Infectivity versus fatality of SARS-CoV-2 mutations and influenza

Current status and clinical outcomes of pharmacotherapies according to SARS-CoV-2 mutations in patients with mild-to-moderate COVID-19: a retrospective single center study

BACKGROUND

During the pandemic period, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutated, leading to changes in the disease's severity and the therapeutic effect of drugs accordingly. This study aimed to present the actual use of therapeutics and clinical outcomes based on the prevalence of each variant using real-world data.

METHODS

We analyzed the electronic medical records of adult patients admitted to Busan Medical Center after confirming coronavirus disease 2019 (COVID-19) from February 1, 2020, to June 30, 2022. Patients with mild-to-moderate COVID-19 who were at a high risk of disease progression were selected as study subjects, and the time period was classified according to the variants as ancestral strain, Delta variant, or Omicron variant. We compared drug use status and clinical outcomes by time period.

RESULTS

Among all 3,091 patients, corticosteroids were the most commonly used therapy (56.0%), being used most frequently in the Delta variant (93.0%), followed by the Omicron variant (42.9%) and ancestral strain (21.2%). Regdanvimab accounted for the majority of therapeutic use in the Delta variant (82.9%) and ancestral strain (76.8%), whereas remdesivir was most frequently used during the Omicron variant period (68.9%). The composite outcomes of death or disease aggravation were ranked in the order of the Delta variant, Omicron variant, and ancestral strain (14.5, 11.9, and 6.0%, respectively, P < 0.001).

CONCLUSION

Regdanvimab was primarily used during the ancestral strain period, regdanvimab plus corticosteroids during the Delta variant period, and remdesivir during the Omicron variant period. The rate of death or disease aggravation was highest in the Delta variant, followed by the Omicron variant and the ancestral strain.

The Clinical Severity of COVID-19 Variants of Concern: Retrospective Population-Based Analysis

BACKGROUND

SARS-CoV-2 variants of concern (VOCs) emerged and rapidly replaced the original strain worldwide. The increased transmissibility of these new variants led to increases in infections, hospitalizations, and mortality. However, there is a scarcity of retrospective investigations examining the severity of all the main VOCs in presence of key public health measures and within various social determinants of health (SDOHs).

OBJECTIVE

This study aims to provide a retrospective assessment of the clinical severity of COVID-19 VOCs in the context of heterogenous SDOHs and vaccination rollout.

METHODS

We used a population-based retrospective cohort design with data from the British Columbia COVID-19 Cohort, a linked provincial surveillance platform. To assess the relative severity (hospitalizations, intensive care unit [ICU] admissions, and deaths) of Gamma, Delta, and Omicron infections during 2021 relative to Alpha, we used inverse probability treatment weighted Cox proportional hazard modeling. We also conducted a subanalysis among unvaccinated individuals, as assessed severity differed across VOCs and SDOHs.

RESULTS

We included 91,964 individuals infected with a SARS-CoV-2 VOC (Alpha: n=20,487, 22.28%; Gamma: n=15,223, 16.55%; Delta: n=49,161, 53.46%; and Omicron: n=7093, 7.71%). Delta was associated with the most severe disease in terms of hospitalization, ICU admissions, and deaths (hospitalization: adjusted hazard ratio [aHR] 2.00, 95% CI 1.92-2.08; ICU: aHR 2.05, 95% CI 1.91-2.20; death: aHR 3.70, 95% CI 3.23-4.25 relative to Alpha), followed generally by Gamma and then Omicron and Alpha. The relative severity by VOC remained similar in the unvaccinated individual subanalysis, although the proportion of individuals infected with Delta and Omicron who were hospitalized was 2 times higher in those unvaccinated than in those fully vaccinated. Regarding SDOHs, the proportion of hospitalized individuals was higher in areas with lower income across all VOCs, whereas among Alpha and Gamma infections, 2 VOCs that cocirculated, differential distributions of hospitalizations were found among racially minoritized groups.

CONCLUSIONS

Our study provides robust severity estimates for all VOCs during the COVID-19 pandemic in British Columbia, Canada. Relative to Alpha, we found Delta to be the most severe, followed by Gamma and Omicron. This study highlights the importance of targeted testing and sequencing to ensure timely detection and accurate estimation of severity in emerging variants. It further sheds light on the importance of vaccination coverage and SDOHs in the context of pandemic preparedness to support the prioritization of allocation for resource-constrained or minoritized groups.

Risk Index of Regional Infection Expansion of COVID-19: Moving Direction Entropy Study Using Mobility Data and Its Application to Tokyo

BACKGROUND

Policies, such as stay home, bubbling, and stay with your community, recommending that individuals reduce contact with diverse communities, including families and schools, have been introduced to mitigate the spread of the COVID-19 pandemic. However, these policies are violated if individuals from various communities gather, which is a latent risk in a real society where people move among various unreported communities.

OBJECTIVE

We aimed to create a physical index to assess the possibility of contact between individuals from diverse communities, which serves as an indicator of the potential risk of SARS-CoV-2 spread when considered and combined with existing indices.

METHODS

Moving direction entropy (MDE), which quantifies the diversity of moving directions of individuals in each local region, is proposed as an index to evaluate a region's risk of contact of individuals from diverse communities. MDE was computed for each inland municipality in Tokyo using mobility data collected from smartphones before and during the COVID-19 pandemic. To validate the hypothesis that the impact of intercommunity contact on infection expansion becomes larger for a virus with larger infectivity, we compared the correlations of the expansion of infectious diseases with indices, including MDE and the densities of supermarkets, restaurants, etc. In addition, we analyzed the temporal changes in MDE in municipalities.

RESULTS

This study had 4 important findings. First, the MDE values for local regions showed significant invariance between different periods according to the Spearman rank correlation coefficient (>0.9). Second, MDE was found to correlate with the rate of infection cases of COVID-19 among local populations in 53 inland regions (average of 0.76 during the period of expansion). The density of restaurants had a similar correlation with COVID-19. The correlation between MDE and the rate of infection was smaller for influenza than for COVID-19, and tended to be even smaller for sexually transmitted diseases (order of infectivity). These findings support the hypothesis. Third, the spread of COVID-19 was accelerated in regions with high-rank MDE values compared to those with high-rank restaurant densities during and after the period of the governmental declaration of emergency (P<.001). Fourth, the MDE values tended to be high and increased during the pandemic period in regions where influx or daytime movement was present. A possible explanation for the third and fourth findings is that policymakers and living people have been overlooking MDE.

CONCLUSIONS

We recommend monitoring the regional values of MDE to reduce the risk of infection spread. To aid in this monitoring, we present a method to create a heatmap of MDE values, thereby drawing public attention to behaviors that facilitate contact between communities during a highly infectious disease pandemic.

Clinical and Genomic Perspective of SARS CoV-2 Infection in Liver Disease Patients: A Single-Centre Retrospective Study

The limited literature on the clinical course of COVID-19 among patients with underlying liver disease (LD) is available from India. The present study aimed to evaluate the clinical and mutational profile of SARS-CoV-2 among LD cases. This was a retrospective study including admitted LD cases in whom SARS-CoV-2 RT-PCR testing was performed. Complete demographic and clinical details were retrieved from Hospital Information System. Detailed mutational analysis was performed by comparing LD COVID-19 positive study group, i.e. LD-CoV(+) with COVID-19 positive outpatients without any underlying LD as control, i.e. NLD-CoV(+). Out of 232 enrolled LD cases, 137 (59.1%) were LD-CoV(+). LD cases with existing co-morbidities were affected more (P = 0.002) and had 2.29 times (OR 2.29, CI 95%, 1.25-4.29) higher odds of succumbing to COVID-19 (P = 0.006). On multivariate regression analysis, ascites (P = 0.05), severe COVID-19 pneumonia (P = 0.046), and an increased levels of bilirubin (P = 0.005) and alkaline phosphatase (P = 0.003) were found to be associated with adverse outcome in LD-CoV(+).On mutational analysis, we found certain differences between LD- and NLD-CoV(+) infected with Delta [LD- and NLD-CoV (+ /D)] and Omicron [LD- and NLD-CoV(+/O)]. More mutations were shared between LD- and NLD-CoV(+/O) compared to LD- and NLD-CoV(+/D). There were differences in prevalence of indel mutations specific to LD-CoV ( +) for both Delta and Omicron. Moreover, we also reported an interesting genic bias between LD- and NLD-CoV( +) in harbouring deleterious/tolerated mutations. To conclude, LD cases with comorbidities were affected more and had higher odds of mortality due to COVID-19. The definite difference between LD- and NLD-CoV(+) groups with respect to frequency of harboured mutations and an inherent genic bias between them is of noteworthy importance.

COVID-19 vaccination strategies in Africa: A scoping review of the use of mathematical models to inform policy

OBJECTIVE

Mathematical models are vital tools to understand transmission dynamics and assess the impact of interventions to mitigate COVID-19. However, historically, their use in Africa has been limited. In this scoping review, we assess how mathematical models were used to study COVID-19 vaccination to potentially inform pandemic planning and response in Africa.

METHODS

We searched six electronic databases: MEDLINE, Embase, Web of Science, Global Health, MathSciNet and Africa-Wide NiPAD, using keywords to identify articles focused on the use of mathematical modelling studies of COVID-19 vaccination in Africa that were published as of October 2022. We extracted the details on the country, author affiliation, characteristics of models, policy intent and heterogeneity factors. We assessed quality using 21-point scale criteria on model characteristics and content of the studies.

RESULTS

The literature search yielded 462 articles, of which 32 were included based on the eligibility criteria. Nineteen (59%) studies had a first author affiliated with an African country. Of the 32 included studies, 30 (94%) were compartmental models. By country, most studies were about or included South Africa (n = 12, 37%), followed by Morocco (n = 6, 19%) and Ethiopia (n = 5, 16%). Most studies (n = 19, 59%) assessed the impact of increasing vaccination coverage on COVID-19 burden. Half (n = 16, 50%) had policy intent: prioritising or selecting interventions, pandemic planning and response, vaccine distribution and optimisation strategies and understanding transmission dynamics of COVID-19. Fourteen studies (44%) were of medium quality and eight (25%) were of high quality.

CONCLUSIONS

While decision-makers could draw vital insights from the evidence generated from mathematical modelling to inform policy, we found that there was limited use of such models exploring vaccination impacts for COVID-19 in Africa. The disparity can be addressed by scaling up mathematical modelling training, increasing collaborative opportunities between modellers and policymakers, and increasing access to funding.

Public acceptance of COVID-19 control measures and associated factors during Omicron-dominant period in China: a cross-sectional survey

OBJECTIVES

This study aims to evaluate the public acceptance of coronavirus disease 2019 (COVID-19) control measures during the Omicron-dominant period and its associated factors.

METHODS

A cross-sectional design was conducted and 1391 study participants were openly recruited to participate in the questionnaire survey. Logistic regression model was performed to assess the association between the public acceptance and potential factors more specifically.

RESULTS

By August 26, 2022, 58.9% of the study participants were less acceptive of the control measures while 41.1% expressed higher acceptance. Factors associated with lower acceptance included young age, such as < 18 (OR = 8.251, 95% CI: 2.009 to 33.889) and 18-29 (OR = 2.349, 95% CI: 1.564 to 3.529), and household per capita monthly income lower than 5000 yuan (OR = 1.512, 95% CI: 1.085 to 2.105). Furthermore, individuals who perceived that the case fatality rate (CFR) of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was very low (OR = 6.010, 95% CI: 2.475 to 14.595) and that the restrictions could be eased once the CFR dropped to 2-3 times of the influenza (OR = 2.792, 95% CI: 1.939 to 4.023) showed greater oppositional attitudes. Likewise, respondents who were dissatisfied with control measures (OR = 9.639, 95% CI: 4.425 to 20.998) or preferred fully relaxation as soon as possible (OR = 13.571, 95% CI: 7.751 to 23.758) had even lower acceptability. By contrast, rural residents (OR = 0.683, 95% CI: 0.473 to 0.987), students (OR = 0.510, 95% CI: 0.276 to 0.941), public (OR = 0.417, 95% CI: 0.240 to 0.727) and private (OR = 0.562, 95% CI: 0.320 to 0.986) employees, and vaccinated participants (OR = 0.393, 95% CI: 0.204 to 0.756) were more compliant with control measures.

CONCLUSION

More than half of the Chinese public were less supportive of COVID-19 control measures during Omicron-dominant period, which varied based on their different demographic characteristics, cognition and overall attitude towards SARS-CoV-2 infection. Control measures that struck a balance between public safety and individual freedom would be more acceptable during the pandemic.

Oral VV116 versus placebo in patients with mild-to-moderate COVID-19 in China: a multicentre, double-blind, phase 3, randomised controlled study

BACKGROUND

Spread of SARS-CoV-2 led to a global pandemic, and there remains unmet medical needs in the treatment of Omicron infections. VV116, an oral antiviral agent that has potent activity against SARS-CoV-2, was compared with a placebo in this phase 3 study to investigate its efficacy and safety in patients with mild-to-moderate COVID-19.

METHODS

This multicentre, double-blind, phase 3, randomised controlled study enrolled adults in hospitals for infectious diseases and tertiary general hospitals in China. Eligible patients were randomly assigned in a 1:1 ratio using permuted block randomisation to receive oral VV116 (0·6 g every 12 h on day 1 and 0·3 g every 12 h on days 2-5) or oral placebo (on the same schedule as VV116) for 5 days. Randomisation stratification factors included SARS-CoV-2 vaccination status and the presence of high-risk factors for progression to severe COVID-19. Inclusion criteria were a positive SARS-CoV-2 test, an initial onset of COVID-19 symptoms 3 days or less before the first study dose, and a score of 2 or more for any target COVID-19-related symptoms in the 24 h before the first dose. Patients who had severe or critical COVID-19 or who had taken any antiviral drugs were excluded from the study. The primary endpoint was the time to clinical symptom resolution for 2 consecutive days. Efficacy analyses were performed on a modified intention-to-treat population, comprising all patients who received at least one dose of VV116 or placebo, tested positive for SARS-CoV-2 nucleic acid, and did not test positive for influenza virus before the first dose. Safety analyses were done on all participants who received at least one dose of VV116 or placebo. This study was registered with ClinicalTrials.gov, NCT05582629, and has been completed.

FINDINGS

A total of 1369 patients were randomly assigned to treatment groups and 1347 received either VV116 (n=674) or placebo (n=673). At the interim analysis, VV116 was superior to placebo in reducing the time to sustained clinical symptom resolution among 1229 patients (hazard ratio [HR] 1·21, 95% CI 1·04-1·40; p=0·0023). At the final analysis, a substantial reduction in time to sustained clinical symptom resolution was observed for VV116 compared with placebo among 1296 patients (HR 1·17, 95% CI 1·04-1·33; p=0·0009), consistent with the interim analysis. The incidence of adverse events was similar between groups (242 [35·9%] of 674 patients vs 283 [42·1%] of 673 patients).

INTERPRETATION

Among patients with mild-to-moderate COVID-19, VV116 significantly reduced the time to sustained clinical symptom resolution compared with placebo, with no observed safety concerns.

FUNDING

Shanghai Vinnerna Biosciences, Shanghai Science and Technology Commission, and the National Key Research and Development Program of China.

TRANSLATION

For the Chinese translation of the abstract see Supplementary Materials section.

Determinants of COVID-19 vaccination worldwide: WORLDCOV, a retrospective observational study

Introduction

The COVID-19 pandemic has resulted in numerous deaths, great suffering, and significant changes in people's lives worldwide. The introduction of the vaccines was a light in the darkness, but after 18 months, a great disparity in vaccination coverage between countries has been observed. As disparities in vaccination coverage have become a global public health issue, this study aimed to analyze several variables to identify possible determinants of COVID-19 vaccination.

Methods

An ecological study was conducted using pooled secondary data sourced from institutional sites. A total of 205 countries and territories worldwide were included. A total of 16 variables from different fields were considered to establish possible determinants of COVID-19 vaccination: sociodemographic, cultural, infrastructural, economic and political variables, and health system performance indicators. The percentage of the population vaccinated with at least one dose and the total doses administered per 100 residents on 15 June 2022 were identified as indicators of vaccine coverage and outcomes. Raw and adjusted values for delivered vaccine doses in the multivariate GLM were determined using R. The tested hypothesis (i.e., variables as determinants of COVID-19 vaccination) was formulated before data collection. The study protocol was registered with the grant number NCT05471635.

Results

GDP per capita [odds = 1.401 (1.299-1.511) CI 95%], access to electricity [odds = 1.625 (1.559-1.694) CI 95%], political stability, absence of violence/terrorism [odds = 1.334 (1.284-1.387) CI 95%], and civil liberties [odds = 0.888 (0.863-0.914) CI 95%] were strong determinants of COVID-19 vaccination. Several other variables displayed a statistically significant association with outcomes, although the associations were stronger for total doses administered per 100 residents. There was a substantial overlap between raw outcomes and their adjusted counterparts.

Discussion

This pioneering study is the first to analyze the association between several different categories of indicators and COVID-19 vaccination coverage in a wide complex setting, identifying strong determinants of vaccination coverage. Political decision-makers should consider these findings when organizing mass vaccination campaigns in a pandemic context to reduce inequalities between nations and to achieve a common good from a public health perspective.

A comprehensive Drosophila resource to identify key functional interactions between SARS-CoV-2 factors and host proteins

Development of effective therapies against SARS-CoV-2 infections relies on mechanistic knowledge of virus-host interface. Abundant physical interactions between viral and host proteins have been identified, but few have been functionally characterized. Harnessing the power of fly genetics, we develop a comprehensive Drosophila COVID-19 resource (DCR) consisting of publicly available strains for conditional tissue-specific expression of all SARS-CoV-2 encoded proteins, UAS-human cDNA transgenic lines encoding established host-viral interacting factors, and GAL4 insertion lines disrupting fly homologs of SARS-CoV-2 human interacting proteins. We demonstrate the utility of the DCR to functionally assess SARS-CoV-2 genes and candidate human binding partners. We show that NSP8 engages in strong genetic interactions with several human candidates, most prominently with the ATE1 arginyltransferase to induce actin arginylation and cytoskeletal disorganization, and that two ATE1 inhibitors can reverse NSP8 phenotypes. The DCR enables parallel global-scale functional analysis of SARS-CoV-2 components in a prime genetic model system.

An Abies Extract Containing Nonvolatile Polyphenols Shows Virucidal Activity against SARS-CoV-2 That Is Enhanced in Increased pH Conditions

Researching the beneficial health properties of wood byproducts can prevent wastage by turning them into valuable resources. In this study, the virucidal activity of two extracts from Abies sachalinensis byproducts, ASE1, and ASE2, against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was investigated. ASE1 is rich in monoterpenoid volatile compounds, whereas ASE2 contains nonvolatile polyphenols. SARS-CoV-2 solutions were mixed with ASE1 or ASE2, and viral titer reduction was evaluated. At their original acidic pH, ASE2 showed stronger virucidal activity than ASE1. The virucidal activity of ASE2 was also significantly enhanced when pH was increased to neutral or basic, which was not the case for ASE1. At a neutral pH, ASE2 induced statistically significant viral titer reduction in 1 min. HCl and NaOH solutions, which had a pH close to that of acidic and basic ASE2 test mixtures, respectively, exhibited no virucidal activity against SARS-CoV-2. Among the SARS-CoV-2 variants, Omicron showed the highest vulnerability to ASE2. Western blotting, RT-PCR, and electron microscopic analysis revealed that neutral ASE2 interacts with SARS-CoV-2 spike proteins and moderately disrupts the SARS-CoV-2 genome and viral envelope. These findings reveal the virucidal potential of ASE2.

Impact of vaccine measures on the transmission dynamics of COVID-19

In many nations, efforts to prevent and control COVID-19 have been significantly impeded by the SARS-CoV-2 virus ongoing mutation. The Omicron strain, a more recent and prevalent strain, has had more significant detrimental effects in countries worldwide. To investigate the impact of the Omicron BA.2 strain on vaccine efficacy, we proposed a model with vaccination and immunological decline in this research. Then, we fitted our model based on the number of daily new instances reported by the government in Jilin and Shanghai, China. We estimated the effective reproduction number Re = 4.71 for the Jilin and Re = 3.32 for Shanghai. Additionally, we do sensitivity analysis to identify the critical factors affecting the effective reproduction number Re. It was found that vaccination rate, effectiveness rate, and declining rate had a significant effect on Re. Further, we investigate the relevant parameter thresholds that make Re lower than unity. Finally, rich numerical experiments were then carried out. We observed that even when vaccine efficiency was not high, increasing vaccination rates had a significant effect on early disease transmission, that limiting social distance was the most economical and rational measure to control the spread of disease, and that for a short period, reducing immune decline was not significant in curbing disease transmission.

Are We Facing a Tsunami of Vaccine Hesitancy or Outdated Pandemic Policy in Times of Omicron? Analyzing Changes of COVID-19 Vaccination Trends in Poland

In this study, we analyzed Polish COVID-19 vaccination data until January 2023 from the European Centre for Disease Prevention and Control to understand individual decision making during the milder Omicron wave. Our findings show a general decline in subsequent vaccine uptake. As the number of government-provided doses increased, completion rates among certain low-risk groups dropped to less than 1%. Elderly individuals, especially those aged 70–79, showed greater adherence but also exhibited decreased interest in subsequent boosters. Healthcare workers exhibited a dramatic shift in their attitude, disregarding the recommended schedule. The overwhelming majority opted out of receiving the second boosters, while the remaining individuals adjusted their timing based on infection trends or the availability of updated boosters. Two factors positively influenced vaccination decisions: societal influence and the availability of updated boosters. Lower-risk individuals were more likely to postpone vaccination until updated boosters were available. Our findings highlight that while Polish policy aligns with international guidelines, it fails to garner significant adherence from the Polish population. Previous studies have shown that vaccinating low-risk groups resulted in more sick days due to adverse events following immunization than the days gained by preventing infection. Consequently, we advocate for the official abandonment of this policy, as its practical abandonment has already taken place, and persisting in pretending otherwise only serves to erode public trust. Therefore, we propose a shift toward treating COVID-19-like influenza with vaccination for vulnerable individuals and those who have close contact with them before the season.

Are We Facing a Tsunami of Vaccine Hesitancy or Outdated Pandemic Policy in Times of Omicron? Analyzing Changes of COVID-19 Vaccination Trends in Poland

In this study, we analyzed Polish COVID-19 vaccination data until January 2023 from the European Centre for Disease Prevention and Control to understand individual decision making during the milder Omicron wave. Our findings show a general decline in subsequent vaccine uptake. As the number of government-provided doses increased, completion rates among certain low-risk groups dropped to less than 1%. Elderly individuals, especially those aged 70-79, showed greater adherence but also exhibited decreased interest in subsequent boosters. Healthcare workers exhibited a dramatic shift in their attitude, disregarding the recommended schedule. The overwhelming majority opted out of receiving the second boosters, while the remaining individuals adjusted their timing based on infection trends or the availability of updated boosters. Two factors positively influenced vaccination decisions: societal influence and the availability of updated boosters. Lower-risk individuals were more likely to postpone vaccination until updated boosters were available. Our findings highlight that while Polish policy aligns with international guidelines, it fails to garner significant adherence from the Polish population. Previous studies have shown that vaccinating low-risk groups resulted in more sick days due to adverse events following immunization than the days gained by preventing infection. Consequently, we advocate for the official abandonment of this policy, as its practical abandonment has already taken place, and persisting in pretending otherwise only serves to erode public trust. Therefore, we propose a shift toward treating COVID-19-like influenza with vaccination for vulnerable individuals and those who have close contact with them before the season.

Low avidity circulating SARS-CoV-2 reactive CD8+ T cells with proinflammatory TEMRA phenotype are associated with post-acute sequelae of COVID-19

The role of adaptive SARS-CoV-2 specific immunity in post-acute sequelae of COVID-19 (PASC) is not well explored, although a growing population of convalescent COVID-19 patients with manifestation of PASC is observed. We analyzed the SARS-CoV-2-specific immune response, via pseudovirus neutralizing assay and multiparametric flow cytometry in 40 post-acute sequelae of COVID-19 patients with non-specific PASC manifestation and 15 COVID-19 convalescent healthy donors. Although frequencies of SARS-CoV-2-reactive CD4+ T cells were similar between the studied cohorts, a stronger SARS-CoV-2 reactive CD8+ T cell response, characterized by IFNγ production and predominant T_EMRA phenotype but low functional TCR avidity was detected in PASC patients compared to controls. Of interest, high avidity SARS-CoV-2-reactive CD4+ and CD8+ T cells were comparable between the groups demonstrating sufficient cellular antiviral response in PASC. In line with the cellular immunity, neutralizing capacity in PASC patients was not inferior compared to controls. In conclusion, our data suggest that PASC may be driven by an inflammatory response triggered by an expanded population of low avidity SARS-CoV-2 reactive pro-inflammatory CD8+ T cells. These pro-inflammatory T cells with TEMRA phenotype are known to be activated by a low or even without TCR stimulation and lead to a tissue damage. Further studies including animal models are required for a better understanding of underlying immunopathogensis. Summary: A CD8+ driven persistent inflammatory response triggered by SARS-CoV-2 may be responsible for the observed sequelae in PASC patients.

Simultaneous Quantitative SARS-CoV-2 Antigen and Host Antibody Detection and Pre-Screening Strategy at the Point of Care

As COVID-19 pandemic public health measures are easing globally, the emergence of new SARS-CoV-2 strains continue to present high risk for vulnerable populations. The antibody-mediated protection acquired from vaccination and/or infection is seen to wane over time and the immunocompromised populations can no longer expect benefit from monoclonal antibody prophylaxis. Hence, there is a need to monitor new variants and its effect on vaccine performance. In this context, surveillance of new SARS-CoV-2 infections and serology testing are gaining consensus for use as screening methods, especially for at-risk groups. Here, we described an improved COVID-19 screening strategy, comprising predictive algorithms and concurrent, rapid, accurate, and quantitative SARS-CoV-2 antigen and host antibody testing strategy, at point of care (POC). We conducted a retrospective analysis of 2553 pre- and asymptomatic patients who were tested for SARS-CoV-2 by RT-PCR. The pre-screening model had an AUC (CI) of 0.76 (0.73-0.78). Despite being the default method for screening, body temperature had lower AUC (0.52 [0.49-0.55]) compared to case incidence rate (0.65 [0.62-0.68]). POC assays for SARS-CoV-2 nucleocapsid protein (NP) and spike (S) receptor binding domain (RBD) IgG antibody showed promising preliminary results, demonstrating a convenient, rapid (<20 min), quantitative, and sensitive (ng/mL) antigen/antibody assay. This integrated pre-screening model and simultaneous antigen/antibody approach may significantly improve accuracy of COVID-19 infection and host immunity screening, helping address unmet needs for monitoring vaccine effectiveness and severe disease surveillance.

Vaccine hesitancy promotes emergence of new SARS-CoV-2 variants

The successive emergence of SARS-CoV-2 mutations has led to an unprecedented increase in COVID-19 incidence worldwide. Currently, vaccination is considered to be the best available solution to control the ongoing COVID-19 pandemic. However, public opposition to vaccination persists in many countries, which can lead to increased COVID-19 caseloads and hence greater opportunities for vaccine-evasive mutant strains to arise. To determine the extent that public opinion regarding vaccination can induce or hamper the emergence of new variants, we develop a model that couples a compartmental disease transmission framework featuring two strains of SARS-CoV-2 with game theoretical dynamics on whether or not to vaccinate. We combine semi-stochastic and deterministic simulations to explore the effect of mutation probability, perceived cost of receiving vaccines, and perceived risks of infection on the emergence and spread of mutant SARS-CoV-2 strains. We find that decreasing the perceived costs of being vaccinated and increasing the perceived risks of infection (that is, decreasing vaccine hesitation) will decrease the possibility of vaccine-resistant mutant strains becoming established by about fourfold for intermediate mutation rates. Conversely, we find increasing vaccine hesitation to cause both higher probability of mutant strains emerging and more wild-type cases after the mutant strain has appeared. We also find that once a new variant has emerged, perceived risk of being infected by the original variant plays a much larger role than perceptions of the new variant in determining future outbreak characteristics. Furthermore, we find that rapid vaccination under non-pharmaceutical interventions is a highly effective strategy for preventing new variant emergence, due to interaction effects between non-pharmaceutical interventions and public support for vaccination. Our findings indicate that policies that combine combating vaccine-related misinformation with non-pharmaceutical interventions (such as reducing social contact) will be the most effective for avoiding the establishment of harmful new variants.

Social implications of a change in the legal classification of COVID-19: The need for pandemic prevention, preparedness, and healthcare system strengthening

In Japan, there has been a discussion of the potential reclassification of the novel coronavirus infectious disease 2019 (COVID-19) as an infectious disease under the Act on the Prevention of Infectious Diseases and Medical Care for Patients with Infectious Diseases (the Infectious Diseases Control Law), beginning in late 2022. To make an informed decision, the societal impact of COVID-19 needs to be carefully considered to ensure that any reclassification does not negatively impact healthcare or society as a whole. The disease burden of COVID-19 remains considerable and is likely to persist for an extended period of time. Consequently, numerous special measures have been taken in the healthcare system to cope with COVID-19. Several of these measures must be implemented. Thus, the healthcare system needs to be strengthened in the future. This will result in adequate prevention, preparation, and a response to future pandemics.

Relative prevalence-based dispersal in an epidemic patch model

In this paper, we propose a two-patch SIRS model with a nonlinear incidence rate: [Formula: see text] and nonconstant dispersal rates, where the dispersal rates of susceptible and recovered individuals depend on the relative disease prevalence in two patches. In an isolated environment, the model admits Bogdanov-Takens bifurcation of codimension 3 (cusp case) and Hopf bifurcation of codimension up to 2 as the parameters vary, and exhibits rich dynamics such as multiple coexistent steady states and periodic orbits, homoclinic orbits and multitype bistability. The long-term dynamics can be classified in terms of the infection rates [Formula: see text] (due to single contact) and [Formula: see text] (due to double exposures). In a connected environment, we establish a threshold [Formula: see text] between disease extinction and uniform persistence under certain conditions. We numerically explore the effect of population dispersal on disease spread when [Formula: see text] and patch 1 has a lower infection rate, our results indicate: (i) [Formula: see text] can be nonmonotonic in dispersal rates and [Formula: see text] ([Formula: see text] is the basic reproduction number of patch i) may fail; (ii) the constant dispersal of susceptible individuals (or infective individuals) between two patches (or from patch 2 to patch 1) will increase (or reduce) the overall disease prevalence; (iii) the relative prevalence-based dispersal may reduce the overall disease prevalence. When [Formula: see text] and the disease outbreaks periodically in each isolated patch, we find that: (a) small unidirectional and constant dispersal can lead to complex periodic patterns like relaxation oscillations or mixed-mode oscillations, whereas large ones can make the disease go extinct in one patch and persist in the form of a positive steady state or a periodic solution in the other patch; (b) relative prevalence-based and unidirectional dispersal can make periodic outbreak earlier.

Genesis, evolution and effectiveness of Singapore's national sorting logic and home recovery policies in handling the COVID-19 Delta and Omicron waves

Singapore developed several novel strategies to transition towards "living with COVID-19", while protecting hospital capacity. The Home Recovery Programme (HRP) was a national, centrally-administered programme that leveraged technology and telemedicine to allow low-risk individuals to safely recover at home. The HRP was subsequently expanded by partnering primary care doctors in caring for more cases in the community. A key enabler was the National Sorting Logic (NSL), a multi-step triage algorithm allowing risk-stratification of large numbers of COVID-19 patients at a national-level. At the core of the NSL was a risk assessment criterion, comprising of Comorbidities-of-concern, Age, Vaccination status, Examination/clinical findings and Symptoms (CAVES). The NSL sorted all COVID-19 cases into the various levels of care – Primary Care, HRP, COVID-19 Treatment Facility and Hospital. By adopting a national approach towards managing healthcare capacities and triaging COVID-19 patients, Singapore was able to prioritize healthcare resources for high-risk individuals and prevent hospital capacities from being overwhelmed. As part of the national response strategy to tackle COVID-19, Singapore set up and integrated key national databases to enable responsive data analysis and support evidence-based policy decisions. Using data collected between 30 August 2021 to 8 June 2022, we conducted a retrospective cohort study to evaluate the outcomes and effectiveness of vaccination policies, NSL and home-based recovery. A total of 1,240,183 COVID-19 cases were diagnosed during this period, spanning both Delta and Omicron waves, Overall, Singapore experienced very low severity (0.51%) and mortality (0.11%) rates. Vaccinations significantly lowered severity and mortality risks across all age groups. The NSL was effective in predicting risk of severe outcomes and was able to right-site >93% of cases into home-based recovery. By leveraging high vaccination rates, technology and telemedicine, Singapore was able to safely navigate through two COVID-19 waves without impacting severity/mortality rates nor overwhelming hospital capacities.

Protective Effect of Inactivated COVID-19 Vaccines against Omicron BA.2 Infection in Guangzhou: A Test-Negative Case-Control Real-World Study

This study aims to explore the relationship between the doses of inactivated COVID-19 vaccines received and SARS-CoV-2 Omicron infection in the real-world setting, so as to preliminarily evaluate the protective effect induced by COVID-19 vaccination. We conducted a test-negative case-control study and recruited the test-positive cases and test-negative controls in the outbreak caused by Omicron BA.2 in April 2022 in Guangzhou, China. All the participants were 3 years and older. The vaccination status between the case group and the control group was compared in the vaccinated and all participants, respectively, to estimate the immune protection of inactivated COVID-19 vaccines. After adjusting for sex and age, compared with a mere single dose, full vaccination of inactivated COVID-19 vaccines (OR = 0.191, 95% CI: 0.050 to 0.727) and booster vaccination (OR = 0.091, 95% CI: 0.011 to 0.727) had a more superior protective effect. Compared with one dose, the second dose was more effective in males (OR = 0.090), as well as two doses (OR = 0.089) and three doses (OR = 0.090) among individuals aged 18–59. Whereas, when compared with the unvaccinated, one dose (OR = 7.715, 95% CI: 1.904 to 31.254) and three doses (OR = 2.055, 95% CI: 1.162 to 3.635) could contribute to the increased risk of Omicron infection after adjusting for sex and age. Meanwhile, by contrast with unvaccinated individuals, the result of increased risk was also manifested in the first dose in males (OR = 12.400) and one dose (OR = 21.500), two doses (OR = 1.890), and a booster dose (OR = 1.945) in people aged 18–59. In conclusion, the protective effect of full and booster vaccination with inactivated COVID-19 vaccines exceeded the incomplete vaccination, of which three doses were more effective. Nevertheless, vaccination may increase the risk of Omicron infection compared with unvaccinated people. This may result from the transmission traits of BA.2, the particularity and stronger protection awareness of the unvaccinated population, as well as the ADE effect induced by the decrease of antibody titers after a long time of vaccination. It is crucial to explore this issue in depth for the formulation of future COVID-19 vaccination strategies.

Comparison of patients admitted to an inner-city intensive care unit across 3 COVID-19 waves

To expand our limited knowledge of COVID-19-related outcomes in patients admitted to inner-city intensive care unit (ICU across multiple infection waves. This retrospective study compared patients admitted to the ICU in Bronx, NY, during 3 COVID-19 waves (March 2020 to February 2022). Outcomes included in hospital mortality, length of stay (LOS), use of mechanical ventilation, and discharge disposition. The study included 716 patients (343, 276, and 97 in the first, second, and third COVID-19 waves, respectively). The number of days on mechanical ventilation and LOS were lower in the first wave. Of the 345 discharged patients, 37% went home directly, whereas 11% were discharged to a skill nursing facility. More patients went home during the second and third waves. Mortality decreased from the first to the third waves (57%-37%; P < .001). Predictors of mortality included age, male gender, COPD, shock, acute kidney injury (AKI), dialysis requirement, and mechanical ventilation. The decreased mortality and better discharge disposition of these inner-city patients during the second and third waves is encouraging, as this population historically had a high COVID-19-related mortality risk.

Change over Time in the Risk of Death among Japanese COVID-19 Cases Caused by the Omicron Variant Depending on Prevalence of Sublineages

To assess temporal changes to the risk of death in COVID-19 cases caused by the Omicron variant, we calculated age-standardized case fatality rates (CFR) in patients aged ≥40 years over nine diagnostic periods (3 January to 28 August 2022) in ten Japanese prefectures (14.8 million residents). Among 552,581 study subjects, we found that there were 1836 fatalities during the isolation period (up to 28 days from date of onset). The highest age-standardized CFR (0.85%, 95% confidence interval (CI):0.78-0.92) was observed in cases diagnosed in the second 4-week period (January 31 to February 27), after which it declined significantly up to the 6th 4-week period (0.23%, 95% CI: 0.13-0.33, May 23 to June 19). The CFR then increased again but remained at 0.39% in the eighth period (July 18 to August 28). The CFR in cases with the BA.2 or BA.5 sublineages in the age range 60-80 years was significantly lower than that with BA.1 infections (60 years: 0.19%, 0.02%, 0.053%, respectively; 70 years: 0.91%, 0.33%, 0.39%; ≥80 years: 3.78%, 1.96%, 1.81%, respectively). We conclude that the risk of death in Japanese COVID-19 patients infected with Omicron variants declined through February to mid-June 2022.

Clinical Severity in Different Waves of SARS-CoV-2 Infection in Sicily: A Model of Smith's "Law of Declining Virulence" from Real-World Data

BACKGROUND

The COVID-19 epidemic had a rapid spread worldwide with a continuous and fast mutation of the virus, resulting in the emergence of several variants of concern (VOC). The aim of this study was to evaluate the severity of each VOC among SARS-CoV-2 infected subjects by investigating deaths, ICU admissions, intubations, and severe critical symptoms.

METHODS

An ecological observational study was performed to evaluate mortality rates and clinical characteristics of 321,490 unvaccinated Sicilian SARS-CoV-2 cases observed from 2 March 2020 to 27 March 2022. Odds ratios (OR) and 95% confidence intervals (CI) were calculated by multivariate logistic regression analysis evaluating factors determining a clinical worsening.

RESULTS

Delta (adj-OR 3.00, 95% Cls 2.70-3.33) and wild-type (adj-OR 2.41, 95% Cls 2.2-2.62) variants had a higher risk than the Omicron strain for developing critical COVID-19 necessitating intubation and eventually undergoing death. Moreover, males appeared to be significantly more susceptible to developing the worst clinical outcome considered, as did older subjects.

CONCLUSIONS

The present study provides evidence of factors implicated in the worsening of SARS-CoV-2-infection-related clinical outcomes. The study highlighted the different roles of VOC, in particular Delta and wild-type, and being male and elderly in the development of a worse clinical outcome.

Towards the light at the end of the tunnel: Changes in clinical settings and political measures regarding COVID-19 from 2021, and future perspectives in Japan

Japan has faced seven waves of the COVID-19 pandemic since 2020. Due to the less severe Omicron variant and the high rate of vaccination nationwide, the death rate has declined compared to that due to previous variants. In early 2022, current Prime Minister Fumio Kishida devised a new concept entitled "Living with COVID-19", encouraging a new lifestyle of living with SARS-CoV-2. Although treatment and prevention options have increased, the Omicron variant still causes deaths among the most vulnerable population. Before accepting life with SARS-CoV-2, challenges remain, especially with regard to communication, the healthcare system, and vaccination. A society-wide strategy involving multiple stakeholders should be adopted to mitigate the damage and achieve a true world where we are "Living with COVID-19".

Health Care Implications of the COVID-19 Pandemic for the Cardiovascular Practitioner

There has been substantial excess morbidity and mortality during the COVID-19 pandemic, not all of which was directly attributable to SARS-CoV-2 infection, and many non-COVID-19 deaths were cardiovascular. The indirect effects of the pandemic have been profound, resulting in a substantial increase in the burden of cardiovascular disease and cardiovascular risk factors, both in individuals who survived SARS-CoV-2 infection and in people never infected. In this report, we review the direct effect of SARS-CoV-2 infection on cardiovascular and cardiometabolic disease burden in COVID-19 survivors as well as the indirect effects of the COVID-19 pandemic on the cardiovascular health of people who were never infected with SARS-CoV-2. We also examine the pandemic effects on health care systems and particularly the care deficits caused (or exacerbated) by health care delayed or foregone during the COVID-19 pandemic. We review the consequences of: (1) deferred/delayed acute care for urgent conditions; (2) the shift to virtual provision of outpatient care; (3) shortages of drugs and devices, and reduced access to: (4) diagnostic testing, (5) cardiac rehabilitation, and (6) homecare services. We discuss the broader implications of the COVID-19 pandemic for cardiovascular health and cardiovascular practitioners as we move forward into the next phase of the pandemic.

Mathematical modeling for COVID-19 with focus on intervention strategies and cost-effectiveness analysis

The realistic assessments of public health intervention strategies are of great significance to effectively combat the COVID-19 epidemic and the formation of intervention policy. In this paper, an extended COVID-19 epidemic model is devised to assess the severity of the pandemic and explore effective control strategies. The model is characterized by ordinary differential equations with seven-state variables, and it incorporates some parameters associated with the interventions (i.e., media publicity, home isolation, vaccination and face-mask wearing) to investigate the impacts of these interventions on the spread of the COVID-19 epidemic. Some dynamic behaviors of the model, such as forward and backward bifurcation, are analyzed. Specifically, we calibrate the model parameters using actual COVID-19 infected data in Brazil by Markov Chain Monte Carlo algorithm such that we can study the effects of interventions on a practical case. Through a comprehensive exploration of model design and analysis, model calibration, sensitivity analysis, implementation of optimal control problems and cost-effectiveness analysis, the rationality of our model is verified, and the effective strategies to combat the epidemic in Brazil are revealed. The results show that the asymptomatic infected individuals are the main drivers of COVID-19 transmission, and rapid detection of asymptomatic infections is critical to combat the COVID-19 epidemic in Brazil. Interestingly, the effect of the vaccination rate associated with pharmaceutical intervention on the basic reproduction number is much lower than that of non-pharmaceutical interventions (NPIs). Our study also highlights the importance of media publicity. To reduce the infected individuals, the multi-pronged NPIs have considerable positive effects on controlling the outbreak of COVID-19. The infections are significantly decreased by the early implementation of media publicity complemented with home isolation and face-mask wearing strategy. When the cost of implementation is taken into account, the early implementation of media publicity complemented with a face-mask wearing strategy can significantly mitigate the second wave of the epidemic in Brazil. These results provide some management implications for controlling COVID-19.

Detection of Influenza in Managed Quarantine in Australia and the Estimated Risk of Importation

BACKGROUND

Influenza circulated at historically low levels during 2020/2021 due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic travel restrictions. In Australia, international arrivals were required to undergo a 14-day hotel quarantine to limit new introduction of SARS-CoV-2.

METHODS

We usedtesting data for travelers arriving on repatriation flights to Darwin, Australia, from 3 January 2021 to 11 October 2021 to identify importations of influenza virus into Australia. We used this information to estimate the risk of a case exiting quarantine while still infectious. Influenza-positive samples were sequenced, and cases were followed up to identify transmission clusters. Data on the number of cases and total passengers were used to infer the risk of influenza cases exiting quarantine while infectious.

RESULTS

Despite very low circulation of influenza globally, 42 cases were identified among 15 026 returned travelers, of which 30 were A(H3N2), 2 were A(H1N1)pdm09, and 10 were B/Victoria. Virus sequencing data identified potential in-flight transmission, as well as independent infections prior to travel. Under the quarantine strategy in place at the time, the probability that these cases could initiate influenza outbreaks in Australia neared 0. However, this probability rose as quarantine requirements relaxed.

CONCLUSIONS

Detection of influenza virus infections in repatriated travelers provided a source of influenza viruses otherwise unavailable and enabled development of the A(H3N2) vaccine seed viruses included in the 2022 Southern Hemisphere influenza vaccine. Failure to test quarantined returned travelers for influenza represents a missed opportunity for enhanced surveillance to better inform public health preparedness.

Response and Assessment of the Effectiveness of the Countermeasures for a COVID-19 Outbreak - Guizhou Province, China, March 2022

WHAT IS ALREADY KNOWN ABOUT THIS TOPIC?

Many regions in China have recently reported outbreaks of the coronavirus disease 2019 (COVID-19) caused by the Omicron variant.

WHAT IS ADDED BY THIS REPORT?

Wuchuan County, Guizhou Province reacted quickly and implemented accurate intervention measures to effectively control the outbreak. The susceptible-exposed-infectious-asymptomatic-removed (SEIAR) model was applied to evaluate the effectiveness of intervention measures.

WHAT ARE THE IMPLICATIONS FOR PUBLIC HEALTH PRACTICE?

Fast response measures should be taken to prevent the spread of outbreaks caused by the Omicron variant.

SARS-CoV-2 and seasonal influenza: similarities and disparities

This report describes the differences in disease severity and clinical presentation between hospitalized patients with coronavirus disease 2019 (COVID-19) and others with seasonal influenza. A total of 136 influenza and 152 COVID-19 patients were included. Patients with influenza more frequently had dyspnea (p = 0.004), hypoxemia (p < 0.001), underlying diseases (p = 0.046), and elevated liver enzymes (p = 0.028). In contrast, patients with COVID-19 were overweight (p < 0.001), lymphopenic (p < 0.001), had elevated CRP (p = 0.011), and radiological abnormalities (p < 0.001). Patients with influenza were more severely ill on admission (NEWS > 5) (p < 0.001). However, length of hospital stay, ventilatory support, and 30-day-mortality were similar. Despite differences in clinical presentation and disease severity between influenza and COVID-19 patients, both groups had similar clinical outcomes.