewater (Takara Bio), which amplified two N-gene regions simultaneously using CDC N1 and N2 assays with a single fluorescence dye, demonstrated better performance in detecting SARS-CoV-2 RNA (positive ratio, 66 %) compared to two-step RT-qPCR using CDC N1 or N2 assay (40 % each, and 52 % when combined), with significantly lower Ct values. The one-step RT-qPCR assay detected SARS-CoV-2 RNA in 59 % (38/64) of influent samples collected from a wastewater treatment plant in Japan between January 2021 and March 2022. The correlation between the concentration of SARS-CoV-2 RNA in the wastewater and the number of COVID-19 cases reported each day for 7 days pre- and post-sampling was significant (p < 0.05, r = 0.76 ± 0.03). Thirty-one influent samples which showed two-well positive for SARS-CoV-2 RNA were further tested by six mutations site-specific one-step RT-qPCR (E484K, L452R, N501Y, T478K, G339D, and E484A mutations). The N501Y mutation was detected between March and June 2021 but was replaced by the L452R and T478K mutations between July and October 2021, reflecting the shift from Alpha to Delta variants in the study region. The G339D and E484A mutations were identified in January 2022 and later when the incidence of the Omicron variant peaked. These findings indicate that wastewater-based epidemiology has the epidemiological potential to complement clinical tests to track the spread of COVID-19 and monitor variants circulating in communities.

SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotype spread in Japan

Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture- or region-specific haplotypes in each of four waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and of geographical prevalence of haplotypes, and aids in developing effective public health control strategies during the global pandemic. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19/.

An integrated chance constraints approach for optimal vaccination strategies under uncertainty for COVID-19

Despite concerted efforts by health authorities worldwide to contain COVID-19, the SARS-CoV-2 virus has continued to spread and mutate into new variants with uncertain transmission characteristics. Therefore, there is a need for new data-driven models for determining optimal vaccination strategies that adapt to the new variants with their uncertain transmission characteristics. Motivated by this challenge, we derive an integrated chance constraints stochastic programming (ICC-SP) approach for finding vaccination strategies for epidemics that incorporates population demographics for any region of the world, uncertain disease transmission and vaccine efficacy. An optimal vaccination strategy specifies the proportion of individuals in a given household-type to vaccinate to bring the reproduction number to below one. The ICC-SP approach provides a quantitative method that allows to bound the expected excess of the reproduction number above one by an acceptable amount according to the decision-maker's level of risk. This new methodology involves a multi-community household based epidemiology model that uses census demographics data, vaccination status, age-related heterogeneity in disease susceptibility and infectivity, virus variants, and vaccine efficacy. The new methodology was tested on real data for seven neighboring counties in the United States state of Texas. The results are promising and show, among other findings, that vaccination strategies for controlling an outbreak should prioritize vaccinating certain household sizes as well as age groups with relatively high combined susceptibility and infectivity.

Effectiveness of feedback control and the trade-off between death by COVID-19 and costs of countermeasures

We provided a framework of a mathematical epidemic modeling and a countermeasure against the novel coronavirus disease (COVID-19) under no vaccines and specific medicines. The fact that even asymptomatic cases are infectious plays an important role for disease transmission and control. Some patients recover without developing the disease; therefore, the actual number of infected persons is expected to be greater than the number of confirmed cases of infection. Our study distinguished between cases of confirmed infection and infected persons in public places to investigate the effect of isolation. An epidemic model was established by utilizing a modified extended Susceptible-Exposed-Infectious-Recovered model incorporating three types of infectious and isolated compartments, abbreviated as SEIIIHHHR. Assuming that the intensity of behavioral restrictions can be controlled and be divided into multiple levels, we proposed the feedback controller approach to implement behavioral restrictions based on the active number of hospitalized persons. Numerical simulations were conducted using different detection rates and symptomatic ratios of infected persons. We investigated the appropriate timing for changing the degree of behavioral restrictions and confirmed that early initiating behavioral restrictions is a reasonable measure to reduce the burden on the health care system. We also examined the trade-off between reducing the cumulative number of deaths by the COVID-19 and saving the cost to prevent the spread of the virus. We concluded that a bang-bang control of the behavioral restriction can reduce the socio-economic cost, while a control of the restrictions with multiple levels can reduce the cumulative number of deaths by infection.

Vaccine-induced neutralizing antibodies against SARS-CoV-2 Omicron variant isolated in Osaka, Japan

To study vaccine-induced neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants isolated in Osaka, Japan, microneutralization tests were performed on serum samples from 32subjects who received a second dose of vaccination, and 10 of those who received the third dose of vaccination. Geometric mean titres (GMTs) for the D614G strain, Alpha variant, Delta variant, and Omicron BA.1 of the subjects after the second dose of vaccination were 19.5, 21.8, 6.3 and 2.0, respectively. The GMT for the Delta variant was significantly lower than that for the D614G strain and Alpha variant, and the GMT for the Omicron BA.1 was significantly lower than that for the Delta variant. Among the subjects who received three doses of vaccination, the GMTs for the Omicron BA.1 (62.8) and BA.2 (38.6) were significantly higher than that for the Omicron BA.1 after the second dose. Thus, in the present study, the second dose of vaccination induced neutralizing antibodies against SARS-CoV-2 strains, and the reactivity of neutralizing antibodies to the variants was thought to be enhanced by the third dose of vaccination. The serum samples used in this study will be useful in evaluating the reactivity of vaccine-induced antibodies to newly emerging variants.

SARS-CoV-2 Omicron (B.1.1.529) Variant: A Challenge with COVID-19

Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there have been multiple peaks of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus virus 2) infection, mainly due to the emergence of new variants, each with a new set of mutations in the viral genome, which have led to changes in the pathogenicity, transmissibility, and morbidity. The Omicron variant is the most recent variant of concern (VOC) to emerge and was recognized by the World Health Organization (WHO) on 26 November 2021. The Omicron lineage is phylogenetically distinct from earlier variants, including the previously dominant Delta SARS-CoV-2 variant. The reverse transcription-polymerase chain reaction (RT-PCR) test, rapid antigen assays, and chest computed tomography (CT) scans can help diagnose the Omicron variant. Furthermore, many agents are expected to have therapeutic benefits for those infected with the Omicron variant, including TriSb92, molnupiravir, nirmatrelvir, and their combination, corticosteroids, and interleukin-6 (IL-6) receptor blockers. Despite being milder than previous variants, the Omicron variant threatens many lives, particularly among the unvaccinated, due to its higher transmissibility, pathogenicity, and infectivity. Mounting evidence has reported the most common clinical manifestations of the Omicron variant to be fever, runny nose, sore throat, severe headache, and fatigue. This review summarizes the essential features of the Omicron variant, including its history, genome, transmissibility, clinical manifestations, diagnosis, management, and the effectiveness of existing vaccines against this VOC.

Association Between Population-Level Factors and Household Secondary Attack Rate of SARS-CoV-2: A Systematic Review and Meta-analysis

Background

Accurate estimation of household secondary attack rate (SAR) is crucial to understand the transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The impact of population-level factors, such as transmission intensity in the community, on SAR estimates is rarely explored.

Methods

In this study, we included articles with original data to compute the household SAR. To determine the impact of transmission intensity in the community on household SAR estimates, we explored the association between SAR estimates and the incidence rate of cases by country during the study period.

Results

We identified 163 studies to extract data on SARs from 326 031 cases and 2 009 859 household contacts. The correlation between the incidence rate of cases during the study period and SAR estimates was 0.37 (95% CI, 0.24-0.49). We found that doubling the incidence rate of cases during the study period was associated with a 1.2% (95% CI, 0.5%-1.8%) higher household SAR.

Conclusions

Our findings suggest that the incidence rate of cases during the study period is associated with higher SAR. Ignoring this factor may overestimate SARs, especially for regions with high incidences, which further impacts control policies and epidemiological characterization of emerging variants.

The P681H Mutation in the Spike Glycoprotein of the Alpha Variant of SARS-CoV-2 Escapes IFITM Restriction and Is Necessary for Type I Interferon Resistance

The appearance of new dominant variants of concern (VOC) of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) threatens the global response to the coronavirus disease 2019 (COVID-19) pandemic. Of these, the alpha variant (also known as B.1.1.7), which appeared initially in the United Kingdom, became the dominant variant in much of Europe and North America in the first half of 2021. The spike (S) glycoprotein of alpha acquired seven mutations and two deletions compared to the ancestral virus, including the P681H mutation adjacent to the polybasic cleavage site, which has been suggested to enhance S cleavage. Here, we show that the alpha spike protein confers a level of resistance to beta interferon (IFN-β) in human lung epithelial cells. This correlates with resistance to an entry restriction mediated by interferon-induced transmembrane protein 2 (IFITM2) and a pronounced infection enhancement by IFITM3. Furthermore, the P681H mutation is essential for resistance to IFN-β and context-dependent resistance to IFITMs in the alpha S. P681H reduces dependence on endosomal cathepsins, consistent with enhanced cell surface entry. However, reversion of H681 does not reduce cleaved spike incorporation into particles, indicating that it exerts its effect on entry and IFN-β downstream of furin cleavage. Overall, we suggest that, in addition to adaptive immune escape, mutations associated with VOC may well also confer a replication and/or transmission advantage through adaptation to resist innate immune mechanisms. IMPORTANCE Accumulating evidence suggests that variants of concern (VOC) of SARS-CoV-2 evolve to evade the human immune response, with much interest focused on mutations in the spike protein that escape from antibodies. However, resistance to the innate immune response is essential for efficient viral replication and transmission. Here, we show that the alpha (B.1.1.7) VOC of SARS-CoV-2 is substantially more resistant to type I interferons than the parental Wuhan-like virus. This correlates with resistance to the antiviral protein IFITM2 and enhancement by its paralogue IFITM3. The key determinant of this is a proline-to-histidine change at position 681 in S adjacent to the furin cleavage site, which in the context of the alpha spike modulates cell entry pathways of SARS-CoV-2. Reversion of the mutation is sufficient to restore interferon and IFITM2 sensitivity, highlighting the dynamic nature of the SARS CoV-2 as it adapts to both innate and adaptive immunity in the humans.

Young Healthy Patient With Severe COVID-19 and Fulminant Community-Acquired Pseudomonas aeruginosa Pneumonia: A Case Report

Community-acquired pneumonia (CAP) caused by Pseudomonas aeruginosa in healthy adults can rapidly lead to severe outcomes. We treated a case of P. aeruginosa-induced CAP and concurrent severe coronavirus disease (COVID-19) in a healthy 39-year-old man without other serious risk factors for severe illness except smoking. Immediately after admission, the patient developed sepsis and received intensive broad-spectrum antibacterial therapy with meropenem and vancomycin, veno-arterial extracorporeal membrane oxygenation (VAECMO), and catecholamine supplementation. Despite receiving multidisciplinary treatment, the patient died within 24 hours. P. aeruginosa with normal antimicrobial susceptibility was identified in blood and sputum cultures of samples taken at admission. Gram staining of the bacteria detected in blood cultures was suspicious for non-glucose-fermenting Gram-negative rods, including P. aeruginosa, and the antimicrobial regimen that was initiated following admission was considered effective. The patient was a plumber and a smoker, which are risk factors for P. aeruginosa-induced CAP, and the clinical course matched those in previous reports of P. aeruginosa-induced CAP, including necrotizing pneumonia with cavities and rapid progression of sepsis. Although COVID-19 can be the sole cause of septic shock, the combination of P. aeruginosa bacteremia and COVID-19 was possibly the cause of septic shock in this case. Even during an infectious disease pandemic, reviewing the patient's occupational history and comorbidities and performing blood and sputum culture tests, including Gram staining, are important for the provision of appropriate treatment.

Assessment of an enhanced COVID-19 case and contact management protocol in controlling a SARS-CoV-2 Alpha (B.1.1.7) variant outbreak on a construction site

BACKGROUND

To control the spread of SARS-CoV-2 variants of concern (VOCs), Kingston, Frontenac, and Lennox & Addington (KFL&A) Public Health implemented a more stringent COVID-19 case and contact management (CCM) protocol than what was used across Ontario at the time. We describe epidemiological data and public health measures employed during one of the largest COVID-19 outbreaks in the KFL&A region at the time, caused by the SARS-CoV-2 Alpha (B.1.1.7) VOC, to assess this enhanced protocol.

METHODS

We obtained line lists of workers associated with the construction site outbreak, and subsequent cases and contacts from case investigators. Case testing, mutation status, and whole genome sequencing were conducted by Public Health Ontario Laboratories.

RESULTS

From 409 high-risk contacts of the outbreak, 109 (27%) developed COVID-19. Three generations of spread were associated with the outbreak, affecting seven public health regions across three provinces. Using an enhanced approach to the CCM, KFL&A Public Health caught 15 cases that could have been missed by standard provincial protocols.

CONCLUSIONS

Rapid initial spread within the construction site produced a relatively high attack rate among workers (26%) and their immediate contacts (34%). KFL&A Public Health's implementation of stringent CCM protocols and fast testing turn-around time effectively curbed the spread of the disease in subsequent generations - illustrated by the large reduction in attack rate (34%-14%) and cases (50-10) between the second and third generations. Lessons learned from this analysis may inform guidance on the CCM for future SARS-CoV-2 VOCs as well as other highly transmissible communicable diseases.

The role of children in household transmission of COVID-19: a systematic review and meta-analysis

OBJECTIVES

To explore household transmissibility of SARS-CoV-2 in children in new-variants dominating periods.

METHODS

Through retrieval in PubMed and Embase, studies were included in two parts: meta-analysis of the household secondary attack rate (SAR) and case analysis of household pediatric infections.

RESULTS

A total of 95 articles were included: 48 for meta-analysis and 47 for case analysis. Pediatric COVID-19 only comprised a minority of the household transmission. The total pooled household SAR of child index cases and contacts were 0.20 (95% confidence interval [CI]: 0.15-0.26) and 0.24 (95% CI: 0.18-0.30). Lower household transmissibility was reported in both child index cases and contacts than in adults (relative risk [RR] = 0.64, 95% CI: 0.50-0.81; RR = 0.74, 95% CI: 0.64-0.85). Younger children were as susceptible as the older children (RR = 0.89, 95% CI: 0.72-1.10). Through subgroup analyses of different variants and periods, increased household SAR was observed in children (Wild: 0.20; Alpha: 0.42; Delta: 0.35; Omicron: 0.56), and no significant difference was found in household SAR between children and adults when new variants dominated.

CONCLUSION

Although children were found not to be dominant in the household transmission, their transmissibility of SARS-CoV-2 appeared to be on the rise as new variants emerged.

The importance of effect sizes when comparing cycle threshold values of SARS-CoV-2 variants

Purpose

We aimed to elaborate whether cycle threshold (Ct) values differ significantly between wild type SARS-CoV-2 (wtV) and certain viral variants and how strong or weak a potential significant effect might be.

Methods

In a retrospective study, we investigated 1873 SARS-CoV-2 positive samples for the occurrence of viral marker mutations. Age, gender, clinical setting, days after onset of symptoms, and Ct values were recorded. Statistical analysis was carried out with special consideration of effect sizes.

Results

During the study period wtV was detected in 1013 samples (54%), while 845 (45%) patients carried the Alpha variant of concern (VOC), and 15 (1%) the Beta VOC. For further analysis, only wtV and the Alpha VOC were included. In a multi-factor ANOVA and post-hoc test with Bonferroni-correction for the age groups we found significant main-effects for Ct values of the viral variant (wtV mean 26.4 (SD 4.27); Alpha VOC mean 25.0 (SD 3.84); F (1,1850) = 55.841; p < .001) and the clinical setting (outpatients: mean 25.7 (SD 4.1); inpatients: mean 27.0 (SD 4.2); F (1,1850) = 8.520, p = .004). However, since the effect sizes were very small (eta squared for the Alpha VOC = .029 and the clinical setting = .004), there was only a slight trend towards higher viral loads of the Alpha VOC compared to wtV.

Conclusions

In order to compare different variants of SARS-CoV-2 the calculation of effect sizes seems to be necessary. A combination of p-values as estimates of the existance of an effect and effect sizes as estimates of the magnitude of a potential effect may allow a better insight into transmission mechanisms of SARS-CoV-2.

Temporal trends in clinical characteristics and in-hospital mortality among patients with COVID-19 in Japan for waves 1, 2, and 3: A retrospective cohort study

INTRODUCTION

Little information is available on the temporal trends in the clinical epidemiology and in-hospital mortality of patients with coronavirus disease 2019 (COVID-19) in Japan for waves 1, 2, and 3.

METHODS

A national claims database was used to analyze the time trends in admission, medical procedure, and in-hospital mortality characteristics among patients with COVID-19. Patients who were ≥18 years and discharged from January 1, 2020 to February 28, 2021 were included.

RESULTS

A multilevel logistic regression analysis of 51,252 patients revealed a decline in mortality in waves 2 and 3 (risk-adjusted mortality range = 2.17-4.07%; relative risk reduction = 23-59%; reference month of April 2020 = 5.32%). In the subgroup analysis, a decline in mortality was also observed in patients requiring oxygen support but not mechanical ventilation (risk-adjusted mortality range = 5.98-11.68%; relative risk reduction = 22-60%; reference month of April 2020 = 15.06%). Further adjustments for medical procedure changes in the entire study population revealed a decrease in mortality in waves 2 and 3 (risk-adjusted mortality range = 2.66-4.05%; relative risk reduction = 24-50%).

CONCLUSIONS

A decline in in-hospital mortality was observed in waves 2 and 3 after adjusting for patient/hospital-level characteristics and medical treatments. The reasons for this decline warrant further research to improve the outcomes of hospitalized patients.

SARS-CoV-2 Transmission and Prevention in the Era of the Delta Variant

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) delta variant transmits much more rapidly than prior SARS-CoV-2 viruses. The primary mode of transmission is via short range aerosols that are emitted from the respiratory tract of an index case. There is marked heterogeneity in the spread of this virus, with 10% to 20% of index cases contributing to 80% of secondary cases, while most index cases have no subsequent transmissions. Vaccination, ventilation, masking, eye protection, and rapid case identification with contact tracing and isolation can all decrease the transmission of this virus.

Modelling the COVID-19 epidemic and the vaccination campaign in Italy by the SUIHTER model

Several epidemiological models have been proposed to study the evolution of COVID-19 pandemic. In this paper, we propose an extension of the SUIHTER model, to analyse the COVID-19 spreading in Italy, which accounts for the vaccination campaign and the presence of new variants when they become dominant. In particular, the specific features of the variants (e.g. their increased transmission rate) and vaccines (e.g. their efficacy to prevent transmission, hospitalization and death) are modeled, based on clinical evidence. The new model is validated comparing its near-future forecast capabilities with other epidemiological models and exploring different scenario analyses.

Structures of Omicron spike complexes and implications for neutralizing antibody development

The emergence of the SARS-CoV-2 Omicron variant is dominant in many countries worldwide. The high number of spike mutations is responsible for the broad immune evasion from existing vaccines and antibody drugs. To understand this, we first present the cryo-electron microscopy structure of ACE2-bound SARS-CoV-2 Omicron spike. Comparison to previous spike antibody structures explains how Omicron escapes these therapeutics. Secondly, we report structures of Omicron, Delta, and wild-type spikes bound to a patient-derived Fab antibody fragment (510A5), which provides direct evidence where antibody binding is greatly attenuated by the Omicron mutations, freeing spike to bind ACE2. Together with biochemical binding and 510A5 neutralization assays, our work establishes principles of binding required for neutralization and clearly illustrates how the mutations lead to antibody evasion yet retain strong ACE2 interactions. Structural information on spike with both bound and unbound antibodies collectively elucidates potential strategies for generation of therapeutic antibodies.

Household Secondary Attack Rates of SARS-CoV-2 by Variant and Vaccination Status: An Updated Systematic Review and Meta-analysis

Importance

An overall household secondary attack rate (SAR) of 18.9% (95% CI, 16.2%-22.0%) through June 17, 2021 was previously reported for SARS-CoV-2. Emerging variants of concern and increased vaccination have affected transmission rates.

Objective

To evaluate how reported household SARs changed over time and whether SARs varied by viral variant and index case and contact vaccination status.

Data Sources

PubMed and medRxiv from June 18, 2021, through March 8, 2022, and reference lists of eligible articles. Preprints were included.

Study Selection

Articles with original data reporting the number of infected and total number of household contacts. Search terms included SARS-CoV-2, COVID-19, variant, vaccination, secondary attack rate, secondary infection rate, household, index case, family contacts, close contacts, and family transmission.

Data Extraction and Synthesis

The Preferred Reporting Items for Systematic Reviews and Meta-Analyses reporting guideline was followed. Meta-analyses used generalized linear mixed models to obtain SAR estimates and 95% CIs.

Main Outcomes and Measures

SAR stratified by covariates according to variant, index case and contact vaccination status, and index case identification period. SARs were used to estimate vaccine effectiveness on the basis of the transmission probability for susceptibility to infection (VES,p), infectiousness given infection (VEI,p), and total vaccine effectiveness (VET,p).

Results

Household SARs were higher for 33 studies with midpoints in 2021 to 2022 (37.3%; 95% CI, 32.7% to 42.1%) compared with 63 studies with midpoints through April 2020 (15.5%; 95% CI, 13.2% to 18.2%). Household SARs were 42.7% (95% CI, 35.4% to 50.4%) for Omicron (7 studies), 36.4% (95% CI, 33.4% to 39.5%) for Alpha (11 studies), 29.7% (95% CI, 23.0% to 37.3%) for Delta (16 studies), and 22.5% (95% CI, 18.6% to 26.8%) for Beta (3 studies). For full vaccination, VES,p was 78.6% (95% CI, 76.0% to 80.9%) for Alpha, 56.4% (95% CI, 54.6% to 58.1%) for Delta, and 18.1% (95% CI, -18.3% to 43.3%) for Omicron; VEI,p was 75.3% (95% CI, 69.9% to 79.8%) for Alpha, 21.9% (95% CI, 11.0% to 31.5%) for Delta, and 18.2% (95% CI, 0.6% to 32.6%) for Omicron; and VET,p was 94.7% (95% CI, 93.3% to 95.8%) for Alpha, 64.4% (95% CI, 58.0% to 69.8%) for Delta, and 35.8% (95% CI, 13.0% to 52.6%) for Omicron.

Conclusions and Relevance

These results suggest that emerging SARS-CoV-2 variants of concern have increased transmissibility. Full vaccination was associated with reductions in susceptibility and infectiousness, but more so for Alpha than Delta and Omicron. The changes in estimated vaccine effectiveness underscore the challenges of developing effective vaccines concomitant with viral evolution.

SARS-CoV-2: Evolution and Emergence of New Viral Variants

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent responsible for the coronavirus disease 2019 (COVID-19). The high rate of mutation of this virus is associated with a quick emergence of new viral variants that have been rapidly spreading worldwide. Several mutations have been documented in the receptor-binding domain (RBD) of the viral spike protein that increases the interaction between SARS-CoV-2 and its cellular receptor, the angiotensin-converting enzyme 2 (ACE2). Mutations in the spike can increase the viral spread rate, disease severity, and the ability of the virus to evade either the immune protective responses, monoclonal antibody treatments, or the efficacy of current licensed vaccines. This review aimed to highlight the functional virus classification used by the World Health Organization (WHO), Phylogenetic Assignment of Named Global Outbreak (PANGO), Global Initiative on Sharing All Influenza Data (GISAID), and Nextstrain, an open-source project to harness the scientific and public health potential of pathogen genome data, the chronological emergence of viral variants of concern (VOCs) and variants of interest (VOIs), the major findings related to the rate of spread, and the mutations in the spike protein that are involved in the evasion of the host immune responses elicited by prior SARS-CoV-2 infections and by the protection induced by vaccination.

Household secondary attack rates of SARS-CoV-2 by variant and vaccination status: an updated systematic review and meta-analysis

We previously reported a household secondary attack rate (SAR) for SARS-CoV-2 of 18.9% through June 17, 2021. To examine how emerging variants and increased vaccination have affected transmission rates, we searched PubMed from June 18, 2021, through January 7, 2022. Meta-analyses used generalized linear mixed models to obtain SAR estimates and 95%CI, disaggregated by several covariates. SARs were used to estimate vaccine effectiveness based on the transmission probability for susceptibility ( VE S,p ), infectiousness ( VE I,p ), and total vaccine effectiveness ( VE T,p ). Household SAR for 27 studies with midpoints in 2021 was 35.8% (95%CI, 30.6%-41.3%), compared to 15.7% (95%CI, 13.3%-18.4%) for 62 studies with midpoints through April 2020. Household SARs were 38.0% (95%CI, 36.0%-40.0%), 30.8% (95%CI, 23.5%-39.3%), and 22.5% (95%CI, 18.6%-26.8%) for Alpha, Delta, and Beta, respectively. VE I,p , VE S,p , and VE T,p were 56.6% (95%CI, 28.7%-73.6%), 70.3% (95%CI, 59.3%-78.4%), and 86.8% (95%CI, 76.7%-92.5%) for full vaccination, and 27.5% (95%CI, -6.4%-50.7%), 43.9% (95%CI, 21.8%-59.7%), and 59.9% (95%CI, 34.4%-75.5%) for partial vaccination, respectively. Household contacts exposed to Alpha or Delta are at increased risk of infection compared to the original wild-type strain. Vaccination reduced susceptibility to infection and transmission to others.

SUMMARY

Household secondary attack rates (SARs) were higher for Alpha and Delta variants than previous estimates. SARs were higher to unvaccinated contacts than to partially or fully vaccinated contacts and were higher from unvaccinated index cases than from fully vaccinated index cases.

Number of public health nurses and COVID-19 incidence rate by variant type: an ecological study of 47 prefectures in Japan

Background

Community health activities by public health nurses (PHNs) are known to improve lifestyle habits of local residents, and may encourage the practice of infectious disease prevention behaviors during the COVID-19 pandemic. We investigated the association between prefecture-level COVID-19 incidence rate and the number of PHNs per population in Japan, by the COVID-19 variant type.

Methods

Our data were based on government surveys where prefectural-level data are accessible to the public. The outcome variable was the COVID-19 incidence rate (i.e., the cumulative number of COVID-19 cases per 100,000 population for each variant type in 47 prefectures). The explanatory variable was the number of PHNs per 100,000 population by prefecture. Covariates included socioeconomic factors, regional characteristics, healthcare resources, and health behaviors. The generalized estimating equations of the multivariable Poisson regression models were used to estimate adjusted incidence rate ratio (IRR) and 95% confidence interval (CI) for the COVID-19 cases. We performed stratified analyses by variant type (i.e., wild type, alpha variant, and delta variant).

Results

A total of 1,705,224 confirmed COVID-19 cases (1351.6 per 100,000 population) in Japan were reported as of September 30, 2021. The number of PHNs per 100,000 population in Japan was 41.9. Multivariable Poisson regression models showed that a lower number of PHNs per population was associated with higher IRR of COVID-19. Among all COVID-19 cases, compared to the highest quintile group of the number of PHNs per population, the adjusted IRR of the lowest quintile group was consistently significant in the models adjusting for socioeconomic factors (IRR: 3.76, 95% CI: 2.55–5.54), regional characteristics (1.73, 1.28–2.34), healthcare resources (3.88, 2.45–6.16), and health behaviors (2.17, 1.39–3.37). These significant associations were unaffected by the variant type of COVID-19.

Conclusion

We found that the COVID-19 incidence rate was higher in prefectures with fewer PHNs per population, regardless of the COVID-19 variant type. By increasing the number of PHNs, it may be possible to contain the spread of COVID-19 in Japan and provide an effective human resource to combat emerging infectious diseases in the future.

Supplementary information

The online version contains supplementary material available at https://doi.org/10.1265/ehpm.22-00013.

Household transmission of COVID-19 cases associated with SARS-CoV-2 delta variant (B.1.617.2): national case-control study

BACKGROUND

The SARS-CoV-2 Delta variant (B.1.617.2), first detected in India, has rapidly become the dominant variant in England. Early reports suggest this variant has an increased growth rate suggesting increased transmissibility. This study indirectly assessed differences in transmissibility between the emergent Delta variant compared to the previously dominant Alpha variant (B.1.1.7).

METHODS

A matched case-control study was conducted to estimate the odds of household transmission (≥ 2 cases within 14 days) for Delta variant index cases compared with Alpha cases. Cases were derived from national surveillance data (March to June 2021). One-to-two matching was undertaken on geographical location of residence, time period of testing and property type, and a multivariable conditional logistic regression model was used for analysis.

FINDINGS

In total 5,976 genomically sequenced index cases in household clusters were matched to 11,952 sporadic index cases (single case within a household). 43.3% (n=2,586) of cases in household clusters were confirmed Delta variant compared to 40.4% (n= 4,824) of sporadic cases. The odds ratio of household transmission was 1.70 among Delta variant cases (95% CI 1.48-1.95, p <0.001) compared to Alpha cases after adjusting for age, sex, ethnicity, index of multiple deprivation (IMD), number of household contacts and vaccination status of index case.

INTERPRETATION

We found evidence of increased household transmission of SARS-CoV-2 Delta variant, potentially explaining its success at displacing Alpha variant as the dominant strain in England. With the Delta variant now having been detected in many countries worldwide, the understanding of the transmissibility of this variant is important for informing infection prevention and control policies internationally.

Treatment and outcome of COVID-19 patients in a specialized hospital during the third wave: advance of age and increased mortality compared with the first/second waves

Purpose

To elucidate the clinical course of patients with coronavirus disease 2019 (COVID-19) treated at a specialized hospital mainly for those with mild and moderate severity during the third wave, and to compare that with the first and second (1st/2nd) waves.

Methods

We retrospectively reviewed the severity on admission, treatment, and outcome of a total of 581 patients from September, 2020, to March, 2021, and examined the risk factors for deterioration of respiratory condition, defined as requiring oxygen ≥ 7 L/min for 12 h.

Results

The median age was 78 (interquartile range 62−83) years, older than in the 1st/2nd waves (53 years), and 50% of the patients was male. The number of patients classified as mild (peripheral oxygen saturation (SpO₂) ≥ 96%), moderate I, II, and severe (requiring admission to the ICU or mechanical ventilation) was 121, 324, 132, and 4, respectively. Favipiravir, ciclesonide, dexamethasone, and/or heparin were administered for treatment. Respiratory condition recovered in 496 (85%) patients. It worsened in 81 patients (14%); 51 (9%) of whom were transferred to tertiary hospitals and 30 (5%) died. Mortality rate increased by fivefold compared during the 1st/2nd waves. Age, male sex, increased body mass index, and C-reactive protein (CRP) on admission were responsible for worsening of the respiratory condition.

Conclusion

Patients were older in the third wave compared with the 1st/2nd waves. Respiratory condition recovered in 85%; whereas 5% of the patients died. Old age, male sex, increased body mass index, and CRP would be responsible for worsening of the respiratory condition.

Application of Artificial Intelligence in COVID-19 Diagnosis and Therapeutics

The coronavirus disease 2019 (COVID-19) pandemic began at the end of December 2019, giving rise to a high rate of infections and causing COVID-19-associated deaths worldwide. It was first reported in Wuhan, China, and since then, not only global leaders, organizations, and pharmaceutical/biotech companies, but also researchers, have directed their efforts toward overcoming this threat. The use of artificial intelligence (AI) has recently surged internationally and has been applied to diverse aspects of many problems. The benefits of using AI are now widely accepted, and many studies have shown great success in medical research on tasks, such as the classification, detection, and prediction of disease, or even patient outcome. In fact, AI technology has been actively employed in various ways in COVID-19 research, and several clinical applications of AI-equipped medical devices for the diagnosis of COVID-19 have already been reported. Hence, in this review, we summarize the latest studies that focus on medical imaging analysis, drug discovery, and therapeutics such as vaccine development and public health decision-making using AI. This survey clarifies the advantages of using AI in the fight against COVID-19 and provides future directions for tackling the COVID-19 pandemic using AI techniques.