Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis

Relative effectiveness of a heterologous booster dose with adenovirus type 5 vectored COVID-19 vaccine versus three doses of inactivated COVID-19 vaccine in adults during a nationwide outbreak of omicron predominance, in China: a retrospective, individually matched cohort-control study

Effectiveness of heterologous booster regimes with ad5 vectored COVID-19 vaccine in a large, diverse population during the national-scale outbreak of SARS-CoV-2 omicron predominance in China has not been reported, yet. We conducted a large-scale cohort-control study in six provinces in China, and did a retrospective survey on the COVID-19 attack risk during this outbreak. Participant aged ≥18 years in five previous trials who were primed with 1 to 3 doses of ICV received heterologous booster with either intramuscular or orally inhaled ad5 vectored COVID-19 vaccine were included in the heterologous-trial cohort. We performed propensity score-matching at a ratio of 1:4 to match participants in the heterologous-trial cohort individually with the community individuals who received three-dose of ICV as a control (ICV-community cohort). From February 4 to April 10, 2023, 41504 (74.5%) of 55710 individuals completed the survey. The median time since the most recent vaccination to the onset of the symptoms of COVID-19 was 303.0 days (IQR 293.0-322.0). The attack rate of COVID-19 in the heterologous-trial cohort was 55.8%, while that in the ICV-community cohort was 64.6%, resulting in a relative effectiveness of 13.7% (95% CI 11.9 to 15.3). In addition, a higher relative effectiveness against COVID-19 associated outpatient visits, and admission to hospital was demonstrated, which was 25.1% (95% CI 18.9 to 30.9), and 48.9% (95% CI 27.0 to 64.2), respectively. The heterologous booster with ad5 vectored COVID-19 vaccine still offered some additional protection in preventing COVID-19 breakthrough infection versus homologous three-dose regimen with ICV, 10 months after vaccination.

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.

Specific immunological characteristics and risk factor of XBB variants re-infection in nasopharyngeal carcinoma patients after BA.5 infection

OBJECTIVES

The specific humoral immune response resulting from inactivated vaccination following by BA.5 infection, and predictors of XBB variants re-infection in BA.5 infection-recovered nasopharyngeal carcinoma (BA.5-RNPC) patients, were explored.

METHODS

Serum SARS-CoV-2 specific antibody levels were assessed using enzyme-linked-immunosorbent-assay. Univariate and multivariate binary logistic regression analyses were conducted to identify factors associated with the magnitude of specific humoral immunity and susceptibility to re-infection by XBB variants.

RESULTS

Our data demonstrates that SARS-CoV-2 specific antibody levels were comparable between BA.5-RNPC patients and BA.5 infection-recovered-non-cancerous (BA.5-RNC) individuals. Specifically, serum levels of anti-ancestral-S1-IgG, anti-ancestral-nucleocapsid-protein (NP)-IgG, anti-BA.5-receptor binding domain (RBD)-IgG and anti-XBB.1.1.6-RBD-IgG were higher in BA.5-RNPC patients compared to those without a prior infection. Compared to BA.5-RNPC patients without vaccination, individuals who received inactivated vaccination exhibited significantly higher levels of anti-ancestral-S1-IgG and anti-XBB.1.16-RBD-IgG. Multivariate logistic regression analysis revealed that inactivated vaccination was the most significant predictor of all tested SARS-CoV-2 specific antibodies response. Subsequent analysis indicated that a low globulin level is an independent risk factor for XBB re-infection in BA.5-RNPC patients.

CONCLUSIONS

The SARS-CoV-2 specific antibodies have been improved in vaccinated BA.5-RNPC patients. However, the baseline immunity status biomarker IgG is an indicators of XBB variant re-infection risk in BA.5-RNPC patients.

Whole genome analysis reveals unique traits of SARS-CoV-2 in pediatric patients

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to challenge the global healthcare with emerging variants and higher infectivity as well as morbidities. This study investigated potential age-related variations through genomic characterization of the virus under common clinical settings. A cohort comprising 71 SARS-CoV-2 strains from both infected infants and accompanying adults, diagnosed via RT-PCR at a tertiary pediatric hospital and research center, underwent Illumina paired-end sequencing. The subsequent analysis involved standard genomic screening, phylogeny construction, and mutational analyses. The analyzed SARSCoV- 2 strains were compared with globally circulating variants. The overall distribution revealed 67.61 % Delta, 25.7 % Omicron, and 1 % either Kappa or Alpha variants. In 2021, Delta predominated at ∼ 94 %, with Alpha/Kappa accounting for around 5 %. However, in 2022, over 94 % of the samples were Omicron variants, signifying a substantial shift from Delta dominance. Delta variants constituted 69.5 % of infections in adults and 78.5 % in infants, while Omicron variants were responsible for 31 % of cases in infants and 18 % in adults. The Spike region harbored the majority of mutations, with T19R being the most prevalent mutation in the Delta lineage. Notably, the frequencies of this mutation varied between infants and adults. In Omicron samples, G142D emerged as the most prevalent mutation. Our dataset predominantly featured clade 21A and lineage B.1.617.2. This study underscores the differential clinical presentations and genomic characteristics of SARS-CoV-2 in pediatric patients and accompanying adults. Understanding the dynamic evolution of the SARS- CoV-2 in both pediatric and adults can help in strengthening prophylactic measures.

Dynamics of anti-SARS-CoV-2 IgG antibody responses following breakthrough infection and the predicted protective efficacy: A longitudinal community-based population study in China

OBJECTIVES

To assess the dynamics of the anti-SARS-CoV-2 IgG antibody levels and their efficacy against COVID-19.

METHODS

We conducted a longitudinal serological analysis of 852 breakthrough COVID-19 infections among the community-based population in Yichang, China. Anti-SARS-CoV-2 IgG levels were measured by chemiluminescence at approximately 3, 4, and 9 months after infection. A linear mixed model predicted IgG antibody decline over 18 months. The effectiveness of antibodies in preventing symptomatic and severe infections was determined using an existing meta-regression model.

RESULTS

IgG antibodies slowly declined after breakthrough infections. Initially high at around 3 months (339.44 AU/mL, IQR: 262.78-382.95 AU/mL), levels remained significant at 9 months (297.74 AU/mL, IQR: 213.22-360.62 AU/mL). The elderly (≥60 years) had lower antibody levels compared to the young (<20 years) (P < 0.001). The protective efficacy of antibodies against symptomatic and severe infections was lower in the elderly (≥60 years) (78.34% and 86.33%) compared to the young (<20 years) (96.56% and 98.75%) after 1 year.

CONCLUSION

The study indicated a slow decline in anti-SARS-CoV-2 IgG antibodies, maintaining considerable efficacy for over 1 year. However, lower levels in the elderly suggest reduced protective effects, underscoring the need for age-specific vaccination strategies.

Repeated Omicron infection dampens immune imprinting from previous vaccination and induces broad neutralizing antibodies against Omicron sub-variants

OBJECTIVE

Similar with influenza virus, antigenic drift is highly relevant to SARS-CoV-2 evolution, and immune imprinting has been found to limit the performance of updated vaccines based on the emerging variants of SARS-CoV-2. We aimed to investigate whether repeated exposure to Omicron variant could reduce the immune imprinting from previous vaccination.

METHODS

A total of 194 participants with different status of vaccination (unvaccinated, regular vaccination and booster vaccination) confirmed for first infection and re-infection with BA.5, BF.7 and XBB variants were enrolled, and the neutralizing profiles against wild type (WT) SARS-CoV-2 and Omicron sub-variants were analyzed.

RESULTS

Neutralizing potency against the corresponding infected variant is significantly hampered along with the doses of vaccination during first infection. However, for the participants with first infection of BA.5/BF.7 variants and re-infection of XBB variant, immune imprinting was obviously alleviated, indicated as significantly increased ratio of the corresponding infected variant/WT ID50 titers and higher percentage of samples with high neutralizing activities (ID50 > 500) against BA.5, BF.7 and XBB variants. Moreover, repeated Omicron infection could induce strong neutralizing potency with broad neutralizing profiles against a series of other Omicron sub-variants, both in the vaccine naive and vaccine experienced individuals.

CONCLUSIONS

Our results demonstrate that repeated Omicron infection dampens immune imprinting from vaccination with WT SARS-CoV-2 and induces broad neutralizing profiles against Omicron sub-variants.

NK Cell Mitochondrial Membrane Potential-Associated Model Predicts Outcomes in Critically Ill Patients with COVID-19

Purpose

This study investigated potential predictive models associated with natural killer (NK) cell mitochondrial membrane potential (MMP or ΔΨm) in predicting death among critically ill patients with COVID-19.

Patients and Methods

We included 97 patients with COVID-19 of different severities attending Peking Union Medical College Hospital from December 2022 to January 2023. Patients were divided into three groups according to oxygen and mechanical ventilation use during specimen collection and were followed for survival and death at 3 months. The lymphocyte subpopulation MMP was detected via flow cytometry. We constructed a joint diagnostic model by integrating identified key indicators and generating receiver operating curves (ROCs) and evaluated its predictive performance for mortality risk in critically ill patients.

Results

The NK-cell MMP median fluorescence intensity (MFI) was significantly lower in critically ill patients who died from COVID-19 (p<0.0001) and significantly and positively correlated with D-dimer content in critically ill patients (r=0.56, p=0.0023). The random forest model suggested that fibrinogen levels and NK-cell MMP MFI were the most important indicators. Integrating the above predictive models for the ROC yielded an area under the curve of 0.94.

Conclusion

This study revealed the potential of combining NK-cell MMP with key clinical indicators (D-dimer and fibrinogen levels) to predict death among critically ill patients with COVID-19, which may help in early risk stratification of critically ill patients and improve patient care and clinical outcomes.

The impact of mild and moderate COVID-19 infection on the progression of kidney dysfunction in patients with IgA nephropathy

Background

Previous research indicates that coronavirus disease 2019 (COVID-19) infection may have a role in triggering immunoglobulin A (IgA) nephropathy. However, limited research has explored the clinical implications of COVID-19 infection in individuals already diagnosed with IgA nephropathy. This study aimed to determine whether COVID-19 infection independently affects the subsequent trajectory of kidney function in IgA nephropathy patients.

Methods

This was a single-center cohort study. The study included 199 patients diagnosed with IgA nephropathy. The COVID-19 infection status was determined using a combined method: a questionnaire and the Health Code application, both administered at the end of 2022 in northern China. Kidney function trajectory was assessed by the estimated glomerular filtration rate (eGFR), calculated based on serum creatinine levels measured during follow-up outpatient visits. The primary endpoint of interest was the eGFR trajectory.

Results

Out of the 199 participants, 75% (n = 181) reported a confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, determined through antigen or polymerase chain reaction tests, accounting for 79% (n = 143) of the infected patients. A significant majority (98%) experienced mild to moderate symptoms. Over a median follow-up period of 10.7 months post-COVID-19 infection, notable clinical events included gross hematuria in 30 patients (16.6%), which normalized within an average of 3 days. Additionally, a 2-fold increase in proteinuria or progression to the nephrotic range was observed in 10 individuals (5.5%). No cases of acute kidney injury were noted. COVID-19 exposure was associated with an absolute change in eGFR of 2.98 mL/min/1.73 m2 per month (95% confidence interval 0.46 to 5.50). However, in a fully adjusted model, the estimated changes in eGFR slope post-COVID-19 were -0.39 mL/min/1.73 m2 per month (95% confidence interval -0.83 to 0.06, P = .088) which included the possibility of no significant effect. Notably, a higher rate of kidney function decline was primarily observed in patients with a baseline eGFR <45 mL/min/1.73 m2 [-0.56 mL/min/1.73 m2 (-1.11 to -0.01), P = .048]. In the cohort, there were few instances of severe COVID-19 cases. The absence of long-term follow-up outcomes was observed.

Conclusions

Overall, mild to moderate COVID-19 infection does not appear to significantly exacerbate the subsequent decline in kidney function among IgA nephropathy patients, particularly in those with preserved baseline kidney function.

Associations between genetic mutations in different SARS-CoV-2 strains and negative conversion time of viral RNA among imported cases in Hangzhou: A cross-sectional study

PURPOSE

Previous studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have focused on factors that influence the achievement of negative conversion of viral RNA. This study aimed to investigate the effects of the genetic mutations in different SARS-CoV-2 strains on the negative conversion time (NCT) among imported cases in Hangzhou, Zhejiang Province, China, in order to provide valuable insights for developing targeted epidemic prevention guidelines.

METHODS

This retrospective study involved 146 imported SARS-CoV-2 cases in Hangzhou from 8 April 2021 to 11 June 2022. We compared the SARS-CoV-2-specific indicators, clinical indexes, and NCT among the wild-type (WT), Delta, and Omicron groups. Spearman correlation analysis was used to identify the correlations of NCT with mutation types/frequencies.

RESULTS

The mean age of the imported cases was 35.3 (SD: 12.3) years, with 71.92 % males and 28.08 % females. The mean cycle threshold (Ct) values of open reading frame 1ab (ORF1ab) and nucleocapsid (N) RNA were 25.17 (SD: 6.44) and 23.4 (SD: 6.76), respectively. The mutations of SARS-CoV-2 strains were mainly located in N, membrane (M), spike (S), ORF1a, ORF1b, ORF3a, ORF6, and ORF9b genes among the WT, Delta, and Omicron groups. NCT was significantly prolonged in the WT and Delta groups compared to the Omicron group. T lymphocyte, white blood cell, eosinophil, and basophil counts were dramatically higher in the WT group than the Delta group. White blood cell, red blood cell, and basophil counts were significantly lower in the Delta group than the Omicron group. Spearman correlation analysis revealed a significant correlation between the NCT of viral RNA and mutation types of viral genes of WT and Omicron strains. Additionally, NCT was markedly negatively correlated with the frequencies of five mutations in Omicron strains (ORF1b:P1223L, ORF1b:R1315C, ORF1b:T2163I, ORF3a:T223I, and ORF6:D61L).

CONCLUSIONS

This study indicates that five mutations in Omicron strains (ORF1b:P1223L/R1315C/T2163I, ORF3a:T223I and ORF6:D61L) shortened NCT in imported SARS-CoV-2 cases.

The contributions of vaccination and natural infection to the production of neutralizing antibodies against the SARS-CoV-2 prototype strain and variants

OBJECTIVES

To evaluate the neutralizing antibody (NAb) levels against the SARS-CoV-2 Omicron variants BF.7, BQ.1, BQ.1.1, XBB.1, and XBB.1.5 after vaccination and natural infection.

METHODS

The NAbs against the different viral strains of 490 individuals with SARS-CoV-2 and 187 without SARS-CoV-2 in the Beijing COVID-19 outbreak during December 2022 to January 2023 were analyzed.

RESULTS

In uninfected individuals, limited levels of NAbs were produced against the prototype and variant strains after two doses vaccine but significantly increased after three or four doses of the vaccine. The infected individuals had high NAbs levels against the BF.7, BQ.1, and BQ.1.1 variants and moderate NAbs levels against the XBB.1 and XBB.1.5 variants. The highest NAbs levels were observed after two inoculation doses. The third and fourth doses vaccine did not result in a significant increase the NAbs levels. After the last dose of vaccination, the NAbs levels peaked at 12 months for the prototype and BF.7 and between 6 to 12 months for the BQ.1, BQ.1.1, XBB.1, and XBB.1.5 variants.

CONCLUSIONS

The immune response decreases as the virus mutates. If booster vaccination is considered necessary, it is suggested for at least 6 months after infection.

Multicenter and multimodal imaging study reveals rare fundus lesions in patients after SARS-CoV-2 infection

To define the characteristics of fundus manifestations in patients after SARS-CoV-2 infection with multimodal imaging techniques. This is a retrospective multicenter and multimodal imaging study including 90 patients. All patients with a visual complaint occurring immediately after SARS-CoV-2 infection were referred to six clinics between December 2022 and February 2023. Demographic information and the temporal relationship between SARS-CoV-2 infection and visual symptoms were documented. The characteristics of the fundus lesions were evaluated using multimodal imaging. Ninety patients from six hospitals were included in this study, including 24 males (26.67%) and 66 (73.33%) females. Seventy-eight patients (86.66%) (146 eyes) were diagnosed with Acute Macular Neuroretinopathy (AMN). The AMN patients were primarily young women (67.95%). Sixty-eight patients (87.18%) had AMN in both eyes. Thirty-eight eyes (24.36%) included Purtscher or Purtscher-like lesions. optical coherence tomography and infrared retinal photographs can show AMN lesions well. Eleven cases were diagnosed with simple Purtscher or Purtscher-like retinopathy (2 cases, 2.22%), Vogt‒Koyanagi‒Harada (VKH) syndrome or VKH-like uveitis (3 cases, 3.33%), multiple evanescent white-dot syndrome (MEWDS) (2 cases, 2.22%), and rhino-orbital-cerebral mucormycosis (ROCM) (5 cases, 5.56%). After SARS-CoV-2 infection, diversified fundus lesions were evident in patients with visual complaints. In this report, AMN was the dominant manifestation, followed by Purtscher or Purtscher-like retinopathy, MEWDS, VKH-like uveitis, and ROCM.

Variant-specific antibody response following repeated SARS-CoV-2 vaccination and infection

The ongoing emergence of SARS-CoV-2 variants poses challenges to the immunity induced by infections and vaccination. We conduct a 6-month longitudinal evaluation of antibody binding and neutralization of sera from individuals with six different combinations of vaccination and infection against BA.5, XBB.1.5, EG.5.1, and BA.2.86. We find that most individuals produce spike-binding IgG or neutralizing antibodies against BA.5, XBB.1.5, EG.5.1, and BA.2.86 2 months after infection or vaccination. However, compared to ancestral strain and BA.5 variant, XBB.1.5, EG.5.1, and BA.2.86 exhibit comparable but significant immune evasion. The spike-binding IgG and neutralizing antibody titers decrease in individuals without additional antigen exposure, and <50% of individuals neutralize XBB.1.5, EG.5.1, and BA.2.86 during the 6-month follow-up. Approximately 57% of the 107 followed up individuals experienced an additional infection, leading to improved binding IgG and neutralizing antibody levels against these variants. These findings provide insights into the impact of SARS-CoV-2 variants on immunity following repeated exposure.

Immune responses and reinfection of SARS-CoV-2 Omicron variant in patients with lung cancer

A significant Omicron wave emerged in China in December 2022. To explore the duration of humoral and cellular response postinfection and the efficacy of hybrid immunity in preventing Omicron reinfection in patients with lung cancer, a total of 447 patients were included in the longitudinal study after the Omicron wave from March 2023 to August 2023. Humoral responses were measured at pre-Omicron wave, 3 months and 7 months postinfection. The detected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) specific antibodies including total antibodies, anti-receptor binding domain (RBD) specific IgG, and neutralizing antibodies against SARS-CoV-2 wild type (WT) and BA.4/5 variant. T cell responses against SARS-CoV-2 WT and Omicron variant were evaluated in 101 patients by ELISpot at 3 months postinfection. The results showed that Omicron-infected symptoms were mild, while fatigue (30.2%), shortness of breath (34.0%) and persistent cough (23.6%) were long-lasting, and vaccines showed efficacy against fever in lung cancer patients. Humoral responses were higher in full or booster vaccinated patients than those unvaccinated (p < .05 for all four antibodies), and the enhanced response persisted for at least 7 months. T cell response to Omicron was higher than WT peptides (21.3 vs. 16.0 SFUs/106 PBMCs, p = .0093). Moreover, 38 (9.74%) patients were reinfected, which had lower antibody responses than non-reinfected patients (all p < .05), and those patients of unvaccinated at late stage receiving anti-cancer immunotherapy alone were at high risk of reinfection. Collectively, these data demonstrate the Omicron infection induces a high and durable immune response in vaccinated patients with lung cancer, which protects vaccinated patients from reinfection.

Omicron neutralization character in patients with breast cancer and liver cancer after the nationwide omicron outbreak

BACKGROUND

The surge in omicron variants has caused nationwide breakthrough infections in mainland China since the December 2022. In this study, we report the neutralization profiles of serum samples from the patients with breast cancer and the patients with liver cancer who had contracted subvariant breakthrough infections.

METHODS

In this real-world study, we enrolled 143 COVID-19-vaccinated (81 and 62 patients with breast and liver cancers) and 105 unvaccinated patients with cancer (58 and 47 patients with breast and liver cancers) after omicron infection. Anti-spike receptor binding domain (RBD) IgGs and 50% pseudovirus neutralization titer (pVNT50) for the preceding (wild type), circulating omicron (BA.4-BA.5, and BF.7), and new subvariants (XBB.1.5) were comprehensively analyzed.

RESULTS

Patients with liver cancer receiving booster doses had higher levels of anti-spike RBD IgG against circulating omicron (BA.4-BA.5, and BF.7) and a novel subvariant (XBB.1.5) compared to patients with breast cancer after breakthrough infection. Additionally, all vaccinated patients produced higher neutralizing antibody titers against circulating omicron (BA.4-BA.5, and BF.7) compared to unvaccinated patients. However, the unvaccinated patients produced higher neutralizing antibody against XBB.1.5 than vaccinated patients after Omicron infection, with this trend being more pronounced in breast cancer than in liver cancer patients. Moreover, we found that there was no correlation between anti-spike RBD IgG against wildtype virus and the neutralizing antibody titer, but a positive correlation between anti-spike RBD IgG and the neutralizing antibody against XBB.1.5 was found in unvaccinated patients.

CONCLUSION

Our study found that there may be differences in vaccine response and protective effect against COVID-19 infection in patients with liver and breast cancer. Therefore, we recommend that COVID-19 vaccine strategies should be optimized based on vaccine components and immunology profiles of different patients with cancer.

Fulminant myocarditis induced by SARS-CoV-2 infection without severe lung involvement: insights into COVID-19 pathogenesis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection often leads to pulmonary complications. Cardiovascular sequelae, including myocarditis and heart failure, have also been reported. Here, the study presents two fulminant myocarditis cases infected by SARS-CoV-2 exhibiting remarkable elevation of cardiac biomarkers without significant pulmonary injury, as determined by imaging examinations. Immunohistochemical staining reveals the viral antigen within cardiomyocytes, indicating that SARS-CoV-2 could directly infect the myocardium. The full viral genomes from respiratory, anal, and myocardial specimens are obtained via next-generation sequencing. Phylogenetic analyses of the whole genome and spike gene indicate that viruses in the myocardium/pericardial effusion and anal swabs are closely related and cluster together yet diverge from those in the respiratory samples. In addition, unique mutations are found in the anal/myocardial strains compared to the respiratory strains, suggesting tissue-specific virus mutation and adaptation. These findings indicate genetically distinct SARS-CoV-2 variants have infiltrated and disseminated within myocardial tissues, independent of pulmonary injury, and point to different infection routes between the myocardium and respiratory tract, with myocardial infections potentially arising from intestinal infection. These findings highlight the potential for systemic SARS-CoV-2 infection and the importance of a thorough multi-organ assessment in patients for a comprehensive understanding of the pathogenesis of COVID-19.

Neutralization of EG.5, EG.5.1, BA.2.86, and JN.1 by antisera from dimeric receptor-binding domain subunit vaccines and 41 human monoclonal antibodies

BACKGROUND

The recently circulating Omicron variants BA.2.86 and JN.1 were identified with more than 30 amino acid changes on the spike protein compared to BA.2 or XBB.1.5. This study aimed to comprehensively assess the immune escape potential of BA.2.86, JN.1, EG.5, and EG.5.1.

METHODS

We collected human and murine sera to evaluate serological neutralization activities. The participants received three doses of coronavirus disease 2019 (COVID-19) vaccines or a booster dose of the ZF2022-A vaccine (Delta-BA.5 receptor-binding domain [RBD]-heterodimer immunogen) or experienced a breakthrough infection (BTI). The ZF2202-A vaccine is under clinical trial study (ClinicalTrials.gov: NCT05850507). BALB/c mice were vaccinated with a panel of severe acute respiratory syndrome coronavirus 2 RBD-dimer proteins. The antibody evasion properties of these variants were analyzed with 41 representative human monoclonal antibodies targeting the eight RBD epitopes.

FINDINGS

We found that BA.2.86 had less neutralization evasion than EG.5 and EG.5.1 in humans. The ZF2202-A booster induced significantly higher neutralizing titers than BTI. Furthermore, BA.2.86 and JN.1 exhibited stronger antibody evasion than EG.5 and EG.5.1 on RBD-4 and RBD-5 epitopes. Compared to BA.2.86, JN.1 further lost the ability to bind to several RBD-1 monoclonal antibodies and displayed further immune escape.

CONCLUSIONS

Our data showed that the currently dominating sub-variant, JN.1, showed increased immune evasion compared to BA.2.86 and EG.5.1, which is highly concerning. This study provides a timely risk assessment of the interested sub-variants and the basis for updating COVID-19 vaccines.

FUNDING

This work was funded by the National Key R&D Program of China, the National Natural Science Foundation of China, the Beijing Life Science Academy, the Bill & Melinda Gates Foundation, and the Postdoctoral Fellowship Program of China Postdoctoral Science Foundation (CPSF).

Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic

OBJECTIVES

The SARS-CoV-2 pandemic and large-scale genomic surveillance provided an exceptional opportunity to analyze mutations that appeared over three years in viral genomes. Here we studied mutations and their epidemic consequences for SARS-CoV-2 genomes from our center.

METHODS

We analyzed 61,397 SARS-CoV-2 genomes we sequenced from respiratory samples for genomic surveillance. Mutations frequencies were calculated using Nextclade, Microsoft Excel, and an in-house Python script.

RESULTS

A total of 22,225 nucleotide mutations were identified, 220 (1.0%) being each at the root of ≥836 genomes, classifying mutations as 'hyperfertile'. Two seeded the European pandemic: P323L in RNA polymerase, associated with an increased mutation rate, and D614G in spike that improved fitness. Most 'hyperfertile' mutations occurred in areas not predicted with increased virulence. Their mean number was 8±6 (0-22) per 1000 nucleotides per gene. They were 3.7-times more frequent in accessory than informational genes (13.8 versus 3.7/1000 nucleotides). Particularly, they were 4.1-times more frequent in ORF8 than in the RNA polymerase gene. Interestingly, stop codons were present in 97 positions, almost only in accessory genes, including ORF8 (21/100 codons).

CONCLUSIONS

most 'hyperfertile' mutations did not predict emergence of a new epidemic, and some were stop codons indicating the existence of so-named 'non-virulence' genes.

Clinical presentation of severe COVID‑19 with heart failure: A single‑center retrospective study

The coronavirus disease-19 (COVID-19) pandemic has led to a global transformation in public health interventions. The present study aimed to evaluate the clinical features as well as the outcomes of severe heart failure (HF) among patients with severe COVID-19. A single-center observational study was carried out at The 904th Hospital of Joint Logistic Support Force (Wuxi, China) from November 2022 to April 2023, and a total of 210 patients diagnosed with severe HF were included. Among these patients, 128 patients had COVID-19 whereas the remaining patients were not diagnosed with COVID-19. The analysis entailed investigated pre-existing medical records, that is, admission and discharge, laboratory values, neuroimaging, length of hospitalization, mortality and costs incurred by patients throughout the COVID-19 pandemic from the records. All the 210 incorporated patients accomplished the follow-up and it was established that there was no significant differences in baseline characteristics between HF combined with COVID-19 and HF without COVID-19 were affirmed (P>0.05). HF coupled with COVID-19 infection demonstrated an increased risk of 30-day mortality (28.91 vs. 14.63%; P=0.017), extended length of hospital stays (22.54±6.73 vs. 19.35±5.69; P<0.001) and higher expenses for hospitalization (P<0.001). Complications related to hospitalization, including pneumonia (76.56 vs. 35.37%; P=1.0x10-4), respiratory failure (47.66 vs. 24.39%; P=0.001), pulmonary embolism (8.59 vs. 2.44%; P=0.031), deep vein thrombosis (30.47 vs. 14.63%; P=0.009), 7 days delirium (60.16 vs. 45.12%; P=0.033), multiple organ dysfunction syndrome (32.81 vs. 18.29%; P=0.021) and neurological deficits (30.47% vs. 17.07%, P=0.029) increased significantly. In conclusion, HF combined with COVID-19, treatment and prognosis are getting worse. Enhancing preparedness for future COVID-19 and other similar pandemics necessitates the comprehension of this to refine care provided to patients with HF (registration no. THH-IPR-20221101 on 01 November 2022).

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.

Time-dependent CT score-based model for identifying severe/critical COVID-19 at a fever clinic after the emergence of Omicron variant

Rationale and objectives

The computed tomography (CT) score has been used to evaluate the severity of COVID-19 during the pandemic; however, most studies have overlooked the impact of infection duration on the CT score. This study aimed to determine the optimal cutoff CT score value for identifying severe/critical COVID-19 during different stages of infection and to construct corresponding predictive models using radiological characteristics and clinical factors.

Materials and methods

This retrospective study collected consecutive baseline chest CT images of confirmed COVID-19 patients from a fever clinic at a tertiary referral hospital from November 28, 2022, to January 8, 2023. Cohorts were divided into three subcohorts according to the time interval from symptom onset to CT examination at the hospital: early phase (0-3 days), intermediate phase (4-7 days), and late phase (8-14 days). The binary endpoints were mild/moderate and severe/critical infection. The CT scores and qualitative CT features were manually evaluated. A logistic regression analysis was performed on the CT score as determined by a visual assessment to predict severe/critical infection. Receiver operating characteristic analysis was performed and the area under the curve (AUC) was calculated. The optimal cutoff value was determined by maximizing the Youden index in each subcohort. A radiology score and integrated models were then constructed by combining the qualitative CT features and clinical features, respectively, using multivariate logistic regression with stepwise elimination.

Results

A total of 962 patients (aged, 61.7 ± 19.6 years; 490 men) were included; 179 (18.6%) were classified as severe/critical COVID-19, while 344 (35.8%) had a typical Radiological Society of North America (RSNA) COVID-19 appearance. The AUCs of the CT score models reached 0.91 (95% confidence interval (CI) 0.88-0.94), 0.82 (95% CI 0.76-0.87), and 0.83 (95% CI 0.77-0.89) during the early, intermediate, and late phases, respectively. The best cutoff values of the CT scores during each phase were 1.5, 4.5, and 5.5. The predictive accuracies associated with the time-dependent cutoff values reached 88% (vs.78%), 73% (vs. 63%), and 87% (vs. 57%), which were greater than those associated with universal cutoff value (all P < 0.001). The radiology score models reached AUCs of 0.96 (95% CI 0.94-0.98), 0.90 (95% CI 0.87-0.94), and 0.89 (95% CI 0.84-0.94) during the early, intermediate, and late phases, respectively. The integrated models including demographic and clinical risk factors greatly enhanced the AUC during the intermediate and late phases compared with the values obtained with the radiology score models; however, an improvement in accuracy was not observed.

Conclusion

The time interval between symptom onset and CT examination should be tracked to determine the cutoff value for the CT score for identifying severe/critical COVID-19. The radiology score combining qualitative CT features and the CT score complements clinical factors for identifying severe/critical COVID-19 patients and facilitates timely hierarchical diagnoses and treatment.

The association of post-embryo transfer SARS-CoV-2 infection with early pregnancy outcomes in in vitro fertilization: a prospective cohort study

BACKGROUND

The influence of SARS-CoV-2 infection after embryo transfer on early pregnancy outcomes in in vitro fertilization or intracytoplasmic sperm injection-embryo transfer treatment remains inadequately understood. This knowledge gap endures despite an abundance of studies investigating the repercussions of preceding SARS-CoV-2 infection on early pregnancy outcomes in spontaneous pregnancies.

OBJECTIVE

This study aimed to investigate the association between SARS-CoV-2 infection within 10 weeks after embryo transfer and early pregnancy outcomes in patients undergoing in vitro fertilization/intracytoplasmic sperm injection treatment.

STUDY DESIGN

This prospective cohort study was conducted at a single public in vitro fertilization center in China. Female patients aged 20 to 39 years, with a body mass index ranging from 18 to 30 kg/m2, undergoing in vitro fertilization/intracytoplasmic sperm injection treatment, were enrolled between September 2022 and December 2022, with follow-up extended until March 2023. The study tracked SARS-CoV-2 infection time (≤14 days, ≤28 days, and ≤10 weeks after embryo transfer), symptoms, vaccination status, the interval between vaccination and embryo transfer, and early pregnancy outcomes, encompassing biochemical pregnancy rate, implantation rate, clinical pregnancy rate, and early miscarriage rate. The study used single-factor analysis and multivariate logistic regression to examine the association between SARS-CoV-2 infection status, along with other relevant factors, and the early pregnancy outcomes.

RESULTS

A total of 857 female patients undergoing in vitro fertilization/intracytoplasmic sperm injection treatment were analyzed. In the first stage, SARS-CoV-2 infection within 14 days after embryo transfer did not have a significant negative association with the biochemical pregnancy rate (adjusted odds ratio, 0.74; 95% confidence interval, 0.51-1.09). In the second stage, SARS-CoV-2 infection within 28 days after embryo transfer had no significant association with the implantation rate (36.6% in infected vs 44.0% in uninfected group; P=.181). No statistically significant association was found with the clinical pregnancy rate after adjusting for confounding factors (adjusted odds ratio, 0.69; 95% confidence interval, 0.56-1.09). In the third stage, SARS-CoV-2 infection within 10 weeks after embryo transfer had no significant association with the early miscarriage rate (adjusted odds ratio, 0.77; 95% confidence interval, 0.35-1.71).

CONCLUSION

Our study suggests that SARS-CoV-2 infection within 10 weeks after embryo transfer may not be negatively associated with the biochemical pregnancy rate, implantation rate, clinical pregnancy rate, and early miscarriage rate in patients undergoing in vitro fertilization/intracytoplasmic sperm injection treatment. It is important to note that these findings are specific to the target population of in vitro fertilization/intracytoplasmic sperm injection patients aged 20 to 39 years, without previous SARS-CoV-2 infection, and with a body mass index of 18 to 30 kg/m2. This information offers valuable insights, addressing current concerns and providing a clearer understanding of the actual risk associated with SARS-CoV-2 infection after embryo transfer.

Risk prediction for severe COVID-19 progressing to critical illness and death in the ICU and efficacy analysis of using traditional Chinese medicine

To reveal the key factors influencing the progression of severe COVID-19 to critical illness and death in the intensive care unit (ICU) and to accurately predict the risk, as well as to validate the efficacy of treatment using traditional Chinese medicine (TCM), thus providing valuable recommendations for the clinical management of patients. A total of 189 patients with COVID-19 in 25 ICUs in Chongqing, China, were enrolled, and 16 eventually died. Statistical models shown that factors influencing the progression of COVID-19 to critical illness include the severity of illness at diagnosis, the mode of respiratory support, and the use of TCM. Risk factors for death include a history of metabolic disease, the use of antiviral drugs and TCM, and invasive endotracheal intubation. The area under curve of the noncollinearity model predicted the risk of progression to critical illness and the risk of death reached 0.847 and 0.876, respectively. The use of TCM is an independent protective factor for the prevention of the progression of severe COVID-19, while uncorrectable hypoxemia and invasive respiratory support are independent risk factors, and antiviral drugs can help reduce mortality. The multifactorial prediction model can assess the risk of critical illness and death in ICU COVID-19 patients, and inform clinicians in choosing the treatment options and medications.

The effect of COVID-19 infection on patients with rheumatic diseases in China

OBJECTIVES

At the end of 2022, the COVID-19 outbreak erupted in China, and BA.5.2 or BF.7 subtypes of Omicron novel variations were implicated in more than 90% of the cases. We created a real-world questionnaire survey to better understand how this new variant pandemic was affecting rheumatic patients in China.

METHODS

During the COVID-19 outbreak in China, the subjects of this study were rheumatic patients and non-rheumatic individuals (control group), who were matched for sex and age. Professional physicians carefully questioned the participants before administering a questionnaire as part of the study. This study focused on the general baseline characteristics, clinical symptoms and treatment after COVID-19 infection, and the target populations' awareness of COVID-19.

RESULTS

The study included 1130 participants, of whom 572 were assigned to the rheumatic group and 558 to the control group. The percentage of vaccinated controls was significantly higher than that of rheumatic patients (90.1% vs. 62.8%, p < 0.001), while the rate of COVID-19 infection was not significantly different between the two groups (82.3% vs. 86.6%, p = 0.051). Patients with rheumatic disease experienced substantially more days of fever following infection (2.87 ± 3.42 vs. 2.18 ± 1.65, p = 0.002) compared to individuals in the control group. The rheumatic patients had a greater prevalence of cough (67.1% vs. 54.0%, p < 0.001), somnipathy (13.8% vs. 6.0%, p < 0.001), and conjunctivitis/ophthalmodynia (5.3% vs. 2.1%, p = 0.008), while dry throat/throat pain/weakness (49.9% vs. 59.4%, p = 0.003), myalgia/osteodynia (33.3% vs. 41.8%, p = 0.003), and dyspnea (14.0% vs. 25.3%, p < 0.001) were more likely to occur in non-rheumatic group after infection. Human immunoglobulin (2.1% vs. 0.2%, p = 0.006), glucocorticoids (19.5% vs. 1.6%, p < 0.001), oxygen support (6.8% vs. 2.1%, p < 0.001), and traditional Chinese medicine (21.9% vs. 16.6%, p = 0.037) were all more frequently used by rheumatic patients with COVID-19 infection. People in the control group were more confused about whether to use masks in following social activities after contracting COVID-19 (14.7% vs. 7.6%, p = 0.001). In the control group, more individuals than patients with rheumatic disease (25.1% vs. 13.4%, p < 0.001) expressed an interest to receive the vaccine again. After being exposed to COVID-19, the majority of rheumatic patients (66.9%) reported no discernible change, only 29.1% reported a worsening of their symptoms, and the remaining 4% indicated an improvement.

CONCLUSIONS

After the COVID-19 outbreak in China, the proportion of patients with rheumatic diseases infected with the virus was similar to that of normal individuals. But the clinical symptoms, follow-up treatment requirements, and awareness of the COVID-19 among rheumatic patients were distinct from those among non-rheumatic patients, necessitating the use of individualized diagnosis and treatment plans as well as health advice by medical professionals in clinical work. Key Points • Despite there were different comorbidities and vaccination rates, the rate of COVID-19 infection in patients with rheumatic disease was similar to that of normal individuals. • After COVID-19 infection, rheumatic patients and normal controls had different clinical symptoms and drug usage. • After being exposed to COVID-19, the majority of rheumatic patients felt no significant change in the primary disease, while the normal controls was more likely to accept a new vaccine injection and confused about whether to use masks in following social activities.

Clinical evaluation of a new COVID-19 antigen rapid test kit for detection of SARS-CoV-2

The antigen rapid diagnostic test (Ag-RDT) is an assay kit for detecting the SARS-COV-2 nucleocapsid proteins, based on the colloidal gold method.Accurate diagnosis has an important role in limiting the transmission of SARS-COV-2, and also helps patients to receive earlier treatment .The object of this study was to perform the clinical evaluation of a novel Ag-RDTs with samples collected from two different swabs.DEEPBLUE®COVID-19 antigen detection kit used for the examination of the subjects in the experiment.For antigen testing on samples collected with nasal swabs, sensitivity was 91.7 % (95 % CI 83.6-96.6 %) and specificity was 100 %(95 %CI 98.1-100 %).For nasopharyngeal swabs, the sensitivity was 96.8 % (95 % CI 93.6-98.7 %) and the specificity was 100 % (95 % CI 98.2-100 %).Fisher Precision test showed a significant correlation between nasopharyngeal swab Ag-RDTs and nasal swab Ag-RDTs and RT-qPCR test (p-value <0.001).The results showed that the patients use the kit for testing were comparable to the RT-qPCR.

Application of next-generation sequencing to identify different pathogens

Early and precise detection and identification of various pathogens are essential for epidemiological monitoring, disease management, and reducing the prevalence of clinical infectious diseases. Traditional pathogen detection techniques, which include mass spectrometry, biochemical tests, molecular testing, and culture-based methods, are limited in application and are time-consuming. Next generation sequencing (NGS) has emerged as an essential technology for identifying pathogens. NGS is a cutting-edge sequencing method with high throughput that can create massive volumes of sequences with a broad application prospects in the field of pathogen identification and diagnosis. In this review, we introduce NGS technology in detail, summarizes the application of NGS in that identification of different pathogens, including bacteria, fungi, and viruses, and analyze the challenges and outlook for using NGS to identify clinical pathogens. Thus, this work provides a theoretical basis for NGS studies and provides evidence to support the application of NGS in distinguishing various clinical pathogens.

Systematic Genomic Surveillance of SARS-CoV-2 at Xiamen International Airport and the Port of Xiamen Reveals the Importance of Incoming Travelers in Lineage Diversity

Sever Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is still a threat to human health globally despite the World Health Organization (WHO) announcing the end of the COVID-19 pandemic. Continued surveillance of SARS-CoV-2 at national borders would be helpful in understanding the epidemics of novel imported variants and updating local strategies for disease prevention and treatment. This study focuses on the surveillance of imported SARS-CoV-2 variants among travelers entering Xiamen International Airport and the Port of Xiamen from February to August 2023. A total of 97 imported SARS-CoV-2 sequences among travelers from 223 cases collected from 12 different countries and regions were identified by real-time RT-PCR. Next-generation sequencing was used to generate high-quality complete sequences for phylogenetic and population dynamic analysis. The study revealed a dominant shift in variant distribution, in which the XBB subvariant (XBB.1.5, XBB.1.16, XBB.1.9, XBB.2.3, and EG.5.1) accounted for approximately 88.8% of the sequenced samples. In detail, clades 23D and 23E accounted for 26.2% and 21.4% of the sequenced samples, respectively, while clades 23B (13.6%) and 23F (10.7%) took the third and fourth spots in the order of imported sequences, respectively. Additionally, the XBB.2.3 variants were first identified in imported cases from the mainland of Xiamen, China on 27 February 2023. The spatiotemporal analyses of recent viral genome sequences from a limited number of travelers into Xiamen provide valuable insights into the situation surrounding SARS-CoV-2 and highlight the importance of sentinel surveillance of SARS-CoV-2 variants in the national border screening of incoming travelers, which serves as an early warning system for the presence of highly transmissible circulating SARS-CoV-2 lineages.

Short-term effectiveness of single-dose intranasal spray COVID-19 vaccine against symptomatic SARS-CoV-2 Omicron infection in healthcare workers: a prospective cohort study

Background

The pivotal phase 3 efficacy clinical trial has demonstrated that a two-dose regimen of dNS1-RBD (Beijing Wantai Biological Pharmacy Enterprise, Beijing, China) is well-tolerated and provides wide protection against SARS-CoV-2 infection. However, the effectiveness of a single-dose regimen is still unknown. We aimed to estimate the effectiveness of one-dose of dNS1-RBD against symptomatic Omicron infections in real-world conditions.

Methods

This prospective cohort study was conducted during an Omicron outbreak among healthcare workers in Xiamen, China, from December 22, 2022 to January 16, 2023. Participants chose to receive single-dose of dNS1-RBD or remain unvaccinated based on personal preference. Healthcare workers daily validated their SARS-CoV-2 infection status, using either RT-PCR or rapid antigen test. A survey questionnaire was conducted to gather information on acute symptoms from individuals infected with SARS-CoV-2. The primary outcome was the symptomatic SARS-CoV-2 infections after enrollment in the dNS1-RBD recipients or the control group among all participants and by prior COVID-19 vaccination status.

Findings

On December 22, 2022, a total of 1391 eligible participants without a history of prior SARS-CoV-2 infection were enrolled. Among them, 550 received single-dose of dNS1-RBD, while 841 remained unvaccinated. In the total cohort, the range of follow-up time was 1∼26 days. During the study period, a total of 880 symptomatic SARS-CoV-2 infections were identified in the total cohort. The adjusted vaccine effectiveness against symptomatic SARS-CoV-2 infections and the infections requiring medical attention were 19.0% (95% CI: 6.7, 29.7, P = 0.004) and 59.4% (95% CI: 25.1, 78.0, P = 0.004) in the total cohort, 11.6% (95% CI: -2.4, 23.7, P = 0.100) and 55.3% (95% CI: 15.3, 76.4, P = 0.014) in the participants with inactivated COVID-19 vaccination history, as well as 87.0% (95% CI: 72.6, 93.9, P < 0.001) and 84.2% (95% CI: -41.8, 98.2, P = 0.099) in the naïve participants, respectively.

Interpretation

When administered as a booster to individuals with a history of inactivated COVID-19 vaccination, a single-dose of dNS1-RBD provides protection against infections requiring medical attention at least in the short-term after vaccination. The data also showed that a single-dose of dNS1-RBD is protective against symptomatic SARS-CoV-2 infections as a primary immunization for individuals without prior exposure, but due to the limited sample size of naïve participants, further research with a larger sample size is needed to make a solid conclusion.

Funding

Xiamen Science and Technology Bureau 2022 General Science and Technology Plan Project and the Bill & Melinda Gates Foundation.

Repeated Omicron exposures override ancestral SARS-CoV-2 immune imprinting

The continuing emergence of SARS-CoV-2 variants highlights the need to update COVID-19 vaccine compositions. However, immune imprinting induced by vaccination based on the ancestral (hereafter referred to as WT) strain would compromise the antibody response to Omicron-based boosters1-5. Vaccination strategies to counter immune imprinting are critically needed. Here we investigated the degree and dynamics of immune imprinting in mouse models and human cohorts, especially focusing on the role of repeated Omicron stimulation. In mice, the efficacy of single Omicron boosting is heavily limited when using variants that are antigenically distinct from WT-such as the XBB variant-and this concerning situation could be mitigated by a second Omicron booster. Similarly, in humans, repeated Omicron infections could alleviate WT vaccination-induced immune imprinting and generate broad neutralization responses in both plasma and nasal mucosa. Notably, deep mutational scanning-based epitope characterization of 781 receptor-binding domain (RBD)-targeting monoclonal antibodies isolated from repeated Omicron infection revealed that double Omicron exposure could induce a large proportion of matured Omicron-specific antibodies that have distinct RBD epitopes to WT-induced antibodies. Consequently, immune imprinting was largely mitigated, and the bias towards non-neutralizing epitopes observed in single Omicron exposures was restored. On the basis of the deep mutational scanning profiles, we identified evolution hotspots of XBB.1.5 RBD and demonstrated that these mutations could further boost the immune-evasion capability of XBB.1.5 while maintaining high ACE2-binding affinity. Our findings suggest that the WT component should be abandoned when updating COVID-19 vaccines, and individuals without prior Omicron exposure should receive two updated vaccine boosters.

Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants

The prolonged course of the COVID-19 pandemic necessitates sustained surveillance of emerging variants. This study aimed to develop a multiplex real-time polymerase chain reaction (rt-PCR) suitable for the real-time tracking of Omicron subvariants in clinical and wastewater samples. Plasmids containing variant-specific mutations were used to develop a MeltArray assay. After a comprehensive evaluation of both analytical and clinical performance, the established assay was used to detect Omicron variants in clinical and wastewater samples, and the results were compared with those of next-generation sequencing (NGS) and droplet digital PCR (ddPCR). The MeltArray assay identified 14 variant-specific mutations, enabling the detection of five Omicron sublineages (BA.2*, BA.5.2*, BA.2.75*, BQ.1*, and XBB.1*) and eight subvariants (BF.7, BN.1, BR.2, BQ.1.1, XBB.1.5, XBB.1.16, XBB.1.9, and BA.4.6). The limit of detection (LOD) of the assay was 50 copies/reaction, and no cross-reactivity was observed with 15 other respiratory viruses. Using NGS as the reference method, the clinical evaluation of 232 swab samples exhibited a clinical sensitivity of > 95.12% (95% CI 89.77-97.75%) and a specificity of > 95.21% (95% CI, 91.15-97.46%). When used to evaluate the Omicron outbreak from late 2022 to early 2023, the MeltArray assay performed on 1408 samples revealed that the epidemic was driven by BA.5.2* (883, 62.71%) and BF.7 (525, 37.29%). Additionally, the MeltArray assay demonstrated potential for estimating variant abundance in wastewater samples. The MeltArray assay is a rapid and scalable method for identifying SARS-CoV-2 variants. Integrating this approach with NGS and ddPCR will improve variant surveillance capabilities and ensure preparedness for future variants.

Was China's zero-COVID policy the right choice? The multiple factor analysis of variables that affected the course of COVID-19 pandemic in China

Background

After 3 years of the COVID-19 pandemic and zero-COVID policy, a rapid increase in the number of daily COVID-19 infections was observed in China from November to December 2022. Therefore, we decided to analyze the factors that have been related to the COVID-19 pandemic in China.

Methods

The multiple factor analysis was conducted, using the data from publicly available databases from the beginning of the COVID-19 pandemic to 30 January 2023.

Results

Our study showed that each year of the pandemic in China had different profiles and can be described by different variables: year 2020 was characterized by restrictions, such as international travel controls, stay at home requirements, and health system policies including contact tracing and protection of older adults; year 2021 was characterized by Alpha, Beta, Gamma, and Delta variants; 2022 was characterized by new cases per million, Omicron lineages, and a few restrictions-related variables; and year 2023 was mainly described by the number of new deaths per million and Omicron variant 22B (BA.5) but also by testing and vaccination policies, as well as the number of people fully vaccinated per 100 and total boosters per 100.

Conclusion

The COVID-19 pandemic has changed over time. Therefore, the anti-pandemic policies implemented must be dynamic and adapted to the current situation.

Contamination dynamics of personal protective equipment (PPE) by SARS-CoV-2 RNA in a makeshift hospital with COVID-19 positive occupants

Background

Personal protective equipment (PPE) helps protect healthcare workers (HCWs) from infection and prevents cross-contamination. Knowledge of the contamination dynamics of PPE during the management of COVID-19 patients in a makeshift hospital is limited.

Aim

To describe the rate of SARS-CoV-2 contamination in PPE and to assess the change of contamination at different time points.

Methods

HCWs were followed up for up to 4 hours with hourly collection of swab samples from PPE surfaces in a makeshift COVID-19 hospital setting. Swabs were tested using quantitative reverse transcription polymerase chain reaction (RT-qPCR) for SARS-CoV-2 RNA.

Results

SARS-CoV-2 was detected on 50.9% of the 1620 swabbed samples from 9 different sites of full-body PPE worn by HCWs. The proportion of sites contaminated with SARS-CoV-2 RNA varied from 10.6% to 95.6%. Viral RNA was most frequently detected from the sole of the outer foot cover (95.6%) and least frequently on the face shield (10.6%). The median Ct values among positive samples were 34.20 (IQR, 32.61-35.22) and 34.05 (IQR, 32.20-35.39) for ORF1ab and N genes, respectively. The highest rate of contamination with SARS-CoV-2 RNA for the PPE swab samples was found after 3 hours of use. The positive rate of outer surface of HEPA filters from air supply device was 82.1% during the full capacity period of the makeshift hospital.

Conclusion

A higher rate of contamination was identified at 3 hours after the entrance to the COVID-19 patient care area. Virus-containing aerosols were trapped in the HEPA filter of air supply equipment, representing a potential protective factor against infection to HCWs.

Epidemiological and clinical features of COVID-19 inpatients in Changsha, China: A retrospective study from 2020 to 2022

Objectives

The spread of SARS-Cov-2 remains a global concern along with the emergence of variants. This study aims to characterize the epidemiological and clinical features of hospitalized patients who were dragonized with five different variants of SARS-CoV-2 during the past 3 years.

Methods

This retrospective study recruited 432 COVID-19 patients who were hospitalized in the First Hospital of Changsha from January 2020 to August 2022. Clinical records on clinical symptoms, laboratory profiles, and chest CT images was collected. The epidemiological and clinical features were compared between COVID-19 patients infected with either the wild-type, Omicron variant or pre- Omicron variants (e.g., Alpha, Beta, Delta).

Results

A total of 432 laboratory-confirmed COVID-19 inpatients were dialogized during three waves, including 247 cases during the wild-type transmission period, 65 cases during the transmission period of pre-Omicron variants, and 119 cases during the transmission period of Omicron variants. The proportion of moderately or severely ill inpatients showed a gradual decline from the wild-type transmission period to the Omicron transmission period. The common symptoms of inpatients infected with SARS-CoV-2 wildtype strains included fever (67.61 %), cough (57.89 %), fatigue (33.60 %), and shortness of breath (12.15 %). In contrast, patients infected with other variants mostly showed upper respiratory symptoms. Based on chest CT images, a lower degree of acute pulmonary infection was observed among inpatients infected with the Omicron variants than those infected with the wild-type strain (31.09 % vs 93.12 %, p-value<0.01).

Conclusions

Compared with the wild-type strain, SARS-CoV-2 variants of concern, especially the Omicron variant, mostly caused a lower degree of acute pulmonary infection, indicating the reduced disease severity and mortality among hospitalized COVID-19 patients.

Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) XBB lineages have achieved dominance worldwide and keep on evolving. Convergent evolution of XBB lineages on the receptor-binding domain (RBD) L455F and F456L is observed, resulting in variants with substantial growth advantages, such as EG.5, FL.1.5.1, XBB.1.5.70, and HK.3. Here, we show that neutralizing antibody (NAb) evasion drives the convergent evolution of F456L, while the epistatic shift caused by F456L enables the subsequent convergence of L455F through ACE2 binding enhancement and further immune evasion. L455F and F456L evade RBD-targeting Class 1 public NAbs, reducing the neutralization efficacy of XBB breakthrough infection (BTI) and reinfection convalescent plasma. Importantly, L455F single substitution significantly dampens receptor binding; however, the combination of L455F and F456L forms an adjacent residue flipping, which leads to enhanced NAbs resistance and ACE2 binding affinity. The perturbed receptor-binding mode leads to the exceptional ACE2 binding and NAb evasion, as revealed by structural analyses. Our results indicate the evolution flexibility contributed by epistasis cannot be underestimated, and the evolution potential of SARS-CoV-2 RBD remains high.

The clinical features of severe COVID-19 with respiratory failure: A Chinese single-center retrospective study

The global pandemic of COVID-19, caused by the novel coronavirus SARS-CoV-2, has resulted in widespread alterations to public health measures worldwide. This observational study aimed to assess the clinical features and results of respiratory failure in patients with severe COVID-19. A single-center observational study was performed at a Chinese hospital between November 1, 2022, and February 31, 2023. All 182 enrolled patients were diagnosed with respiratory failure, 84 patients were infected with COVID-19, and the other 98 patients were not infected. A review of available medical records at admission and discharge, including neuroimaging, laboratory values at admission, mortality, length of hospitalization, and hospital costs, was conducted during the COVID-19 pandemic. All 182 eligible patients completed the follow-up. There was no significant difference in baseline characteristics between respiratory failure combined with COVID-19 (P > .05). Respiratory failure combined with COVID-19 infection may lead to higher 30-day mortality (16.36% vs 7.14%, P = .005), longer hospital stays (22.5 ± 5.9 vs 12.8 ± 4.2, P < .001), larger hospitalization costs (P < .001), and increased hospitalization complications, such as pulmonary embolism (10.30% vs 4.76%, P = .039), deep vein thrombosis (33.33% vs 18.57%, P = .001), incidence of 7-day delirium (69.70% vs 46.19%, P < .001), and respiratory failure (38.18% vs 24.77%, P = .005). If respiratory failure occurs while the patient is infected with COVID-19, treatment and prognosis worsen. Our understanding of COVID-19 and the care we provide to patients with respiratory failure is crucial to better prepare for a potential pandemic.

Assessment of vaccinations and breakthrough infections after adjustment of the dynamic zero-COVID-19 strategy in China: an online survey

Coronavirus disease 2019 (COVID-19) cases in China has grown rapidly after adjustment of the dynamic zero-COVID-19 strategy. However, how different vaccination states affect symptoms, severity and post COVID conditions was unclear. Here, we used an online questionnaire to investigate the infection status of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among 11,897 participants, with 55.55% positive and 28.42% negative. The common COVID-19 symptoms were fatigue (73.31%), cough (70.02%), fever (65.25%) and overall soreness (58.64%); self-reported asymptomatic infection accounted for 0.7% of participants. The persistent symptoms at 1 month after infection included fatigue (48.7%), drowsiness (34.3%), cough (30.1%), decreased exercise ability (23.1%) and pharyngeal discomfort (19.4%), which was reduced by more than 200% at 2 months. Participants with complications such as chronic obstructive pulmonary disease, respiratory diseases, diabetes, hypertension, etc. have a higher proportion of hospitalization and longer recovery time (p < = 0.01). Multiple vaccination statuses reduced the infection (p < 0.001) and severity rates (p = 0.022) by varying degrees as well as reduced the risk of high fever (>39.1 °C), chills, diarrhea and ageusia/anosmia, respectively (p < 0.05). Vaccination may enhance some upper respiratory symptoms, including sore throat, nasal congestion and runny nose, respectively (p < 0.05). Participants who had been vaccinated within 3 months were better protected by helping reduce their risk of overall soreness, chills and ageusia/anosmia, respectively (p < 0.05). In conclusion, our work has updated the epidemic characteristics of the breakthrough infection (BTI) wave after the dynamic zero-COVID-19 strategy, providing data and insights on how different vaccination statuses affect COVID-19 symptoms and disease prognosis.

Separation and quantification of Azvudine in plasma of patients with COVID-19 using LC-MS/MS

Azvudine (FNC) is a new drug conditionally approved in 2022 for the treatment of coronavirus disease 2019 (COVID-19) in China. However, the exposure level of FNC in COVID-19 patients in clinical practice is still obscure, and there is no liquid chromatography-tandem mass spectrometry (LC-MS/MS) or LC method reported for quantifying the FNC. In this study, a simple, fast, and reliable LC-MS/MS method using L-phenylalanine-D5 (Phe-D5) as the internal standard (IS) was developed for the quantification of FNC in plasma from COVID-19 patients. After simple protein precipitation with methanol, the analyte in the supernatant was separated on Waters Atlantis® T3 (2.1 ×100 mm, 3.0 µm) column with the mobile phase consisting of acetonitrile (ACN) - aqueous solution (containing 0.03% heptafluorobutyric acid and 0.2% formic acid). The mobile phase was delivered at 0.3 mL/min in an isocratic elution program (15:85, V: V). The linear relationship of FNC was good within the calibration range of 2.0 - 2000.0 ng/mL, with the recovery of FNC ranging from 81.37% to 103.31% and the matrix effect was 94.77%- 109.83%. The short-term, long-term, and freeze-thaw stability of the FNC assessed in method was acceptable, and all other items met the requirements of validation of the biological analytical method. Finally, the method was applied to detect the exposure level of FNC in plasma samples from patients diagnosed with COVID-19, and the results, which are within the linear range of the method, showed huge inter-individual variation, supporting the significance of therapeutic drug monitoring of FNC.

Effects of the response to the COVID-19 pandemic in chest trauma patients in China: a multicenter retrospective study

BACKGROUND

An international pandemic of severe coronavirus disease (COVID-19) has been caused by the novel coronavirus SARS-CoV-2. A large number of patients with chest trauma were infected with COVID-19. The COVID-19 pandemic had a significant impact on the management of chest trauma.

OBJECTIVE

The present observational study was conducted to evaluate the clinical characteristics and outcomes of chest trauma patients with or without COVID-19 infection.

METHODS

A multicenter observational study was performed at three Chinese hospitals between November 1, 2022, and January 31, 2023. All enrolled patients were diagnosed with chest trauma. We analyzed data from existing medical records, including all baseline data and prognostic follow-up data, such as 30-day mortality, hospital stays, hospitalization costs, and complications.

RESULTS

All 375 eligible patients completed the follow-up. There was no significant difference in baseline characteristics between chest trauma combined with COVID-19 (p > 0.05). Chest trauma combined with COVID-19 infection may lead to higher 30-day mortality (16.36% vs. 7.14%, p = 0.005), longer hospital stays (22.5 ± 5.9 vs. 12.8 ± 4.2, p < 0.001), larger hospitalization costs (p < 0.001), and increased hospitalization complications, such as pulmonary embolism (10.30% vs. 4.76%, p = 0.039), deep vein thrombosis (DVT, 33.33% vs. 18.57%, p = 0.001), the incidence of 7-day delirium (69.70% vs. 46.19%, p < 0.001), and respiratory failure (38.18% vs. 24.77%, p = 0.005).

CONCLUSIONS

Compared to chest trauma alone, it may lead to higher mortality, larger hospitalization costs, and more complications. To better respond to the future of COVID-19 or other similar virus-borne disease pandemics, it is important to understand the clinical characteristics and complications, such as pulmonary embolism, DVT, and respiratory failure after COVID-19 infection. To guide the future treatment of chest trauma combined with COVID-19 infection or other infectious diseases.

Genomic evolution of BA.5.2 and BF.7.14 derived lineages causing SARS-CoV-2 outbreak at the end of 2022 in China

Since the end of 2022, when China adjusted its COVID-19 response measures, the SARS-CoV-2 epidemic has rapidly grown in the country. It is very necessary to monitor the evolutionary dynamic of epidemic variants. However, detailed reports presenting viral genome characteristics in China during this period are limited. In this study, we examined the epidemiological, genomic, and evolutionary characteristics of the SARS-CoV-2 genomes from China. We analyzed nearly 20,000 genomes belonging to 17 lineages, predominantly including BF.7.14 (22.3%), DY.2 (17.3%), DY.4 (15.5%), and BA.5.2.48 (11.9%). The Rt value increased rapidly after mid-November 2022, reaching its peak at the end of the month. We identified forty-three core mutations in the S gene and forty-seven core mutations in the ORF1ab gene. The positive selection of all circulating lineages was primarily due to non-synonymous substitutions in the S1 region. These findings provide insights into the genomic characteristics of SARS-CoV-2 genomes in China following the relaxation of the 'dynamic zero-COVID' policy and emphasize the importance of ongoing genomic monitoring.

Characteristics and Prognostic Factors of SARS-CoV-2 Omicron Variant Infection in Hemodialysis Patients: A Single-Center Study in China

INTRODUCTION

This study aimed to evaluate the characteristics and prognostic factors for coronavirus disease 2019 (COVID-19) patients on maintenance hemodialysis (HD).

METHODS

All admitted HD patients who were infected with SARS-CoV-2 from December 1, 2022, to January 31, 2023, were included. Patients with pneumonia were further classified into the mild, moderate, severe, and critical illness. Clinical symptoms, laboratory results, radiologic findings, treatment, and clinical outcomes were collected. Independent risk factors for progression to critical disease and in-hospital mortality were determined by the multivariate regression analysis. The receiver operating characteristic analysis with the area under the curve was used to evaluate the predictive performance of developing critical status and in-hospital mortality.

RESULTS

A total of 182 COVID-19 patients with HD were included, with an average age of the 61.55 years. Out of the total, 84 (46.1%) patients did not have pneumonia and 98 (53.8%) patients had pneumonia. Among patients with pneumonia, 48 (49.0%) had moderate illness, 26 (26.5%) severe illness, and 24 (24.5%) critical illness, respectively. Elder age [HR (95% CI): 1.07 (1.01-1.13), p <0.01], increased levels of lactate dehydrogenase (LDH) [1.01 (1.003-1.01), p <0.01], and C-reactive protein (CRP) [1.01 (1.00-1.01), p = 0.04] were risk factors for developing critical illness. Elder age [1.11 (1.03-1.19), p = 0.01], increased procalcitonin (PCT) [1.07 (1.02-1.12), p = 0.01], and LDH level [1.004 (1-1.01), p = 0.03] were factors associated with increased risk of in-hospital mortality.

CONCLUSION

Age, CRP, PCT, and LDH can be used to predict negative clinical outcomes for HD patients with COVID-19 pneumonia.

Genomic surveillance of SARS-CoV-2 in Weihai, China, march 2022 to march 2023

COVID-19 is an acute respiratory infectious disease caused by SARS-CoV-2. It was first reported in Wuhan, China in December 2019 and rapidly spread globally in early 2020, triggering a global pandemic. In December 2022, China adjusted the dynamic COVID-zero strategy that lasted for three years. The number of positive cases in China increased rapidly in the short term. Weihai was also affected during this period. We conducted genomic surveillance of SARS-CoV-2 variants in Weihai during this period, hoping to understand the changes in the genomic characteristics of SARS-CoV-2 before and after the adjustment of the epidemic policy. In this study,we collected SARS-CoV-2 positive samples from March 2022 to March 2023 in Weihai and performed SARS-CoV-2 whole genome sequencing on these samples using next-generation sequencing technology. we obtained a total of 704 SARS-CoV-2 whole genome sequences, and selected 581 high-quality sequences for further analysis. The analysis results showed that from March 2022 to November 2022, before the adjustment of epidemic policy, the COVID-19 cases in Weihai were mainly from four local clusters,which were caused by four variants, including BA.2,BA.1.1,P.1.15 and BA.5.2.1. Phylogenetic analysis showed that: In the same cluster,the sequences between each other were highly homologous, and the whole genome sequence were almost identical. After December 2022, the epidemic policy was adjusted, BF.7 and BA.5.2 became the dominant variants in Weihai, consistent with the main domestic strains in China during the same period. Phylodynamic analysis showed that BF.7 and BA.5.2 had a large amount of genetic diversities in December, and the effective population size of BF.7 and BA.5.2 also showed explosive growth in December. In conclusion, we reported the composition and dynamic trend of SARS-CoV-2 variants in Weihai from March 2022 to March 2023. We found that there have been significant changes in the variants and expansion patterns of SARS-CoV-2 before and after the adjustment of epidemic policies. But the dominant variants in Weihai were the same as the SARS-CoV-2 variants circulating globally at the same time and we found no persistently dominant variants or new lineages during this period.

SARS-CoV-2-specific antibody and T-cell immunity in convalescents after infection wave in Beijing in late 2022

OBJECTIVES

To evaluate SARS-CoV-2-specific antibody and T-cell responses in convalescents 5 months after infection wave in Beijing from December 2022 to January 2023 to prevent reinfection and severe disease.

METHODS

Convalescents and uninfected individuals vaccinated with different doses were enrolled to assess the IFNγ T-cell responses against SARS-CoV-2 prototype strain, BF.7, BQ.1, and XBB. Neutralizing antibodies against prototype strain, BF.7, BA.5, and XBB and immunoglobulin G antibody were further analyzed.

RESULTS

In convalescents, the IFNγ T-cell response was significantly higher than that of uninfected individuals (all P < 0.001), and the T-cell response against XBB had no significant difference from that of SARS-CoV-2 prototype strain and BF.7 and BQ.1 (all P > 0.05). The seropositive rates of IgG antibodies were 100% (303/303) with a median concentration of 90.52 (95% CI, 82.52-99.37). The neutralizing antibodies titers of convalescents against BF.7 and BA.5 were higher than that against the prototype strain (both P < 0.001), while XBB.1.5 was lower (P < 0.001). T-cell response, IgG and neutralizing antibodies had no significant difference in convalescents vaccinated with different doses (all P > 0.05).

CONCLUSIONS

The immunities may have some protective effect against possible future outbreaks and severe diseases of COVID-19.

Application of Internet hospitals for first-visit patients with COVID-19 during the pandemic in China

BACKGROUND

There has been controversy over whether to carry out online medical inquiries and electronic prescription for first-visit patients. While Internet hospitals have become crucial to ensure providing online diagnosis and prescription needs for first-visit COVID-positive patients.

OBJECTIVE

We describe the results and advantages of online medical treatment during the coronavirus disease 2019 (COVID-19) outbreak and analyse the results and advantages of online medical treatment.

METHODS

Data were collected from the patients who received online medical inquiry services through the COVID-19 Special Section of our Internet hospital. The user demographic characteristics, user behaviour, clinical symptoms and medical records were collected. Baseline data of offline outpatient patients were also collected.

RESULTS

A total of 16 173 online medical inquiries were included. The daily online outpatient service volume reached a peak of 2446 person-times. The median age was 29.92 years (SD 15.59), ranging from 20-39 years (n = 8870, 54.84%). A total of 89.20% (n = 14 426/16 173) patients had epidemic-related symptoms. Moreover, 23.35% of the people were diagnosed as COVID-19-positive through antigen or nucleic acid testing. Furthermore, 86.61% (14 008/16 173) of the patients visited our hospital for the first time or had no offline physical outpatient service record within the past 3 months. The demand for medical inquiries was mainly for drug dispensing, followed by medication guidance and disease diagnosis. And 2.07% (334/16 173) of the patients needed to go to the offline hospital for further treatment.

CONCLUSION

The service model of the COVID-19 Special Section based on Internet hospitals provided the public with the necessary medical support during the COVID-19 outbreak. It provides a reference for future pandemics or public health emergencies.

Clinical Characteristics and Postoperative Complications in Patients Undergoing Colorectal Cancer Surgery with Perioperative COVID-19 Infection

With the emergence of novel variants, there have been widespread COVID-19 infections in the Chinese mainland recently. Compared to ancestral COVID-19 variants, Omicron variants become more infectious, but less virulent. Previous studies have recommended postponing non-emergency surgery for at least 4-8 weeks after COVID-19 infection. However, delayed surgery has been shown to be associated with tumor progression and worse overall survival for cancer patients. Here, we examined surgery risk and optimal timing for colorectal cancer patients with perioperative COVID-19 infection. A total of 211 patients who underwent colorectal cancer surgery from 1 October 2022 to 20 January 2023 at Xinhua Hospital were included. In addition, COVID-19-infected patients were further categorized into three groups based on infected time (early post-COVID-19 group, late post-COVID-19 group and postoperative COVID-19 group). The complication rate in patients with COVID-19 infection was 26.3%, which was significantly higher than in control patients (8.4%). The most common complications in COVID-19-infected patients were pneumonia, ileus and sepsis. Patients who underwent surgery close to the time of infection had increased surgery risks, whereas surgery performed over 1 week after recovery from COVID-19 did not increase the risk of postoperative complications. In conclusion, surgery performed during or near the time of COVID-19 infection is associated with an increased risk of developing postoperative complications. We recommend that the safe period for patients with recent COVID-19 infection in colorectal cancer surgery be at least 1 week after recovery from COVID-19.

Safety, immunogenicity and protection of heterologous boost with an aerosolised Ad5-nCoV after two-dose inactivated COVID-19 vaccines in adults: a multicentre, open-label phase 3 trial

BACKGROUND

Aerosolised Ad5-nCoV is one of the first licensed mucosal respiratory vaccine against SARS-CoV-2 in the world; however, the safety profile of this vaccine has not been reported in a large population yet.

METHODS

This multicentre, open-label phase 3 trial, done in 15 centres in six provinces (Jiangsu, Hunan, Anhui, Chongqing, Yunnan, Shandong) in China, aimed to evaluate the safety and immunogenicity of aerosolised Ad5-nCoV in healthy adults (members of the general population with no acute febrile disorders, infectious disease, serious cardiovascular diseases, serious chronic diseases or progressive diseases that cannot be controlled) at least 18 years old, who had received two doses of inactivated COVID-19 vaccine as their primary regimen. This study contained a non-randomly assigned safety cohort and a centrally randomly assigned (1:1) immunogenicity subcohort. The patients in the immunogenicity subcohort received aerosolised Ad5-nCov (aerosolised Ad5-nCoV group) or inactivated vaccine (inactivated COVID-19 group) The primary endpoints were the incidence of adverse reactions within 28 days following the booster vaccination with aerosolised Ad5-nCoV in the safety population (collected through a daily record of any solicited or unsolicited adverse events filled by each participant) and the geometric mean titre of neutralising antibodies at day 28 after the booster dose in the immunogenicity subcohort (measured with a pseudovirus neutralisation test). This study was registered with ClinicalTrials.gov, NCT05204589.

FINDINGS

Between Jan 22, 2022, and March 12, 2022, we recruited 11 410 participants who were screened for eligibility, of whom 10 267 (99·8%) participants (5738 [55·9%] men, 4529 [44·1%] women; median age 53 years [18-92]) received the study drugs: 9847 (95·9%) participants in the open-label cohort to receive aerosolised Ad5-nCoV, and 420 (4·1%) in the immunogenicity subcohort (212 in the aerosolised Ad5-nCoV group and 208 in the inactivated vaccine group). Adverse reactions were reported by 1299 (13%) of 10 059 participants within 28 days after receiving the booster vaccination with aerosolised Ad5-nCoV, but most of the adverse reactions reported were mild to moderate in severity. Participants in the aerosolised Ad5-nCoV group had a significantly higher level of the neutralising antibodies against omicron BA.4/5 (GMT 107·7 [95% CI 88·8-130·7]) than did those in the inactivated vaccine group (17·2 [16·3-18·2]) at day 28.

INTERPRETATION

The heterologous booster regimen with aerosolised Ad5-nCoV is safe and highly immunogenic, boosting both systemic and mucosal immunity against omicron subvariants.

FUNDING

National Natural Science Foundation of China, Jiangsu Provincial Science Fund for Distinguished Young Scholars, and Jiangsu Provincial Key Project of Science and Technology Plan.

TRANSLATION

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

Patients with chronic myeloid leukemia and coronavirus disease 2019 in the Omicron era

To explore the prevalence and severity of COVID-19 and the mental health during the Omicron pandemic in patients with chronic myeloid leukemia (CML), a cross-sectional survey from 2609 respondents with CML was performed. A total of 1725 (66%) reported that they had COVID-19 during this period. Among them, 1621 (94%) were mild; 97 (6%), moderate; 7 (0.4%), severe; and 0, critical or death. Four hundred three (15%), 199 (8%), and 532 (20%) had moderate to severe depression, anxiety, and distress, respectively. Eight hundred ninety (34%), 667 (26%), and 573 (22%), avoidance, intrusion, and hyper-arousal, respectively. In multivariate analyses, longer TKI-therapy duration was significantly associated with a lower prevalence of COVID-19 (odds ratio [OR] = 0.98; 95% confidence interval [CI], 0.95, 0.99; p = 0.043); however, living in urban areas (OR = 1.6 [1.3, 2.0]; p < 0.001) and having family members with COVID-19 (OR = 18.6 [15.1, 22.8]; p < 0.001), a higher prevalence of COVID-19. Increasing age (OR = 1.2 [1.1, 1.4]; p = 0.009), comorbidity(ies) (OR = 1.7 [1.1, 2.7]; p = 0.010), and multi-TKI-resistant patients receiving 3rd-generation TKIs or investigational agents (OR = 2.2 [1.2, 4.2]; p = 0.010) were significantly associated with moderate or severe COVID-19. Female, comorbidity(ies), unvaccinated, and moderate or severe COVID-19 were significantly associated with almost all adverse mental health consequences; increasing age or forced TKI dose reduction because of various restriction during the pandemic, moderate to severe distress, avoidance, or intrusion; however, mild COVID-19, none or mild anxiety, distress, avoidance, or intrusion. In conclusion, shorter TKI-therapy duration, increasing age, comorbidity(ies), or multi-TKI-resistant patients receiving 3rd-generation TKIs or investigational agents had a higher prevalence of COVID-19 or higher risk of moderate or severe disease in patients with CML; increasing age, female, comorbidity(ies), forced TKI dose reduction due to the pandemic, moderate or severe COVID-19, unvaccinated, a higher likelihood of worse mental health.

CoronaVac and BBIBP-CorV vaccines against SARS-CoV-2 during predominant circulation of Omicron BA.5.2 and BF.7 in China, a retrospective cohort study

Pandemic of COVID-19 hit China at the end of 2022. According to China Center for Disease Control and Prevention, Omicron BA.5.2 and BF.7 were the main circulating variants. Chinese people had a high COVID-19 vaccination rate, and the most widely used vaccines were CoronaVac (Sinovac) and BBIBP-CorV (Sinopharm). An online questionnaire was distributed to survey the vaccination history and infection information of China mainland residents during this pandemic. A total of 4250 subjects were included for propensity score matching, 566 unvaccinated subjects and 1072 vaccinated subjects were finally included to analyze the effects of the two vaccines on BA.5.2 and BF.7. The SARS-CoV-2 infection rate was 84.5% in the vaccinated group and 82.3% in the unvaccinated group (p = 0.255). Vaccinated subjects had significantly higher rates of COVID-19-related symptoms, including fever, cough, nasal obstruction, runny nose, and sore throat. However, vaccinated people had lower risk of pneumonia (odds ratio [OR]: 0.467, 95% confidence interval [CI]: 0.286-0.762) and hospitalization (OR: 0.290, 95% CI: 0.097-0.870) due to COVID-19. In general, the current study did not observe the protective effect of CoronaVac and BBIBP CorV against BA.5.2 and BF.7 infection. However, these vaccines can still reduce the risk of adverse outcomes such as pneumonia and hospitalization.