Global emerging Omicron variant of SARS-CoV-2: Impacts, challenges and strategies

Enhanced immunity against SARS-CoV-2 in returning Chinese individuals

Global COVID-19 vaccination programs effectively contained the fast spread of SARS-CoV-2. Characterizing the immunity status of returned populations will favor understanding the achievement of herd immunity and long-term management of COVID-19 in China. Individuals were recruited from 7 quarantine stations in Guangzhou, China. Blood and throat swab specimens were collected from participants, and their immunity status was determined through competitive ELISA, microneutralization assay and enzyme-linked FluoroSpot assay. A total of 272 subjects were involved in the questionnaire survey, of whom 235 (86.4%) were returning Chinese individuals and 37 (13.6%) were foreigners. Blood and throat swab specimens were collected from 108 returning Chinese individuals. Neutralizing antibodies against SARS-CoV-2 were detected in ~90% of returning Chinese individuals, either in the primary or the homologous and heterologous booster vaccination group. The serum NAb titers were significantly decreased against SARS-CoV-2 Omicron BA.5, BF.7, BQ.1 and XBB.1 compared with the prototype virus. However, memory T-cell responses, including specific IFN-γ and IL-2 responses, were not different in either group. Smoking, alcohol consumption, SARS-CoV-2 infection, COVID-19 vaccination, and the time interval between last vaccination and sampling were independent influencing factors for NAb titers against prototype SARS-CoV-2 and variants of concern. The vaccine dose was the unique common influencing factor for Omicron subvariants. Enhanced immunity against SARS-CoV-2 was established in returning Chinese individuals who were exposed to reinfection and vaccination. Domestic residents will benefit from booster homologous or heterologous COVID-19 vaccination after reopening of China, which is also useful against breakthrough infection.

Human monoclonal antibody F61 nasal spray effectively protected high-risk populations from SARS-CoV-2 variants during the COVID-19 pandemic from late 2022 to early 2023 in China

Following the national dynamic zero-COVID strategy adjustment, the utilization of broad-spectrum nasal neutralizing antibodies may offer an alternative approach to controlling the outbreak of Omicron variants between late 2022 and early 2023 in China. This study involved an investigator-initiated trial (IIT) to assess the pharmacokinetic, safety and efficacy of the F61 nasal spray. A total of 2,008 participants were randomly assigned to receive F61 nasal spray (24 mg/0.8 mL/dose) or normal saline (0.8 mL/dose) and 1336 completed the follow-up in the IIT. Minimal absorption of F61 antibody into the bloodstream was detected in individuals receiving F61 nasal spray for seven consecutive days. No treatment-emergent adverse reactions of grade 3 severity or higher were reported. In the one-dose cohort, the 7-day cumulative SARS-CoV-2 infection rate was 79.0% in the F61 group and 82.6% in the placebo group, whereas, in the multiple-dose (once daily for 7 consecutive days) cohort, the rates were 6.55% in the F61 group and 23.83% in the placebo group. The laboratory-confirmed efficacy of F61 was 3.78% (-3.74%-10.75%) in the one-dose cohort and 72.19% (57.33%-81.87%) in the multiple-dose cohort. In the real-world study, 60,225 volunteers in four different regions were administered the F61 nasal spray based on the subject's wishes, over 90% efficacy rate was observed against different Omicron variants. The F61 nasal spray, with its favourable safety profile, could be a promising prophylactic monoclonal antibody against SARS-CoV-2 VOCs.

Estimate the number of lives saved by a SARS-CoV-2 vaccination campaign in six states in the United States with a simple model

Objectives

Vaccination and the emergence of the highly transmissible Omicron variant changed the fate of the COVID-19 pandemic. It is very challenging to estimate the number of lives saved by vaccination given the multiple doses of vaccination, the time-varying nature of transmissibility, the waning of immunity, and the presence of immune evasion.

Methods

We established a S-SV-E-I-T-D-R model to simulate the number of lives saved by vaccination in six states in the United States (U.S.) from March 5, 2020, to March 23, 2023. The cumulative number of deaths were estimated under three vaccination scenarios based on two assumptions. Additionally, immune evasion by the Omicron and loss of protection afforded by vaccination or infection were considered.

Results

The number of deaths averted by COVID-19 vaccinations (including three doses) ranged from 0.154-0.295% of the total population across six states. The number of deaths averted by the third dose ranged from 0.008-0.017% of the total population.

Conclusions

Our estimate of death averted by COVID-19 vaccination in the U.S. was largely in line with an official estimate (at a level of 0.15-0.20% of the total population). We found that the additional contribution of the third dose was small but significant.

A Natural Bioactive Peptide from Pinctada fucata Pearls Can Be Used as a Potential Inhibitor of the Interaction between SARS-CoV-2 and ACE2 against COVID-19

The frequent occurrence of viral infections poses a serious threat to human life. Identifying effective antiviral components is urgent. In China, pearls have been important traditional medicinal ingredients since ancient times, exhibiting various therapeutic properties, including detoxification properties. In this study, a peptide, KKCH, which acts against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was derived from Pinctada fucata pearls. Molecular docking showed that it bound to the same pocket of the SARS-CoV-2 S protein and cell surface target angiotensin-converting enzyme II (ACE2). The function of KKCH was analyzed through surface plasmon resonance (SPR), Enzyme-Linked Immunosorbent Assays, immunofluorescence, and simulation methods using the SARS-CoV-2 pseudovirus and live virus. The results showed that KKCH had a good affinity for ACE2 (KD = 6.24 × 10-7 M) and could inhibit the binding of the S1 protein to ACE2 via competitive binding. As a natural peptide, KKCH inhibited the binding of the SARS-CoV-2 S1 protein to the surface of human BEAS-2B and HEK293T cells. Moreover, viral experiments confirmed the antiviral activity of KKCH against both the SARS-CoV-2 spike pseudovirus and SARS-CoV-2 live virus, with half-maximal inhibitory concentration (IC50) values of 398.1 μM and 462.4 μM, respectively. This study provides new insights and potential avenues for the prevention and treatment of SARS-CoV-2 infections.

Effect of occupational stress and resilience on insomnia among nurses during COVID-19 in China: a structural equation modelling analysis

OBJECTIVES

To explore the effects of occupational stress and resilience on insomnia among Chinese nurses during the COVID-19 pandemic.

DESIGN, SETTINGS AND PARTICIPANTS

A quantitative description study. The data were collected via a cross-sectional survey. A total of 725 front-line nurses at three tertiary hospitals in western China were included from December 2022 to January 2023. The Connor-Davidson Resilience Scale, Job Content Questionnaire, and Athens Insomnia Scale were used to collect data from a self-reported online questionnaire.

OUTCOME MEASURES

The outcome variable was insomnia, and structural equation modelling was used to assess the associations among resilience, occupational stress and insomnia.

RESULTS

The prevalence of insomnia among the participants was 58.76%. The structural equation model showed that resilience had a negative direct effect on insomnia and occupational stress, and occupational stress had a positive direct effect on insomnia. Involvement in COVID-19-related work has a positive effect on insomnia through occupational stress. In contrast, higher education levels improved insomnia through increased resilience.

CONCLUSION

A significantly higher prevalence of insomnia has been observed among Chinese nurses during the COVID-19 pandemic. Our study suggests that better resilience may improve insomnia by relieving occupational stress, and implementing measures to promote resilience is essential to reduce occupational stress in nurses and improve their sleep quality.

SARS-CoV-2 Molecular Evolution: A Focus on Omicron Variants in Umbria, Italy

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 6 million deaths worldwide, and the spread of new variants over time increased the ability of this virus to cause infection. The Omicron variant was detected for the first time in Umbria, a region of central Italy, in November 2021 and it induced an unprecedented increase in the number of infection cases. Here, we analysed 3300 SARS-CoV-2 positive samples collected in Umbria between April 2022 and December 2023. We traced the molecular evolution of SARS-CoV-2 variants over time through the Next-Generation Sequencing (NGS) approach. We assessed correlation between SARS-CoV-2 infection and patients' health status. In total, 17.3% of our samples came from patients hospitalised as a consequence of COVID-19 infection even though 81.4% of them received at least three vaccine doses. We identified only Omicron variants, and the BA.5 lineage was detected in the majority of our samples (49.2%). Omicron variants outcompeted each other through the acquisition of mutations especially in Spike glycoprotein that are fingerprints of each variant. Viral antigenic evolution confers higher immunological escape and makes a continuous improvement of vaccine formulation necessary. The continuous update of international genomic databases with sequencing results obtained by emergent pathogens is essential to manage a possible future pandemic.

Comparative analysis of prognostic scoring systems in predicting severity and outcomes of Omicron variant COVID-19 pneumonia

Background

The global spread of Coronavirus Disease 2019 (COVID-19) underscores the urgent need for reliable methods to forecast the disease's severity and outcome, thereby facilitating timely interventions and reducing mortality rates. This study focuses on evaluating the clinical and laboratory profiles of patients with Omicron variant-induced COVID-19 pneumonia and assessing the efficacy of various scoring systems in prognosticating disease severity and mortality.

Methods

In this retrospective analysis, we examined the clinical records of 409 individuals diagnosed with Omicron variant COVID-19 pneumonia. We documented the Pneumonia Severity Index, CURB-65, and MuLBSTA scores within the first 24 h and analyzed the sensitivity, specificity, positive predictive value, negative predictive value, and the area under the receiver operating characteristic curve for each scoring system to ascertain their predictive accuracy for disease severity and fatality risk.

Results

The cohort's median age was 78 years, predominantly presenting with fever, cough, expectoration, fatigue, and gastrointestinal symptoms. Factors such as expectoration, fatigue, Glasgow Coma Scale score, lactate dehydrogenase levels, procalcitonin, creatinine levels, and co-occurrence of acute respiratory distress syndrome were identified as independent predictors of disease severity. Furthermore, age, oxygenation index, glucose levels, lactate dehydrogenase, and septic shock were independently associated with mortality. For severe disease prediction, the CURB-65, PSI, and MuLBSTA scores demonstrated sensitivities of 65.9%, 63.8%, and 79.7%, respectively, with specificities of 63.8%, 76.8%, and 60.9%, and AUROCs of 0.707, 0.750, and 0.728. To predict mortality risk, these scores at cutoffs of 1.5, 102.5, and 12.5 exhibited sensitivities of 83.3%, 96.3%, and 70.4%, specificities of 59.4%, 60.8%, and 65.4%, and AUROCs of 0.787, 0.850, and 0.736, respectively.

Conclusion

The study cohort predominantly comprised elderly individuals with pre-existing health conditions. Elevated lactate dehydrogenase emerged as a significant marker for both disease severity and prognosis, sputum production, gastrointestinal symptoms, GCS score, creatinine, PCT, and ARDS as independent predictors of disease severity, and age, oxygenation index, glucose levels, and septic shock as independent mortality predictors in COVID-19 pneumonia patients. Among the scoring systems evaluated, Pneumonia Severity Index demonstrated superior predictive capability for both disease severity and mortality, suggesting its utility in forecasting the clinical outcomes of Omicron variant COVID-19 pneumonia.

Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia: A Retrospective Genomic Surveillance Study

Mutations have driven the evolution and development of new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with potential implications for increased transmissibility, disease severity and vaccine escape among others. Genome sequencing is a technique that allows scientists to read the genetic code of an organism and has become a powerful tool for studying emerging infectious diseases. Here, we conducted a cross-sectional study in selected districts of the Eastern Province of Zambia, from November 2021 to February 2022. We analyzed SARS-CoV-2 samples (n = 76) using high-throughput sequencing. A total of 4097 mutations were identified in 69 SARS-CoV-2 genomes with 47% (1925/4097) of the mutations occurring in the spike protein. We identified 83 unique amino acid mutations in the spike protein of the seven Omicron sublineages (BA.1, BA.1.1, BA.1.14, BA.1.18, BA.1.21, BA.2, BA.2.23 and XT). Of these, 43.4% (36/83) were present in the receptor binding domain, while 14.5% (12/83) were in the receptor binding motif. While we identified a potential recombinant XT strain, the highly transmissible BA.2 sublineage was more predominant (40.8%). We observed the substitution of other variants with the Omicron strain in the Eastern Province. This work shows the importance of pandemic preparedness and the need to monitor disease in the general population.

Managing and treating COVID-19 in patients with hematological malignancies: a narrative review and expert insights

Patients with hematologic malignancies (HMs) are at a significantly higher risk of contracting COVID-19 and experiencing severe outcomes compared to individuals without HMs. This heightened risk is influenced by various factors, including the underlying malignancy, immunosuppressive treatments, and patient-related factors. Notably, immunosuppressive regimens commonly used for HM treatment can lead to the depletion of B cells and T cells, which is associated with increased COVID-19-related complications and mortality in these patients. As the pandemic transitions into an endemic state, it remains crucial to acknowledge and address the ongoing risk for individuals with HMs. In this review, we aim to summarize the current evidence to enhance our understanding of the impact of HMs on COVID-19 risks and outcomes, identify particularly vulnerable individuals, and emphasize the need for specialized clinical attention and management. Furthermore, the impaired immune response to COVID-19 vaccination observed in these patients underscores the importance of implementing additional mitigation strategies. This may include targeted prophylaxis and treatment with antivirals and monoclonal antibodies as indicated. To provide practical guidance and considerations, we present two illustrative cases to highlight the real-life challenges faced by physicians caring for patients with HMs, emphasizing the need for individualized management based on disease severity, type, and the unique circumstances of each patient.

Urban Wastewater-Based Surveillance of SARS-CoV-2 Virus: A Two-Year Study Conducted in City of Patras, Greece

Wastewater-based epidemiology, during the COVID-19 pandemic years, has been applied as a complementary approach, worldwide, for tracking SARS-CoV-2 virus into the community and used as an early warning of the prevalence of COVID-19 infection. The present study presents the results of the 2-year surveillance project, in the city of Patras, Greece. The purpose of the study was to monitor SARS-CoV-2 and implement WBE as an early warning method of monitoring Public Health impact. The presence of SARS-CoV-2 was determined and quantified in 310 samples using RT-qPCR assays. For the years 2022 and 2023, 93.5% and 78.7% of samples were found positive, respectively. Comparison of detection methods have been conducted to select the method with the highest recovery of the viral load. A seasonal variation of the virus was recorded, showing a recession in summer months confirming the country's epidemiological data as indicated by positive correlation of wastewater viral load with registered cases of COVID-19 infections during these years (p < 0.05) and moreover sealed with a significant negative correlation observed with Daily Average (p < 0.01) and Daily Maximum Temperature (p < 0.01). More research was carried out to elucidate a possible association of physicochemical characteristics of wastewater with viral load showing positive correlation with Chlorides (p < 0.01) advocating possible increased use of chlorine-based disinfectants and Electrical Conductivity (p < 0.01) indicates that wastewater during periods of increased infections is more heavily loaded with ions from chemical and biological pollutants. No correlation found with rainfall and physicochemical indicators, such as COD, BOD5, Total Phosphorus, Total Nitrogen, and Total Suspended Solids. According to the findings, WBE represents a useful tool in the management of epidemics based on an environmental approach and it can also shed light on the interacting parameters that capture Public Health since any infections that may lead to epidemics lead to a parallel change in the use of pharmaceuticals, antimicrobials, disinfectants, and microbial load in urban wastewater.

Prediction of potential public health risk of the recent multicountry monkeypox outbreak: An update after the end declaration of global public health emergency

Background and Aims

A double-stranded DNA virus called monkeypox virus (MPV) belonging to the Poxviridae family and Orthopoxvirus genus causes monkeypox (mpox) infection. This virus used to infect only Central, East, and West Africa. However, it has spread to an extent outside Africa recently. The range of MPV outbreaks was so high that on July 23, 2022, the World Health Organization (WHO) declared it a Public Health Emergency of International Concern (PHEIC). About a year later, the WHO notified the end of a global public health emergency for mpox on May 11, 2023. Here, we aimed to assess the current pathogenicity and potential risk of MPV causing public health emergencies.

Methods

We searched information from published articles available in PubMed, Scopus, and ScienceDirect. We used monkeypox, mpox, monkeypox outbreak, and monkeypox virus as keywords during the literature search.

Results

Many new variants of MPV have emerged throughout the world that created PHEIC for mpox. Considering the low lethality and transmission rate, mpox is no longer a global public health threat. In addition, the availability of therapeutic and preventive measures helped the healthcare authorities fight the mpox infection in an efficient manner. In this review, we have portrayed the history and evolution of mpox from past to present and an idea of its future outcomes. Also, we have discussed the symptoms related to mpox and approved antiviral treatment strategies to fight off the infection in this piece. This review also emphasized the preventive guidelines set by the WHO for patients, caregivers, and healthcare providers to control the outbreak of mpox infection.

Conclusion

We believe this article would give an idea about the potential public health threats of the recent multi-country monkeypox outbreak to the healthcare authorities for taking measures accordingly.

New variants of COVID-19 (XBB.1.5 and XBB.1.16, the "Arcturus"): A review of highly questioned concerns, a brief comparison between different peaks in the COVID-19 pandemic, with a focused systematic review on expert recommendations for prevention, vaccination, and treatment measures in the general population and at-risk groups

INTRODUCTION

The COVID-19 pandemic has taken many forms and continues to evolve, now around the Omicron wave, raising concerns over the globe. With COVID-19 being declared no longer a "public health emergency of international concern (PHEIC)," the COVID pandemic is still far from over, as new Omicron subvariants of interest and concern have risen since January of 2023. Mainly with the XBB.1.5 and XBB.1.16 subvariants, the pandemic is still very much "alive" and "breathing."

METHODS

This review consists of five highly concerning questions about the current state of the COVID Omicron peak. We searched four main online databases to answer the first four questions. For the last one, we performed a systematic review of the literature, with keywords "Omicron," "Guidelines," and "Recommendations."

RESULTS

A total of 31 articles were included. The main symptoms of the current Omicron wave include a characteristically high fever, coughing, conjunctivitis (with itching eyes), sore throat, runny nose, congestion, fatigue, body ache, and headache. The median incubation period of the symptoms is shorter than the previous peaks. Vaccination against COVID can still be considered effective for the new subvariants.

CONCLUSION

Guidelines recommend continuation of personal protective measures, third and fourth dose boosters, along with administration of bivalent messenger RNA vaccine boosters. The consensus antiviral treatment is combination therapy using Nirmatrelvir and Ritonavir, and the consensus for pre-exposure prophylaxis is Tixagevimab and Cilgavimab combination. We hope the present paper raises awareness for the continuing presence of COVID and ways to lower the risks, especially for at-risk groups.

Clinical and prognostic implications of hyaluronic acid in patients with COVID-19 reinfection and first infection

Objective

Previous research has shown that human identical sequences of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) promote coronavirus disease 2019 (COVID-19) progression by upregulating hyaluronic acid (HA). However, the association of HA with mortality and long COVID in SARS-CoV-2 reinfection and first infection is unclear.

Methods

Patients with COVID-19 at Beijing Ditan Hospital from September 2023 to November 2023 were consecutively enrolled. SARS-CoV-2 reinfections were matched 1:2 with first infections using a nearest neighbor propensity score matching algorithm. We compared the hospital outcomes between patients with COVID-19 reinfection and first infection. The association between HA levels and mortality and long COVID in the matched cohort was analyzed.

Results

The reinfection rate among COVID-19 hospitalized patients was 25.4% (62 cases). After propensity score matching, we found that reinfection was associated with a better clinical course and prognosis, including lower levels of C-reactive protein and erythrocyte sedimentation rate, fewer cases of bilateral lung infiltration and respiratory failure, and shorter viral clearance time and duration of symptoms (p < 0.05). HA levels were significantly higher in patients with primary infection [128.0 (90.5, 185.0) vs. 94.5 (62.0, 167.3), p = 0.008], those with prolonged viral clearance time [90.5 (61.5, 130.8) vs. 130.0 (95.0, 188.0), p < 0.001], and deceased patients [105.5 (76.8, 164.5) vs. 188.0 (118.0, 208.0), p = 0.002]. Further analysis showed that HA was an independent predictor of death (AUC: 0.789), and the risk of death increased by 4.435 times (OR = 5.435, 95% CI = 1.205-24.510, p = 0.028) in patients with high HA levels. We found that patients with HA levels above 116 ng/mL had an increased risk of death. However, the incidence of long COVID was similar in the different HA level groups (p > 0.05).

Conclusion

Serum HA may serve as a novel biomarker for predicting COVID-19 mortality in patients with SARS-CoV-2 reinfection and first infection. However, HA levels may not be associated with long COVID.

Combination of spironolactone and DPP-4 inhibitors for treatment of SARS-CoV-2 infection: a literature review

Coronavirus disease 2019 (COVID-19) is still causing hospitalization and death, and vaccination appears to become less effective with each emerging variant. Spike, non-spike, and other possible unrecognized mutations have reduced the efficacy of recommended therapeutic approaches, including monoclonal antibodies, plasma transfusion, and antivirals. SARS-CoV-2 binds to angiotensin-converting enzyme 2 (ACE2) and probably dipeptidyl peptidase 4 (DPP-4) to initiate the process of endocytosis by employing host proteases such as transmembrane serine protease-2 (TMPRSS-2) and ADAM metallopeptidase domain 17 (ADAM17). Spironolactone reduces the amount of soluble ACE2 and antagonizes TMPRSS-2 and ADAM17. DPP-4 inhibitors play immunomodulatory roles and may block viral entry. The efficacy of treatment with a combination of spironolactone and DPP-4 inhibitors does not appear to be affected by viral mutations. Therefore, the combination of spironolactone and DPP-4 inhibitors might improve the clinical outcome for COVID-19 patients by decreasing the efficiency of SARS-CoV-2 entry into cells and providing better anti-inflammatory, antiproliferative, and antifibrotic effects than those achieved using current therapeutic approaches such as antivirals and monoclonal antibodies.

Reverse Zoonotic Transmission of SARS-CoV-2 and Monkeypox Virus: A Comprehensive Review

Reverse zoonosis reveals the process of transmission of a pathogen through the human-animal interface and the spillback of the zoonotic pathogen. In this article, we methodically demonstrate various aspects of reverse zoonosis, with a comprehensive discussion of SARS-CoV-2 and MPXV reverse zoonosis. First, different components of reverse zoonosis, such as humans, different pathogens, and numerous animals (poultry, livestock, pets, wild animals, and zoo animals), have been demonstrated. Second, it explains the present status of reverse zoonosis with different pathogens during previous occurrences of various outbreaks, epidemics, and pandemics. Here, we present 25 examples from literature. Third, using several examples, we comprehensively illustrate the present status of the reverse zoonosis of SARS-CoV-2 and MPXV. Here, we have provided 17 examples of SARS-CoV-2 reverse zoonosis and two examples of MPXV reverse zoonosis. Fourth, we have described two significant aspects of reverse zoonosis: understanding the fundamental aspects of spillback and awareness. These two aspects are required to prevent reverse zoonosis from the current infection with two significant viruses. Finally, the One Health approach was discussed vividly, where we urge scientists from different areas to work collaboratively to solve the issue of reverse zoonosis.

The second dose of COVID-19 vaccine booster hesitancy among health care workers in China: A multicenter cross-sectional study

BACKGROUND

The COVID-19 outbreak in China exposed health care workers (HCWs) to an increased risk of infection. The acquired immunity rapidly diminishes after the previous COVID-19 vaccination and the second booster vaccination has been recommended in several countries. HCWs are a priority group for vaccination because they are at increased risk of being infected, however, a certain amount of HCWs were hesitant.

METHODS

The survey was conducted among 5805 HCWs in China from January 5 to February 9, 2023. Questionnaire included sociodemographic information, COVID-19-related variables, psychological factors, and the COVID-19 vaccine hesitancy scale. Multiple logistic regression analysis was used to assess the influencing factors of the second dose of COVID-19 vaccine booster hesitancy.

RESULTS

42.2% of HCWs self-reported having the second dose of COVID-19 vaccine booster hesitancy. Occupations, years of working, COVID-19 infection status were associated with less vaccine hesitancy. HCWs who had received 3 doses of COVID-19 vaccine were less likely to be hesitant compared to those had not received. HCWs with PTSD symptoms and anxiety symptoms were more likely to be hesitant. No relation was observed between COVID-19 vaccine booster hesitancy and age, marriage, salary, and perceived an increased risk of COVID-19 infection due to work (all P > 0.05).

CONCLUSIONS

A considerable proportion of HCWs were hesitant to accept the second dose of the COVID-19 booster vaccine. Incorporating vaccine knowledge and new evidence into routine health educations and procedures to raise confidence and reduce complacency may be effective and feasible in promoting the vaccination and implementing future vaccination programs.

A universal recombinant adenovirus type 5 vector-based COVID-19 vaccine

A universal recombinant adenovirus type-5 (Ad5) vaccine against COVID19 (Ad-US) was constructed, and immunogenicity and broad-spectrum of Ad5-US were evaluated with both intranasal and intramuscular immunization routes. The humoral immune response of Ad5-US in serum and bronchoalveolar lavage fluid were evaluated by the enzyme-linked immunosorbent assay (ELISA), recombinant vesicular stomatitis virus based pseudovirus neutralization assay, and angiotensin-converting enzyme-2 (ACE2) -binding inhibition assay. The cellular immune response and Th1/Th2 biased immune response of Ad5-US were evaluated by the IFN-γ ELISpot assay, intracellular cytokine staining, and Meso Scale Discovery (MSD) profiling of Th1/Th2 cytokines. Intramuscular priming followed by an intranasal booster with Ad5-US elicited the broad-spectrum and high levels of IgG, IgA, pseudovirus neutralizing antibody (PNAb), and Th1-skewing of the T-cell response. Overall, the adenovirus type-5 vectored universal SARS-CoV-2 vaccine Ad5-US was successfully constructed, and Ad5-US was highly immunogenic and broad spectrum. Intramuscular priming followed by an intranasal booster with Ad5-US induced the high and broad spectrum systemic immune responses and local mucosal immune responses.

PASC (Post Acute Sequelae of COVID-19) is associated with decreased neutralizing antibody titers in both biological sexes and increased ANG-2 and GM-CSF in females

Post-acute sequelae of COVID-19 (PASC) or the continuation of COVID-19 (Coronavirus disease 2019) symptoms past 12 weeks may affect as many as 30% of people recovering from a SARS-CoV-2 (severe acute respiratory coronavirus 2) infection. The mechanisms regulating the development of PASC are currently not known; however, hypotheses include virus reservoirs, pre-existing conditions, microblood clots, immune dysregulation, as well as poor antibody responses. Importantly, virus neutralizing antibodies are essential for COVID-19 recovery and protection from reinfection but there is currently limited information on these immune regulators and associated cytokines in PASC patients. Understanding the key drivers of general and specific symptoms associated with Long COVID and the presence of virus neutralizing antibodies in PASC will aid in the development of therapeutics, diagnostics, and vaccines which currently do not exist. We designed a cross-sectional study to investigate systemic antibody and cytokine responses during COVID-19 recovery and PASC. In total, 195 participants were recruited in one of four groups: (1) Those who never had COVID-19 (No COVID); (2) Those in acute COVID-19 recovery (Acute Recovery) (4-12 weeks post infection); (3) Those who recovered from COVID-19 (Recovered) (+ 12 weeks from infection); and (4) those who had PASC (PASC) (+ 12 weeks from infection). Participants completed a questionnaire on health history, sex, gender, demographics, experiences with COVID-19 acute and COVID-19 recovery/continuing symptoms. Serum samples collected were evaluated for antibody binding to viral proteins, virus neutralizing antibody titers, and serum cytokine levels using Ella SimplePlex Immunoassay™ panels. We found participants with PASC reported more pre-existing conditions (e.g. such as hypertension, asthma, and obesity), and PASC symptoms (e.g. fatigue, brain fog, headaches, and shortness of breath) following COVID-19 than COVID-19 Recovered individuals. Importantly, we found PASC individuals to have significantly decreased levels of neutralizing antibodies toward both SARS-CoV-2 and the Omicron BA.1 variant. Sex analysis indicated that female PASC study participants had sustained antibody levels as well as levels of the inflammatory cytokines GM-CSF and ANG-2 over time following COVID-19. Our study reports people experiencing PASC had lower levels of virus neutralizing antibodies; however, the results are limited by the collection time post-COVID-19 and post-vaccination. Moreover, we found females experiencing PASC had sustained levels of GM-CSF and ANG-2. With lower levels of virus neutralizing antibodies, this data suggests that PASC individuals not only have had a suboptimal antibody response during acute SARS-CoV-2 infection but may also have increased susceptibility to subsequent infections which may exacerbate or prolong current PASC illnesses. We also provide evidence suggesting GM-CSF and ANG-2 to play a role in the sex-bias of PASC. Taken together, our findings maybe important for understanding immune molecular drivers of PASC and PASC subgroups.

Real life experience on the use of Remdesivir in patients admitted to COVID-19 in two referral Italian hospital: a propensity score matched analysis

Remdesivir (RDV) was the first Food and Drug Administration (FDA)-approved medication for COVID-19, with discordant data on efficacy in reducing mortality risk and disease progression. In the context of a dynamic and rapidly changing pandemic landscape, the utilization of real-world evidence is of utmost importance. The objective of this study is to evaluate the impact of RDV on patients who have been admitted to two university referral hospitals in Italy due to COVID-19. All patients older than 18 years and hospitalized at two different universities (Bari and Palermo) were enrolled in this study. To minimize the effect of potential confounders, we used propensity score matching with one case (Remdesivir) and one control that never experienced this kind of intervention during hospitalization. Mortality was the primary outcome of our investigation, and it was recorded using death certificates and/or medical records. Severe COVID-19 was defined as admission to the intensive care unit or a qSOFAscore ≥ 2 or CURB65scores ≥ 3. After using propensity score matching, 365 patients taking Remdesivir and 365 controls were included. No significant differences emerged between the two groups in terms of mean age and percentage of females, while patients taking Remdesivir were less frequently active smokers (p < 0.0001). Moreover, the patients taking Remdesivir were less frequently vaccinated against COVID-19. All the other clinical, radiological, and pharmacological parameters were balanced between the two groups. The use of Remdesivir in our cohort was associated with a significantly lower risk of mortality during the follow-up period (HR 0.56; 95% CI 0.37-0.86; p = 0.007). Moreover, RDV was associated with a significantly lower incidence of non-invasive ventilation (OR 0.27; 95% CI 0.20-0.36). Furthermore, in the 365 patients taking Remdesivir, we observed two cases of mild renal failure requiring a reduction in the dosage of Remdesivir and two cases in which the physicians decided to interrupt Remdesivir for bradycardia and for QT elongation. Our study suggests that the use of Remdesivir in hospitalized COVID-19 patients is a safe therapy associated with improved clinical outcomes, including halving of mortality and with a reduction of around 75% of the risk of invasive ventilation. In a constantly changing COVID-19 scenario, ongoing research is necessary to tailor treatment decisions based on the latest scientific evidence and optimize patient outcomes.

Acceptance, safety, and immunogenicity of a booster dose of inactivated SARS-CoV-2 vaccine in patients with primary biliary cholangitis

Inactivated coronavirus disease 2019 (COVID-19) vaccines showed impaired immunogenicity in some autoimmune diseases, but it remains unclear in primary biliary cholangitis (PBC). This study aimed to explore the antibody response to the inactivated COVID-19 vaccine in individuals with PBC, as well as to evaluate coverage, safety, and attitudes toward the COVID-19 vaccine among them. Two cohorts of patients with PBC were enrolled in this study. One cohort was arranged to evaluate the immunogenicity of the inactivated COVID-19 vaccine, another cohort participated in an online survey. The titers of the anti-receptor-binding domain (RBD)-specific immunoglobulin G (IgG), neutralizing antibody (NAb) toward severe acute respiratory syndrome coronavirus 2 wild-type, and NAb toward Omicron BA.4/5 subvariants were detected to assess antibody response from the vaccine. After booster vaccination for more than six months, patients with PBC had significantly lowered levels of anti-RBD-specific IgG compared to HCs, and the inhibition rates of NAb toward wild-type also declined in individuals with PBC. The detected levels of NAb toward Omicron BA.4/5 were below the positive threshold in patients with PBC and HCs. Laboratory parameters did not significantly correlate with any of the three antibodies. The online survey revealed that 24% of patients with PBC received three COVID-19 vaccines, while 63% were unimmunized. Adverse effect rates after the first, second, and third vaccine doses were 6.1%, 10.3%, and 9.5%, respectively. Unvaccinated patients with PBC were more worried about the safety of the vaccine than those who were vaccinated (P = 0.004). As a result, this study fills the immunological assessment gap in patients with PBC who received inactivated COVID-19 vaccines.

A mini review of reinfection with the SARS-CoV-2 Omicron variant

Background

COVID-19 has caused severe morbidity and mortality worldwide. After the end of the dynamic zero-COVID policy in China in December, 2022, concerns regarding reinfection were raised while little was known due to the lack of surveillance data in this country.

Aims

This study reviews the probability, risk factors, and severity of severe acute respiratory syndrome coronavirus 2 Omicron variant reinfection, as well as the interval between infections, risk of onward transmission by reinfected cases, and the role of booster vaccination against reinfection.

Sources

References for this review were identified through searches of PubMed and Web of Science up to September 24, 2023.

Results

The rate of reinfection ranges from 3.1% to 13.0%. Factors associated with a higher risk of reinfection include being female, having comorbidities, and being unvaccinated. Reinfection with the BA.4 or BA.5 variant occurs approximately 180 days after the initial infection. Reinfections are less clinically severe than primary infections, and there is evidence of lower transmissibility. The debate surrounding the effectiveness and feasibility of booster vaccinations in preventing reinfection continues.

Conclusions

The reinfection rate during the Omicron epidemic is significantly higher than in previous epidemic periods. However, the symptoms and infectivity of reinfection were weaker than those of the prior infection. Medical staff and individuals at high risk of reinfection should be vigilant. The efficacy of booster vaccinations in reducing reinfection is currently under debate.

Detection of SARS-CoV-2 and Omicron variant RNA in wastewater samples from Manila, Philippines

Manila, a highly urbanized city, is listed as one of the top cities with the highest recorded number of coronavirus disease 2019 (COVID-19) cases in the Philippines. This study aimed to detect and quantify the RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the Omicron variant in 51 wastewater samples collected from three locations in Manila, namely Estero de Santa Clara, Estero de Pandacan, which are open drainages, and a sewage treatment plant (STP) at De La Salle University-Manila, between July 2022 and February 2023. Using one-step reverse transcription-quantitative polymerase chain reaction, SARS-CoV-2 and Omicron variant RNA were detected in 78 % (40/51; 4.9 ± 0.5 log10 copies/L) and 60 % (24/40; 4.4 ± 0.3 log10 copies/L) of wastewater samples collected from all sampling sites, respectively. SARS-CoV-2 RNA was detected frequently at Estero de Santa Clara (88 %, 15/17); its highest concentration was at the STP (6.3 log10 copies/L). The Omicron variant RNA was present in the samples collected (4.4 ± 0.3 log10 copies/L) from all sampling sites, with the highest concentration at the STP (4.9 log10 copies/L). Regardless of normalization, using concentrations of pepper mild mottle virus RNA, SARS-CoV-2 RNA concentrations exhibited the highest positive correlation with COVID-19 reported cases in Manila 5 days after the clinical report. These findings revealed that wastewater-based epidemiology may aid in identifying and monitoring of the presence of pathogens in open drainages and STPs in the Philippines. This paper provides the first documentation on SARS-CoV-2 and the Omicron variant in wastewater from Manila.

Current Progress, Challenges and Prospects in the Development of COVID-19 Vaccines

The COVID-19 pandemic has resulted in over 772 million confirmed cases, including nearly 7 million deaths, according to the World Health Organization (WHO). Leveraging rapid development, accelerated vaccine approval processes, and large-scale production of various COVID-19 vaccines using different technical platforms, the WHO declared an end to the global health emergency of COVID-19 on May 5, 2023. Current COVID-19 vaccines encompass inactivated, live attenuated, viral vector, protein subunit, nucleic acid (DNA and RNA), and virus-like particle (VLP) vaccines. However, the efficacy of these vaccines is diminishing due to the constant mutation of SARS-CoV-2 and the heightened immune evasion abilities of emerging variants. This review examines the impact of the COVID-19 pandemic, the biological characteristics of the virus, and its diverse variants. Moreover, the review underscores the effectiveness, advantages, and disadvantages of authorized COVID-19 vaccines. Additionally, it analyzes the challenges, strategies, and future prospects of developing a safe, broad-spectrum vaccine that confers sufficient and sustainable immune protection against new variants of SARS-CoV-2. These discussions not only offer insight for the development of next-generation COVID-19 vaccines but also summarize experiences for combating future emerging viruses.

Prevalence, outcomes and associated factors of SARS-CoV-2 infection in psoriasis patients of Southwest China: a cross-sectional survey

In this study we aimed to investigate the prevalence of SARS-CoV-2 infection in psoriasis patients, and outcomes of SARS-CoV-2 infection and associated risk factors. A cross-sectional survey was conducted from February 2023 to March 2023. Information was obtained with online questionnaire about psoriasis patients on demographic characteristics, clinical characteristics, SARS-CoV-2 infection and outcomes, vaccination, and routine protection against COVID-19. Logistic regression analysis was used to explore risk factors with SARS-CoV-2 infection and exacerbation of psoriasis. A total of 613 participants were recruited. 516 (84.2%) were infected, and associated factors were sex, working status, routine protection against COVID-19, COVID-19 vaccination, impaired nail, infection exacerbate psoriasis, and severity of psoriasis. Among the patients infected with SARS-CoV-2, 30 (5.8%) required hospitalization, 122 (23.6%) had psoriasis exacerbation due to SARS-CoV-2 infection, and associated factors were subtype of psoriasis, discontinuation of psoriasis treatment during SARS-CoV-2 infection, response following COVID-19 vaccination, and severity of psoriasis. Booster dose vaccination contributed a low probability of COVID-19 sequelae. COVID-19 vaccine's effectiveness was unsatisfactory, while booster dose vaccination reduced the occurrence of COVID-19 sequelae in psoriasis patients of Southwest China. Patients treated with psoriasis shown to be safe, without a higher incidence of SARS-CoV-2 infection or COVID-19hospitalization compared to untreated patients. Stopping treatment during SARS-CoV-2 infection led to psoriasis exacerbation, so psoriasis treatment could be continued except severe adverse reaction.

SARS-CoV-2 specific antibody response after an mRNA vaccine as the third dose: Homologous versus heterologous boost

The aim of this study was to evaluate immunogenicity and longevity of the humoral immune response within six months after the homologous (BNT162b2/BNT162b2) or heterologous (BBIBP-CorV/BNT162b2) third dose, and to assess breakthrough infections among vaccinees during the Omicron wave in Serbia. Serum samples were analyzed at four timepoints: five months after the primary series; three weeks, three months, and six months after the boost. IgG antibodies against the receptor-binding domain of the spike protein were detected using enzyme-linked fluorescence assay. Both homologous (n = 55) and heterologous group (n = 36) showed a highly significant increase in antibody concentrations (p < 0.001) three weeks after the boost. A moderate inverse correlation between the age of recipients and the antibody levels at three weeks post-boost was observed in the homologous group (p = 0.02, r = -0.37), while the same correlation was not significant for heterologous group (p = 0.55, r = -0.15). Heterologous group had significantly higher antibody concentrations than homologous group at three weeks (Median 851.4(IQR 766.6-894.1); 784.3(676.9-847.4); p = 0.03) and three months post-boost (766.6(534.8-798.9); 496.8(361.6-664.0); p < 0.001). However, a significant decline in antibody response over time was noted for both strategies. The overall incidence of breakthrough cases was estimated at 36.36% (20/55) for homologous, and 16.67% (6/36) for heterologous group, but none of them required hospitalization. Although observed incidence in the homologous group was more than double when compared to the heterologous group, this difference was not statistically significant, most likely due to the small sample size. In conclusion, waning immunity after inactivated vaccine can be recovered by BNT162b2 heterologous boost regardless of the age of recipients, and both boost strategies induced potent humoral immune response and protection against severe COVID-19 during the Omicron wave. However, as the observed incidence of breakthrough infections was higher in the homologous group, although non-significant, this finding could indicate an advantage of heterologous approach.

Assessment of the predictive value of plasma calprotectin in the evolution of SARS-Cov-2 primo-infection

BACKGROUND

The COVID-19 epidemic still calls for anticipation aimed at preventing the overloading of critical care services. With this in mind, the predictive value of easily accessible biomarkers is to be assessed.

OBJECTIVE

Secretion of calprotectin is stimulated during an inflammatory process, especially in the cytokine storm. We tried to determine whether early plasma concentration of calprotectin in patients with primary SARS-CoV-2 infection could predict an adverse outcome in cases of COVID-19.

METHODS

We included 308 patients with a primary diagnosis of SARS-CoV-2 confirmed by PCR. Heparinized tube samples, collected within the first 24 h of hospitalization, were used for biomarker assays, in which plasma calprotectin was included. Data from the patients' medical records and severity groups established subsequent to diagnosis at the end of hospitalization were collected.

RESULTS

Early plasma calprotectin concentration is significantly associated with progression to a severe form of COVID-19 in patients with primary infection (Relative Risk: 2.2 [1.6-2.7]). In multivariate analysis, however, it does not appear to provide additional information compared to other parameters (age, GFR, CRP…).

CONCLUSION

Our study shows that while an early single blood test for calprotectin could help to predict the progression of a primary SARS-CoV-2 infection, it is not superior to the other parameters currently used in emergency medicine. However, it paves the way for future considerations, such as the interest of this biomarker for high-risk infected patients (immunocompromised individuals…). Finally, the usefulness of early serial measurements of plasma calprotectin to assess progression towards severity of COVID-19 requires further assessment.

Innovative applications of artificial intelligence during the COVID-19 pandemic

The COVID-19 pandemic has created unprecedented challenges worldwide. Artificial intelligence (AI) technologies hold tremendous potential for tackling key aspects of pandemic management and response. In the present review, we discuss the tremendous possibilities of AI technology in addressing the global challenges posed by the COVID-19 pandemic. First, we outline the multiple impacts of the current pandemic on public health, the economy, and society. Next, we focus on the innovative applications of advanced AI technologies in key areas such as COVID-19 prediction, detection, control, and drug discovery for treatment. Specifically, AI-based predictive analytics models can use clinical, epidemiological, and omics data to forecast disease spread and patient outcomes. Additionally, deep neural networks enable rapid diagnosis through medical imaging. Intelligent systems can support risk assessment, decision-making, and social sensing, thereby improving epidemic control and public health policies. Furthermore, high-throughput virtual screening enables AI to accelerate the identification of therapeutic drug candidates and opportunities for drug repurposing. Finally, we discuss future research directions for AI technology in combating COVID-19, emphasizing the importance of interdisciplinary collaboration. Though promising, barriers related to model generalization, data quality, infrastructure readiness, and ethical risks must be addressed to fully translate these innovations into real-world impacts. Multidisciplinary collaboration engaging diverse expertise and stakeholders is imperative for developing robust, responsible, and human-centered AI solutions against COVID-19 and future public health emergencies.

Deciphering the omicron variant: integrated omics analysis reveals critical biomarkers and pathophysiological pathways

BACKGROUND

The rapid emergence and global dissemination of the Omicron variant of SARS-CoV-2 have posed formidable challenges in public health. This scenario underscores the urgent need for an enhanced understanding of Omicron's pathophysiological mechanisms to guide clinical management and shape public health strategies. Our study is aimed at deciphering the intricate molecular mechanisms underlying Omicron infections, particularly focusing on the identification of specific biomarkers.

METHODS

This investigation employed a robust and systematic approach, initially encompassing 15 Omicron-infected patients and an equal number of healthy controls, followed by a validation cohort of 20 individuals per group. The study's methodological framework included a comprehensive multi-omics analysis that integrated proteomics and metabolomics, augmented by extensive bioinformatics. Proteomic exploration was conducted via an advanced Ultra-High-Performance Liquid Chromatography (UHPLC) system linked with mass spectrometry. Concurrently, metabolomic profiling was executed using an Ultra-Performance Liquid Chromatography (UPLC) system. The bioinformatics component, fundamental to this research, entailed an exhaustive analysis of protein-protein interactions, pathway enrichment, and metabolic network dynamics, utilizing state-of-the-art tools such as the STRING database and Cytoscape software, ensuring a holistic interpretation of the data.

RESULTS

Our proteomic inquiry identified eight notably dysregulated proteins (THBS1, ACTN1, ACTC1, POTEF, ACTB, TPM4, VCL, ICAM1) in individuals infected with the Omicron variant. These proteins play critical roles in essential physiological processes, especially within the coagulation cascade and hemostatic mechanisms, suggesting their significant involvement in the pathogenesis of Omicron infection. Complementing these proteomic insights, metabolomic analysis discerned 146 differentially expressed metabolites, intricately associated with pivotal metabolic pathways such as tryptophan metabolism, retinol metabolism, and steroid hormone biosynthesis. This comprehensive metabolic profiling sheds light on the systemic implications of Omicron infection, underscoring profound alterations in metabolic equilibrium.

CONCLUSIONS

This study substantially enriches our comprehension of the physiological ramifications induced by the Omicron variant, with a particular emphasis on the pivotal roles of coagulation and platelet pathways in disease pathogenesis. The discovery of these specific biomarkers illuminates their potential as critical targets for diagnostic and therapeutic strategies, providing invaluable insights for the development of tailored treatments and enhancing patient care in the dynamic context of the ongoing pandemic.

A retrospective analysis of children with mild and asymptomatic Omicron infections under 14: A single-center study

Omicron BA.5 subvariant has been proven to be more transmissible than other Omicron subvariants. But the studies on the spread of the Omicron BA.5 subvariant in children are still limited. This study aimed to analyze the clinical features of children infected with Omicron BA.5.2 variant in the mobile cabin hospital and the influence factors of the infections. Children with mild and asymptomatic Omicron infections under 14 years old who were admitted to the mobile cabin hospital from October 30 to December 7, 2022 were retrospectively collected. A total of 741 children, 424 boys (57.2%) and 317 girls (42.8%) were enrolled, including 145 asymptomatic cases (22.7%) and 493 (77.3%) mild cases. Upper respiratory tract infection was the dominant manifestation. Fever was the most common presenting symptom (80.7%), followed by cough (52.5%). The average time to symptom disappearance was 3.76 days, and the average negative conversion time of nucleic acid was 12.3 days. Univariate analysis showed that the negative conversion time of nucleic acid differed significantly across the age groups. The multivariate analysis showed that the older the age, the longer the negative conversion time of nucleic acid. Among those with the negative conversion time of nucleic acid longer than 12 days, age was positively correlated to the negative conversion time of nucleic acid, while the number of vaccine doses received was negatively correlated to the negative conversion time of nucleic acid. Omicron infection occurred in children of any age group, with good prospect for recovery. Age and number of vaccine doses received were risk factors influencing the negative conversion time of nucleic acid.

Recent advances in chemometric modelling of inhibitors against SARS-CoV-2

The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused great harm to all countries worldwide. This disease can be prevented by vaccination and managed using various treatment methods, including injections, oral medications, or aerosol therapies. However, the selection of suitable compounds for the research and development of anti-SARS-CoV-2 drugs is a daunting task because of the vast databases of available compounds. The traditional process of drug research and development is time-consuming, labour-intensive, and costly. The application of chemometrics can significantly expedite drug R&D. This is particularly necessary and important for drug development against pandemic public emergency diseases, such as COVID-19. Through various chemometric techniques, such as quantitative structure-activity relationship (QSAR) modelling, molecular docking, and molecular dynamics (MD) simulations, compounds with inhibitory activity against SARS-CoV-2 can be quickly screened, allowing researchers to focus on the few prioritised candidates. In addition, the ADMET properties of the screened candidate compounds should be further explored to promote the successful discovery of anti-SARS-CoV-2 drugs. In this case, considerable time and economic costs can be saved while minimising the need for extensive animal experiments, in line with the 3R principles. This paper focuses on recent advances in chemometric modelling studies of COVID-19-related inhibitors, highlights current limitations, and outlines potential future directions for development.

Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia

During the Covid-19 pandemic, the resurgence of SARS-CoV-2 was due to the development of novel variants of concern (VOC). Thus, genomic surveillance is essential to monitor continuing evolution of SARS-CoV-2 and to track the emergence of novel variants. In this study, we performed phylogenetic, mutation, and selection pressure analyses of the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 isolates circulating in Yogyakarta and Central Java provinces, Indonesia from May 2021 to February 2022. Various bioinformatics tools were employed to investigate the evolutionary dynamics of distinct SARS-CoV-2 isolates. During the study period, 213 and 139 isolates of Omicron and Delta variants were identified, respectively. Particularly in the Spike gene, mutations were significantly more abundant in Omicron than in Delta variants. Consistently, in all of four genes studied, the substitution rates of Omicron were higher than that of Delta variants, especially in the Spike and nsp12 genes. In addition, selective pressure analysis revealed several sites that were positively selected in particular genes, implying that these sites were functionally essential for virus evolution. In conclusion, our study demonstrated a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia.

High production MBL2 polymorphisms protect against COVID-19 complications in critically ill patients: A retrospective cohort study

Mannose-binding lectin (MBL) binds to SARS-CoV-2, inhibits infection of susceptible cells, and activates the complement system via the lectin pathway. In this study, we investigated the association of MBL2 polymorphisms with the risk of hospitalization and clinical worsening in patients with COVID-19. A total of 550 patients with COVID-19 were included (94 non-hospitalized and 456 hospitalized). Polymorphisms in MBL2 exon 1 (codons 52, 54 and 57) and promoter region (-550, -221, and +4) were determined by real-time PCR. MBL and complement proteins were measured by Luminex. A higher frequency of the H/H genotype and the HYPA haplotype was observed in non-hospitalized patients when compared to hospitalized. In addition, critically ill patients carrying haplotypes associated with high MBL levels (HYPA/HYPA + HYPA/LYPA + HYPA/LYQA + LYPA/LYQA + LYPA/LYPA + LYQA/LYQA + LXPA/HYPA + LXPA/LYQA + LXPA/LYPA) were protected against lower oxygen saturation levels (P = 0.02), use of invasive ventilation use (P = 0.02, OR 0.38), and shock (P = 0.01, OR 0.40), independent of other potential confounders adjusted by multivariate analysis. Our results suggest that variants in MBL2 associated with high MBL levels may play a protective role in the clinical course of COVID-19.

Development and clinical application of loop-mediated isothermal amplification combined with lateral flow assay for rapid diagnosis of SARS-CoV-2

BACKGROUND

The diagnostic assay leveraging multiple reverse transcription loop-mediated isothermal amplification (RT-LAMP) could meet the requirements for rapid nucleic acid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

METHODS

The devised assay merged the lateral flow assay with the RT-LAMP technology and designed specific primers for the simultaneous detection of the target and human-derived internal reference genes within a single reaction. An inquiry into the assay's limit of detection (LOD), sensitivity, and specificity was carried out. The effectiveness of this assay was validated using 498 clinical specimens.

RESULTS

This LOD of the assay was determined to be 500 copies/mL, and there was no observed cross-reaction with other respiratory pathogens. The detection results derived from clinical specimens showed substantial concordance with those from real-time reverse transcription-polymerase chain reaction (RT-qPCR) (Cohen's kappa, 0.876; 95% CI: 0.833-0.919; p<0.005). The diagnostic sensitivity and specificity were 87.1% and 100%, respectively.

CONCLUSION

The RT-LAMP assay, paired with a straightforward and disposable lateral immunochromatographic strip, achieves visual detection of dual targets for SARS-CoV-2 immediatly. Moreover, the entire procedure abstains from nucleic acids extraction. The samples are lysed at room temperature and subsequently proceed directly to the RT-LAMP reaction, which can be executed within 30 minutes at a constant temperature of 60-65°C. Then, the RT-LAMP amplification products are visualized using colloidal gold test strips.

TRIAL REGISTRATION

This study was registered at the Chinese Clinical Trial Registry (Registration number: ChiCTR2200060495, Date of registration 2022-06-03).

COVID-19 mRNA Vaccines: Lessons Learned from the Registrational Trials and Global Vaccination Campaign

Our understanding of COVID-19 vaccinations and their impact on health and mortality has evolved substantially since the first vaccine rollouts. Published reports from the original randomized phase 3 trials concluded that the COVID-19 mRNA vaccines could greatly reduce COVID-19 symptoms. In the interim, problems with the methods, execution, and reporting of these pivotal trials have emerged. Re-analysis of the Pfizer trial data identified statistically significant increases in serious adverse events (SAEs) in the vaccine group. Numerous SAEs were identified following the Emergency Use Authorization (EUA), including death, cancer, cardiac events, and various autoimmune, hematological, reproductive, and neurological disorders. Furthermore, these products never underwent adequate safety and toxicological testing in accordance with previously established scientific standards. Among the other major topics addressed in this narrative review are the published analyses of serious harms to humans, quality control issues and process-related impurities, mechanisms underlying adverse events (AEs), the immunologic basis for vaccine inefficacy, and concerning mortality trends based on the registrational trial data. The risk-benefit imbalance substantiated by the evidence to date contraindicates further booster injections and suggests that, at a minimum, the mRNA injections should be removed from the childhood immunization program until proper safety and toxicological studies are conducted. Federal agency approval of the COVID-19 mRNA vaccines on a blanket-coverage population-wide basis had no support from an honest assessment of all relevant registrational data and commensurate consideration of risks versus benefits. Given the extensive, well-documented SAEs and unacceptably high harm-to-reward ratio, we urge governments to endorse a global moratorium on the modified mRNA products until all relevant questions pertaining to causality, residual DNA, and aberrant protein production are answered.

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

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

Molecular Epidemiology of SARS-CoV-2 and Clinical Manifestations among Organ Transplant Recipients with COVID-19

RNA viruses, including SARS-CoV-2, rely on genetic mutation as a major evolutionary mechanism, leading to the emergence of variants. Organ transplant recipients (OTRs) may be particularly vulnerable to such mutations, making it crucial to monitor the spread and evolution of SARS-CoV-2 in this population. This cohort study investigated the molecular epidemiology of SARS-CoV-2 by comparing the SARS-CoV-2 whole genome, demographic characteristics, clinical conditions, and outcomes of COVID-19 illness among OTRs (n = 19) and non-OTRs with (n = 38) or without (n = 30) comorbid conditions. Most patients without comorbidities were female, whereas most OTRs were male. Age varied significantly among the three groups: patients with comorbidities were the oldest, and patients without comorbidities were the youngest. Whole-genome sequencing revealed that OTRs with mild disease had higher numbers of unusual mutations than patients in the other two groups. Additionally, OTRs who died had similar spike monoclonal antibody resistance mutations and 3CLpro mutations, which may confer resistance to nirmatrelvir, ensitrelvir, and GC37 therapy. The presence of those unusual mutations may impact the severity of COVID-19 illness in OTRs by affecting the virus's ability to evade the immune system or respond to treatment. The higher mutation rate in OTRs may also increase the risk of the emergence of new virus variants. These findings highlight the importance of monitoring the genetic makeup of SARS-CoV-2 in all immunocompromised populations and patients with comorbidity.

Obesity and COVID-19 Pandemics: Epidemiology, Mechanisms, and Management

Obesity is a principle causative factor of various metabolic dysfunctions, chronic inflammation, and multi-organ impairment. The global epidemic of obesity has constituted the greatest threat to global health. Emerging evidence has associated obesity with an increased risk of severe infection and poor outcomes from coronavirus disease 2019 (COVID-19). During current COVID-19 pandemic, the interaction between COVID-19 and obesity has exaggerated the disease burden of obesity more than ever before. Thus, there is an urgent need for consideration of universal measures to reduce the risk of complications and severe illness from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in obesity population. In this review, we first summarized the clinical evidence on the effect of obesity on susceptibility, severity, and prognosis of COVID-19. Then we discussed and the underlying mechanisms, including respiratory pathophysiology of obesity, dysregulated inflammation, upregulated angiotensin-converting enzyme 2 (ACE2) expression, hyperglycemia, and adipokines. Finally, we proposed recommendations on how to reduce the spread and pandemic of SARS-CoV-2 infection by prevention and treatment of obesity.

Spatiotemporal observations of host-pathogen interactions in mucosa during SARS-CoV-2 infection indicate a protective role of ILC2s

IMPORTANCE

Our study revealed the spatial interaction between humanized ACE2 and pseudovirus expressing Spike, emphasizing the role of type 2 innate lymphoid cells during the initial phase of viral infection. These findings provide a foundation for the development of mucosal vaccines and other treatment approaches for both pre- and post-infection management of coronavirus disease 2019.

Association between salivary proteases and protease inhibitors linked with viral infections and oral inflammatory diseases

INTRODUCTION

Despite the role of transmembrane protease, serine 2 (TMPRSS2) in facilitating the entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the primary cause of the global COVID-19 pandemic, the interaction of extracellular and intracellular proteases in this process remains poorly elucidated. Thus, we monitored the salivary expression concentration (SEC) of TMPRSS2 and its inhibitor, alpha-1 antitrypsin (A1AT), and investigated whether oral inflammatory diseases affected the SEC of both proteins.

MATERIALS AND METHODS

We collected saliva samples before and after surgical treatment of inflammatory cystic diseases (radicular and inflammatory dentigerous cysts) in 25 patients. The SEC of TMPRSS2 and A1AT was measured using enzyme-linked immunosorbent assay. SEC in multiple patient status groups and subgroups of each status were investigated. Finally, the correlation between TMPRSS2 and A1AT SEC was analyzed.

RESULTS

The TMPRSS2 and A1AT SEC did not significantly change pre- or post-treatment. The TMPRSS2 SEC was significantly higher before and after treatment in patients aged >50 years, patients with radicular cysts, and patients with the basic disease. A1AT SEC was significantly decreased after treatment in the acute inflammation, large-sized, and patients without basic disease groups. No significant correlation was observed between the SEC of either protein before and after treatment.

DISCUSSION

Individual-specific SEC for TMPRSS2 may be influenced by age, lesion type, and basic disease; however, oral inflammatory diseases may not have a direct effect. Moreover, the extent of oral inflammatory diseases and the presence of basic diseases may be associated with A1AT SEC. Furthermore, the SEC between the two proteins may be independent.

Exploring the structural and molecular interaction landscape of nirmatrelvir and Mpro complex: The study might assist in designing more potent antivirals targeting SARS-CoV-2 and other viruses

BACKGROUND

Several therapeutics have been developed and approved against SARS-CoV-2 occasionally; nirmatrelvir is one of them. The drug target of nirmatrelvir is Mpro, and therefore, it is necessary to comprehend the structural and molecular interaction of the Mpro-nirmatrelvir complex.

METHODS

Integrative bioinformatics, system biology, and statistical models were used to analyze the macromolecular complex.

RESULTS

Using two macromolecular complexes, the study illustrated the interactive residues, H-bonds, and interactive interfaces. It informed of six and nine H-bond formations for the first and second complex, respectively. The maximum bond length was observed as 3.33 Å. The ligand binding pocket's surface area and volume were noted as 303.485 Å2 and 295.456 Å3 for the first complex and 308.397 Å2 and 304.865 Å3 for the second complex. The structural proteome dynamics were evaluated by analyzing the complex's NMA mobility, eigenvalues, deformability, and B-factor. Conversely, a model was created to assess the therapeutic status of nirmatrelvir.

CONCLUSIONS

Our study reveals the structural and molecular interaction landscape of Mpro-nirmatrelvir complex. The study will guide researchers in designing more broad-spectrum antiviral molecules mimicking nirmatrelvir, which assist in fighting against SARS-CoV-2 and other infectious viruses. It will also help to prepare for future epidemics or pandemics.

Mid-term follow-up after COVID-19 vaccination in adults with CHD: a prospective study

BACKGROUND

Long-term data on COVID-19 vaccine safety, immunogenicity, and acceptance in adults with CHD are lacking.

METHODS

This is a prospective study including adults with CHD patients undergoing COVID-19 vaccination from January 2021 to June 2022. Data on adverse events, antispike IgG titre, previous or subsequent COVID-19 infection, booster doses, and patients' attitude towards vaccination were collected.

RESULTS

Four hundred and ninety CHD patients (36 ± 13 years, 53% male, 94% with moderate/complex defects) were prospectively included: 433 (88%) received a Pfizer-BioNTech mRNA vaccine, 31 (6%) Moderna mRNA vaccine, 23 (5%) AstraZeneca-Oxford ChAdOx1 nCov-19 vaccine, and 3 (0.6%) Janssen Vaccine; 310 (63%) received a booster dose. Median follow-up after vaccination was 1.53 [1.41-1.58] years. No major adverse event was reported. Eighty-two fully vaccinated patients contracted COVID-19 during follow-up after a median of 5.4 [4.3-6.5] months from the last dose. One patient with Ebstein's disease died from severe COVID-19. Symptoms' duration in patients who tested positive after vaccination was significantly shorter than in the group tested positive before vaccination (5.5 [3-8] versus 9 [2.2-15] days, p = 0.04). Median antispike IgG titre measured in 280 individuals (57%) at a median of 1.4 [0.7-3.3] months from the last dose was 2381 [901-8307] BAU/ml. Sixty patients (12%) also showed positive antinucleocapsid antibodies, demonstrating previous SARS-COV2 exposure. Twenty-nine percent appeared to have concerns regarding vaccine safety and 42% reported fearing potential effects of the vaccine on their cardiac disease before discussing with their CHD cardiologist.

CONCLUSION

COVID-19 vaccines appear safe in the mid-term follow-up in adults with CHD with satisfactory immunogenicity and reduction of symptoms' duration in case of infection.

Knowledge, attitude and practices towards SARS-CoV-2 genetic mutations and emerging variants among the population in Bangladesh: a cross-sectional study

OBJECTIVES

The coronavirus is continuously mutating and creating new SARS-CoV-2 variants. Public awareness about SARS-CoV-2 mutation is essential for effective preventive measures. The present study aimed to assess the knowledge, attitude and practices (KAP) towards SARS-CoV-2 variants among the general population in Bangladesh.

DESIGN

We conducted this online survey between 9 April 2021 and 10 May 2021 using structured questionnaires to collect the information.

SETTING

We distributed the survey link among the participants from all 64 districts of Bangladesh using social media platforms.

PARTICIPANTS

A total of 1,090 respondents completed this survey. After careful evaluation, we excluded 18 responses due to partial or incomplete information, and 1,072 responses entered into the final analysis.

PRIMARY OUTCOME

The KAP of participants towards SARS-CoV-2 variants depends on their demographic backgrounds. Associations between demographic characteristics and the likelihood of having adequate KAP were estimated using adjusted logistic regressions.

RESULTS

Among the participants, 42% had a poor knowledge level, 4% had a low attitude level and 14% had a poor practice score. The average knowledge, attitude and practice score were 2.65, 4.194 and 4.464 on a scale of 5, respectively. Only 51.8% of the participants knew about mutant strains, and only 47.6% knew about the effectiveness of vaccines against new variants. The key factors associated with poor knowledge levels were educational levels, area of residence, geographic location, and concern regarding COVID-19. Sociodemographic factors for poor attitude levels were geographic location, vaccination and concern regarding COVID-19. The pivotal factors in determining poor practice scores were the residence area of people and concern regarding COVID-19.

CONCLUSIONS

The knowledge level and positive attitude are associated with better preventive measures against SARS-CoV-2 variants. Based on these findings, we recommended several awareness programmes on SARS-CoV-2 mutations and variants for the rural population in Bangladesh to increase overall awareness levels.

Comparative Computational Analysis of Spike Protein Structural Stability in SARS-CoV-2 Omicron Subvariants

The continuous emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with multiple spike (S) protein mutations pose serious threats to current coronavirus disease 2019 (COVID-19) therapies. A comprehensive understanding of the structural stability of SARS-CoV-2 variants is vital for the development of effective therapeutic strategies as it can offer valuable insights into their potential impact on viral infectivity. S protein mediates a virus' attachment to host cells by binding to angiotensin-converting enzyme 2 (ACE2) through its receptor-binding domain (RBD), and mutations in this protein can affect its stability and binding affinity. We analyzed S protein structural stability in various Omicron subvariants computationally. Notably, the S protein sequences analyzed in this work were obtained directly from our own sample collection. We evaluated the binding free energy between S protein and ACE2 in several complex forms. Additionally, we measured distances between the RBD of each chain in S protein to analyze conformational changes. Unlike most of the prior studies, we analyzed full-length S protein-ACE2 complexes instead of only RBD-ACE2 complexes. Omicron subvariants including BA.1, BA.2, BA.2.12.1, BA.4/BA.5, BA.2.75, BA.2.75_K147E, BA.4.6 and BA.4.6_N658S showed enhanced stability compared to wild type, potentially due to distinct S protein mutations. Among them, BA.2.75 and BA.4.6_N658S exhibited the highest and lowest level of stability, respectively.

Significant increase in anti-SARS-CoV-2 antibodies after administration of heterologous mRNA-based vaccine booster in individuals receiving two doses of inactivated COVID-19 vaccine: A single-center study in healthcare workers in Jakarta, Indonesia

BACKGROUND

Vaccine plays an important role in breaking SARS-CoV-2 transmission and accelerating the path to pandemic recovery. Currently, there is still limited data on heterologous COVID-19 booster vaccination efficacy and effectiveness in Indonesia.

METHODS

Antibody response was retrospectively analyzed from 156 serum collected from healthcare workers that have received mRNA-1273 vaccine as the booster against SARS-CoV-2. These individuals had previously received the full two doses of inactivated anti-SARS-CoV-2 vaccine. Serological analysis was performed to measure total antibody, as well as IgA and IgG antibodies specific to spike (S) protein using ECLIA and ELISA methods.

RESULTS

A significant increase in total, IgA, and IgG antibody titers was reported in vaccine receiving a third heterologous booster dose of mRNA-based COVID-19 vaccine following two doses of inactivated type.

CONCLUSION

The third heterologous booster dose of vaccine may be beneficial to individuals with or without previous history of SARS-CoV-2 infection.

Chemoprophylactic Assessment of Combined Intranasal SARS-CoV-2 Polymerase and Exonuclease Inhibition in Syrian Golden Hamsters

Pibrentasvir (PIB) has been demonstrated to block exonuclease activity of the SARS-CoV-2 polymerase, protecting favipiravir (FVP) and remdesivir (RDV) from post-incorporation excision and eliciting antiviral synergy in vitro. The present study investigated the chemoprophylactic efficacy of PIB, FVP, RDV, FVP with PIB, or RDV with PIB dosed intranasally twice a day, using a Syrian golden hamster contact transmission model. Compared to the saline control, viral RNA levels were significantly lower in throat swabs in FVP (day 7), RDV (day 3, 5, 7), and RDV+PIB (day 3, 5) treatment groups. Similarly, findings were evident for nasal turbinate after PIB and RDV treatment, and lungs after PIB, FVP, and FVP+PIB treatment at day 7. Lung viral RNA levels after RDV and RDV+PIB treatment were only detectable in two animals per group, but the overall difference was not statistically significant. In situ examination of the lungs confirmed SARS-CoV-2 infection in all animals, except for one in each of the RDV and RDV+PIB treatment groups, which tested negative in all virus detection approaches. Overall, prevention of transmission was observed in most animals treated with RDV, while other agents reduced the viral load following contact transmission. No benefit of combining FVP or RDV with PIB was observed.

Cell-mediated and Neutralizing Antibody Responses to the SARS-CoV-2 Omicron BA.4/BA.5-adapted Bivalent Vaccine Booster in Kidney and Liver Transplant Recipients

Background

The immunogenicity elicited by the Omicron BA.4/BA.5-adapted bivalent booster vaccine after solid organ transplantation (SOT) has not been characterized.

Methods

We assessed cell-mediated and neutralizing IgG antibody responses against the BA.4/BA.5 spike receptor-binding domain at baseline and 2 wk after the administration of an mRNA-based bivalent (ancestral strain and BA.4/BA.5 subvariants) vaccine among 30 SOT recipients who had received ≥3 monovalent vaccine doses. Previous coronavirus disease 2019 history was present in 46.7% of them. We also recruited a control group of 19 nontransplant healthy individuals. Cell-mediated immunity was measured by fluorescent ELISpot assay for interferon (IFN)-γ secretion, whereas the neutralizing IgG antibody response against the BA.4/BA.5 spike receptor-binding domain was quantified with a competitive ELISA.

Results

The median number of BA.4/BA.5 spike-specific IFN-γ-producing spot-forming units (SFUs) increased from baseline to 2 wk postbooster (83.8 versus 133.0 SFUs/106 peripheral blood mononuclear cells; P = 0.0017). Seropositivity rate also increased (46.7%-83.3%; P = 0.001), as well as serum neutralizing activity (4.2%-78.3%; P < 0.0001). Patients with no prior coronavirus disease 2019 history experienced higher improvements in cell-mediated and neutralizing responses after booster vaccination. There was no correlation between BA.4/BA.5 spike-specific IFN-γ-producing SFUs and neutralizing activity. Nontransplant controls showed more robust postbooster cell-mediated immunity than SOT recipients (591.1 versus 133.0 IFN-γ-producing SFUs/106 peripheral blood mononuclear cells; P < 0.0001), although no differences were observed for antibody responses in terms of postbooster seropositivity rates or neutralizing activity.

Conclusions

Booster with the BA.4/BA.5-adapted bivalent vaccine generated strong subvariant-specific responses among SOT recipients. Booster-induced cell-mediated immunity, however, remained lower than in immunocompetent individuals.

Adapting Neutralizing Antibodies to Viral Variants by Structure-Guided Affinity Maturation Using Phage Display Technology

Neutralizing monoclonal antibodies have achieved great efficacy and safety for the treatment of numerous infectious diseases. However, their neutralization potency is often rapidly lost when the target antigen mutates. Instead of isolating new antibodies each time a pathogen variant arises, it can be attractive to adapt existing antibodies, making them active against the new variant. Potential benefits of this approach include reduced development time, cost, and regulatory burden. Here a methodology is described to rapidly evolve neutralizing antibodies of proven activity, improving their function against new pathogen variants without losing efficacy against previous ones. The reported procedure is based on structure-guided affinity maturation using combinatorial mutagenesis and phage display technology. Its use against the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is demonstrated, but it is suitable for any other pathogen. As proof of concept, the method is applied to CoV-X2, a human bispecific antibody that binds with high affinity to the early SARS-CoV-2 variants but lost neutralization potency against Delta. Antibodies emerging from the affinity maturation selection exhibit significantly improved neutralization potency against Delta and no loss of efficacy against the other viral sequences tested. These results illustrate the potential application of structure-guided affinity maturation in facilitating the rapid adaptation of neutralizing antibodies to pathogen variants.

The immunogenicity of Alum+CpG adjuvant SARS-CoV-2 inactivated vaccine in mice

The ongoing evolution and emergence of SARS-CoV-2 variants have raised concerns regarding the efficacy of existing vaccines and therapeutic agents. This study aimed to investigate the immunogenicity of an aluminum hydroxide (Alum) and CpG adjuvanted inactivated vaccine (IAV) candidate against SARS-CoV-2 in mice. A comparison was made between the immune response of mice vaccinated with the Alum+CpG adjuvant IAV and those vaccinated with the Alum adjuvant IAV. Mice immunized with Alum+CpG adjuvant IAV demonstrated high antibody titers and a durable humoral immune response, as well as a Th1-type cellular immune response. Notably, compared to Alum alone vaccine, the Alum+CpG adjuvant IAV induced significantly higher proportions of GC B cells in the splenocytes of immunized mice. Importantly, the changes in inflammatory cytokine levels in the sera of mice vaccinated with the Alum+CpG adjuvant IAV followed a similar trend to that of the Alum adjuvant IAV, which had been proven safe in clinical trials. Overall, our results demonstrate that Alum+CpG adjuvant has the potential to serve as a novel adjuvant, thereby providing valuable insights into the development of vaccine formulations.

A weapon to fight against pervasive Omicron: systematic actions transiting to pre-COVID normal

The Coronavirus Disease-2019 (COVID-19) pandemic is not just a health crisis but also a social crisis. Confronted with the resurgence of variants with massive infections, the triggered activities from personal needs may promote the spread, which should be considered in risk management. Meanwhile, it is important to ensure that the policy responses on citizen life to a lower level. In the face of Omicron mutations, we need to sum up the control experience accumulated, adapting strategies in the dynamic coevolution process while balancing life resumption and pandemic control, to meet challenges of future crises. We collected 46 cases occurring between 2021 and 2022, mainly from China, but also including five relevant cases from other countries around the world. Based on case studies, we combine micro-view individual needs/behaviors with macro-view management measures linking Maslow's hierarchy of needs with the transmission chain of Omicron clusters. The proposed loophole chain could help identify both individual and management loopholes in the spread of the virus. The systematic actions that were taken have effectively combated these ubiquitous vulnerabilities at lower costs and lesser time. In the dynamic coevolution process, the Chinese government has made effective and more socially acceptable prevention policies while meeting the divergent needs of the entire society at the minimum costs. Systematic actions do help maintain the balance between individuals' satisfaction and pandemic containment. This implies that risk management policies should reasonably consider individual needs and improve the cooperation of various stakeholders with targeted flexible measures, securing both public health and life resumption.