Epidemiology of Infections with SARS-CoV-2 Omicron BA.2 Variant, Hong Kong, January-March 2022

Experiences and reflections of doctors on the operations of designated clinics during the COVID-19 pandemic in Hong Kong: a qualitative study

BACKGROUND

The conversion of General Out-patient Clinics (GOPC) into COVID-19 designated clinics played a crucial role in combating COVID-19 pandemic in Hong Kong in 2022. This qualitative research aimed to contribute valuable perspectives from doctors on the operations of designated clinics for the preparedness of future outbreaks and health emergencies.

METHODS

This research adopted an interpretive phenomenological approach. Participants were purposively recruited from the doctors who worked in designated clinics during the COVID-19 pandemic in the Cluster of New Territories West, Hong Kong. Individual semi-structured interviews were conducted using an interview guide informed by the researchers' past experiences and the Donabedian framework. The verbatim transcripts were imported into NVivo 12 for data organizing, coding and thematic analysis.

RESULTS

Sixteen participants were recruited and interviewed until data sufficiency. Eight themes were elicited and grouped under the three domains of the Donabedian framework: structure (availability of facilities, supportive training and education, and flexible manpower allocation), process (challenges in clinical practices, communication and collaboration, and effectiveness of operations), and outcome (patient outcomes and impact to healthcare workers).

CONCLUSIONS

Overall, participants thought that the operations in the designated clinics were smooth, efficient, and achieving satisfactory outcomes. However, improvements could be made in upgrading facilities to better manage more severe future outbreaks, enhancing government roles in information centralization and public communication and improving collaboration between designated clinics and ambulance services. This research provided valuable insights for the preparedness of future outbreaks and health emergencies.

Burden of Acute Respiratory Infections Caused by Influenza Virus, Respiratory Syncytial Virus, and SARS-CoV-2 with Consideration of Older Adults: A Narrative Review

Influenza virus, respiratory syncytial virus (RSV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are acute respiratory infections (ARIs) that can cause substantial morbidity and mortality among at-risk individuals, including older adults. In this narrative review, we summarize themes identified in the literature regarding the epidemiology, seasonality, immunity after infection, clinical presentation, and transmission for these ARIs, along with the impact of the COVID-19 pandemic on seasonal patterns of influenza and RSV infections, with consideration of data specific to older adults when available. As the older adult population increases globally, it is of paramount importance to fully characterize the true disease burden of ARIs in order to develop appropriate mitigation strategies to minimize their impact in vulnerable populations. Challenges associated with characterizing the burden of these diseases include the shared symptomology and clinical presentation of influenza virus, RSV, and SARS-CoV-2, which complicate accurate diagnosis and highlight the need for improved testing and surveillance practices. To this end, multiple regional, national, and global virologic and disease surveillance systems have been established to provide accurate knowledge of viral epidemiology, support appropriate preparedness and response to potential outbreaks, and help inform prevention strategies to reduce disease severity and transmission. Beyond the burden of acute illness, long-term health consequences can also result from influenza virus, RSV, and SARS-CoV-2 infection. These include cardiovascular and pulmonary complications, worsening of existing chronic conditions, increased frailty, and reduced life expectancy. ARIs among older adults can also place a substantial financial burden on society and healthcare systems. Collectively, the existing data indicate that influenza virus, RSV, and SARS-CoV-2 infections in older adults present a substantial global health challenge, underscoring the need for interventions to improve health outcomes and reduce the disease burden of respiratory illnesses.Graphical abstract and video abstract available for this article.

Durability for 12 months of antibody response to a booster dose of monovalent BNT162b2 in adults who had initially received 2 doses of inactivated vaccine

This study examined the strength and durability of antibody responses in 277 adults who received a heterologous third dose of the BNT162b2 vaccine, following two doses of an inactivated vaccine. Neutralizing antibody levels against both the ancestral virus and Omicron BA.2 subvariant decreased from one month to 6 months after the third dose, and were then maintained at 12 months. Participants who received both a fourth dose and reported a SARS-CoV-2 infection had the highest antibody titers at 365 days after the third dose. Individuals with chronic medical conditions had lower antibody levels against the Omicron BA.2 subvariant at 12 months after the third dose. The results suggest that the heterologous third dose provides durable neutralizing antibody responses, which may be influenced by subsequent infection or vaccination and pre-existing medical conditions. These findings may help explain the differences in immune protection between vaccination and natural infection.

Community-level variability in Bronx COVID-19 hospitalizations associated with differing population immunity during the second year of the pandemic

The Bronx, New York, exhibited unique peaks in the number of coronavirus disease 2019 (COVID-19) cases and hospitalizations compared to national trends. To determine which features of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus might underpin this local disease epidemiology, we conducted a comprehensive analysis of the genomic epidemiology of the four dominant strains of SARS-CoV-2 (Alpha, Iota, Delta, and Omicron) responsible for COVID-19 cases in the Bronx between March 2020 and January 2023. Genomic analysis revealed similar viral fitness for Alpha and Iota variants in the Bronx despite nationwide data showing higher cases of Alpha. However, Delta and Omicron variants had increased fitness within the borough. While the transmission dynamics of most variants in the Bronx corresponded with mutational fitness-based predictions of transmissibility, the Delta variant presented as an exception. Epidemiological modeling confirms Delta's advantages of higher transmissibility in Manhattan and Queens, but not the Bronx; wastewater analysis suggests underdetection of cases in the Bronx. The Alpha variant had slightly faster growth but a lower carrying capacity compared to Iota and Delta in all four boroughs, suggesting stronger limitations on Alpha's growth in New York City (NYC). The founder effect of Iota varied between higher vaccinated and lower vaccinated boroughs with longer delay, shorter duration, and lower fitness of the Alpha variant in lower vaccinated boroughs. Amino acid changes in T-cell and antibody epitopes revealed Delta and Iota having larger antigenic variability and antigenic profiles distant from local previously circulating lineages compared to Alpha. In concert with transmission modeling, our data suggest that the limited spread of Alpha may be due to a lack of adaptation to immunity in NYC. Overall, our study demonstrates that localized analyses and integration of orthogonal community-level datasets can provide key insights into the mechanisms of transmission and immunity patterns associated with regional COVID-19 incidence and disease severity that may be missed when analyzing broader datasets.

Real-World Effectiveness and Safety of Tixagevimab-Cilgavimab: A Target Trial Emulation Study

BACKGROUND

Immunocompromised individuals are at high risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and subsequent severe or fatal coronavirus disease 2019 (COVID-19), yet they have suboptimal responses to mRNA and inactivated COVID-19 vaccines. The efficacy of tixagevimab-cilgavimab in reducing symptomatic SARS-CoV-2 infection was demonstrated in phase III clinical trials. Nevertheless, real-world data on the effectiveness and safety of tixagevimab-cilgavimab remain limited.

OBJECTIVE

The aim was to evaluate the effectiveness and safety of tixagevimab-cilgavimab among immunocompromised individuals.

METHODS

Adults who were immunocompromised or receiving immunosuppressive therapies were included in this target trial emulation using territory-wide electronic health records in Hong Kong. A sequential trial emulation approach was adopted to compare effectiveness and safety outcomes between individuals who received tixagevimab-cilgavimab and individuals who did not.

RESULTS

A total of 746 tixagevimab-cilgavimab recipients and 2980 controls were included from 1 May 2022 to 30 November 2022. Tixagevimab-cilgavimab significantly reduced the risk of COVID-19 infection (hazard ratio [HR] 0.708, 95% confidence interval [CI] 0.527-0.951) during a median follow-up of 60 days. No significant difference was observed in the risk of COVID-19-related hospitalisation. Zero versus eight COVID-19 mortality cases and zero versus two severe COVID-19 cases were observed in tixagevimab-cilgavimab recipients and controls, respectively. Notably, significant risk reduction in COVID-19 infection was also observed among immunocompromised individuals who had been previously vaccinated with three or more doses of COVID-19 vaccine, or had no prior COVID-19 infection history.

CONCLUSIONS

Tixagevimab-cilgavimab was effective in reducing COVID-19 infection among immunocompromised patients during the Omicron wave. Findings were consistent among individuals who previously received three or more doses of COVID-19 vaccine, or had no previous history of COVID-19 infection.

Evaluating the impact of extended dosing intervals on mRNA COVID-19 vaccine effectiveness in adolescents

BACKGROUND

Extending the dosing interval of a primary series of mRNA COVID-19 vaccination has been employed to reduce myocarditis risk in adolescents, but previous evaluation of impact on vaccine effectiveness (VE) is limited to risk after second dose.

METHODS

We quantified the impact of the dosing interval based on case notifications and vaccination uptake in Hong Kong from January to April 2022, based on calendar-time proportional hazards models and matching approaches.

RESULTS

We estimated that the hazard ratio (HR) and odds ratio (OR) of infections after the second dose for extended (28 days or more) versus regular (21-27 days) dosing intervals ranged from 0.86 to 0.99 from calendar-time proportional hazards models, and from 0.85 to 0.87 from matching approaches, respectively. Adolescents in the extended dosing groups (including those who did not receive a second dose in the study period) had a higher hazard of infection than those with a regular dosing interval during the intra-dose period (HR 1.66; 95% CI 1.07, 2.59; p = 0.02) after the first dose.

CONCLUSIONS

Implementing an extended dosing interval should consider multiple factors including the degree of myocarditis risk, the degree of protection afforded by each dose, and the extra protection achievable using an extended dosing interval.

Chronic Obstructive Pulmonary Disease and the Omicron Variant of COVID-19 Prognosis: A Retrospective Cohort Study

BACKGROUND AND AIM

This retrospective cohort study aimed to investigate the association between chronic obstructive pulmonary disease (COPD) and the prognosis of COVID-19 patients infected with the Omicron variant. The primary objective was to determine if COVID-19 patients with COPD had higher mortality rates compared to those without COPD. Secondary objectives included assessing the risk of respiratory failure, hospital stay length, intensive care unit (ICU) admission, and oxygen requirements in COPD patients with COVID-19.

MATERIALS AND METHODS

The study included 2761 COVID-19 patients admitted to the Princess Margaret Hospital, Hong Kong, between January 1 and June 30, 2022. Among them, 7.4% (n = 205) had COPD. Demographic and clinical data, including vaccination status and comorbidities, were collected. The primary outcome was 30-day mortality, and secondary outcomes included respiratory support requirement, hospital stay length, and ICU admission. Logistic regression analyses were conducted, adjusting for potential confounders.

RESULTS

COPD did not independently increase the risk of COVID-19 mortality after adjusting for confounders. Instead, older age, male sex, incomplete vaccination, long-term oxygen therapy use, and specific comorbidities were identified as significant predictors of 30-day mortality. COPD patients were more likely to require oxygen and noninvasive ventilation, but there were no significant differences in other secondary outcomes compared to non-COPD patients.

CONCLUSION

COPD itself was not an independent risk factor for COVID-19 mortality. Age, sex, vaccination status, comorbidities, and long-term oxygen therapy use were important predictors of mortality. These findings underscore the importance of considering multiple factors when assessing the impact of COPD on COVID-19 prognosis, particularly with the Omicron variant.

Transmission Patterns of Co-Circulation of Omicron Sub-Lineages in Hong Kong SAR, China, a City with Rigorous Social Distancing Measures, in 2022

OBJECTIVE

This study aimed to characterize the changing landscape of circulating SARS-CoV-2 lineages in the local community of Hong Kong throughout 2022. We examined how adjustments to quarantine arrangements influenced the transmission pattern of Omicron variants in a city with relatively rigorous social distancing measures at that time.

METHODS

In 2022, a total of 4684 local SARS-CoV-2 genomes were sequenced using the Oxford Nanopore GridION sequencer. SARS-CoV-2 consensus genomes were generated by MAFFT, and the maximum likelihood phylogeny of these genomes was determined using IQ-TREE. The dynamic changes in lineages were depicted in a time tree created by Nextstrain. Statistical analysis was conducted to assess the correlation between changes in the number of lineages and adjustments to quarantine arrangements.

RESULTS

By the end of 2022, a total of 83 SARS-CoV-2 lineages were identified in the community. The increase in the number of new lineages was significantly associated with the relaxation of quarantine arrangements (One-way ANOVA, F(5, 47) = 18.233, p < 0.001)). Over time, Omicron BA.5 sub-lineages replaced BA.2.2 and became the predominant Omicron variants in Hong Kong. The influx of new lineages reshaped the dynamics of Omicron variants in the community without fluctuating the death rate and hospitalization rate (One-way ANOVA, F(5, 47) = 2.037, p = 0.091).

CONCLUSION

This study revealed that even with an extended mandatory quarantine period for incoming travelers, it may not be feasible to completely prevent the introduction and subsequent community spread of highly contagious Omicron variants. Ongoing molecular surveillance of COVID-19 remains essential to monitor the emergence of new recombinant variants.

Evaluating the impact of extended dosing intervals on mRNA COVID-19 vaccine effectiveness in adolescents

Extending the dosing interval of a primary series of mRNA COVID-19 vaccination has been employed to reduce myocarditis risk in adolescents, but previous evaluation of impact on vaccine effectiveness (VE) is limited to risk after second dose. Here, we quantified the impact of the dosing interval based on case notifications and vaccination uptake in Hong Kong from January to April 2022. We estimated that the hazard ratio (HR) and odds ratio (OR) of infections after the second dose for extended (28 days or more) versus regular (21-27 days) dosing intervals ranged from 0.86 to 0.99 from calendar-time proportional hazards models, and from 0.85 to 0.87 from matching approaches, respectively. Adolescents in the extended dosing groups (including those who did not receive a second dose in the study period) had a higher hazard of infection than those with a regular dosing interval during the intra-dose period (HR: 1.66; 95% CI: 1.07, 2.59; p = 0.02) after the first dose. Implementing an extended dosing interval should consider multiple factors including the degree of myocarditis risk, the degree of protection afforded by each dose, and the extra protection achievable using an extended dosing interval.

Vaccination Shapes Within-Host SARS-CoV-2 Diversity of Omicron BA.2.2 Breakthrough Infection

BACKGROUND

Low-frequency intrahost single-nucleotide variants of SARS-CoV-2 have been recognized as predictive indicators of selection. However, the impact of vaccination on the intrahost evolution of SARS-CoV-2 remains uncertain at present.

METHODS

We investigated the genetic variation of SARS-CoV-2 in individuals who were unvaccinated, partially vaccinated, or fully vaccinated during Shanghai's Omicron BA.2.2 wave. We substantiated the connection between particular amino acid substitutions and immune-mediated selection through a pseudovirus neutralization assay or by cross-verification with the human leukocyte antigen-associated T-cell epitopes.

RESULTS

In contrast to those with immunologic naivety or partial vaccination, participants who were fully vaccinated had intrahost variant spectra characterized by reduced diversity. Nevertheless, the distribution of mutations in the fully vaccinated group was enriched in the spike protein. The distribution of intrahost single-nucleotide variants in individuals who were immunocompetent did not demonstrate notable signs of positive selection, in contrast to the observed adaptation in 2 participants who were immunocompromised who had an extended period of viral shedding.

CONCLUSIONS

In SARS-CoV-2 infections, vaccine-induced immunity was associated with decreased diversity of within-host variant spectra, with milder inflammatory pathophysiology. The enrichment of mutations in the spike protein gene indicates selection pressure exerted by vaccination on the evolution of SARS-CoV-2.

Assessing the impact of interventions on the major Omicron BA.2 outbreak in spring 2022 in Shanghai

Background

Shanghai experienced a significant surge in Omicron BA.2 infections from March to June 2022. In addition to the standard interventions in place at that time, additional interventions were implemented in response to the outbreak. However, the impact of these interventions on BA.2 transmission remains unclear.

Methods

We systematically collected data on the daily number of newly reported infections during this wave and utilized a Bayesian approach to estimate the daily effective reproduction number. Data on public health responses were retrieved from the Oxford COVID-19 Government Response Tracker and served as a proxy for the interventions implemented during this outbreak. Using a log-linear regression model, we assessed the impact of these interventions on the reproduction number. Furthermore, we developed a mathematical model of BA.2 transmission. By combining the estimated effect of the interventions from the regression model and the transmission model, we estimated the number of infections and deaths averted by the implemented interventions.

Results

We found a negative association (-0.0069, 95% CI: 0.0096 to -0.0045) between the level of interventions and the number of infections. If interventions did not ramp up during the outbreak, we estimated that the number of infections and deaths would have increased by 22.6% (95% CI: 22.4-22.8%), leading to a total of 768,576 (95% CI: 768,021-769,107) infections and 722 (95% CI: 722-723) deaths. If no interventions were deployed during the outbreak, we estimated that the number of infections and deaths would have increased by 46.0% (95% CI: 45.8-46.2%), leading to a total of 915,099 (95% CI: 914,639-915,518) infections and 860 (95% CI: 860-861) deaths.

Conclusion

Our findings suggest that the interventions adopted during the Omicron BA.2 outbreak in spring 2022 in Shanghai were effective in reducing SARS-CoV-2 transmission and disease burden. Our findings emphasize the importance of non-pharmacological interventions in controlling quick surges of cases during epidemic outbreaks.

Projecting the future impact of emerging SARS-CoV-2 variants under uncertainty: Modeling the initial Omicron outbreak

Over the past several years, the emergence of novel SARS-CoV-2 variants has led to multiple waves of increased COVID-19 incidence. When the Omicron variant emerged, there was considerable concern about its potential impact in the winter of 2021-2022 due to its increased fitness. However, there was also considerable uncertainty regarding its likely impact due to questions about its relative transmissibility, severity, and degree of immune escape. We sought to evaluate the ability of an agent-based model to forecast incidence in the context of this emerging pathogen variant. To project COVID-19 cases and deaths in Indiana, we calibrated our model to COVID-19 hospitalizations, deaths, and test-positivity rates through November 2021, and then projected COVID-19 incidence through April 2022 under four different scenarios that covered the plausible ranges of Omicron's severity, transmissibility, and degree of immune escape. Our initial projections from December 2021 through March 2022 indicated that under a pessimistic scenario with high disease severity, the peak in weekly COVID-19 deaths in Indiana would be larger than the previous peak in December 2020. However, retrospective analyses indicate that Omicron's severity was closer to the optimistic scenario, and even though cases and hospitalizations reached a new peak, fewer deaths occurred than during the previous peak. According to our results, Omicron's rapid spread was consistent with a combination of higher transmissibility and immune escape relative to earlier variants. Our updated projections starting in January 2022 accurately predicted that cases would peak in mid-January and decline rapidly over the next several months. The performance of our projections shows that following the emergence of a new pathogen variant, models can help quantify the potential range of outbreak magnitudes and trajectories. Agent-based models are particularly useful in these scenarios because they can efficiently track individual vaccination and infection histories with multiple variants with varying degrees of cross-protection.

Clinical evaluation of a multiplex droplet digital PCR for pathogen detection in critically ill COVID-19 patients with bloodstream infections

BACKGROUND

Nosocomial bloodstream infections (nBSI) have emerged as a clinical concern for physicians treating COVID-19 patients. In this study, we aimed to evaluate the effectiveness of a multiplex ddPCR in detecting bacterial pathogens in the blood of COVID-19 critically ill patients.

METHODS

This prospective diagnostic study included RT-PCR-confirmed COVID-19 patients admitted to our hospital from December 2022 to February 2023. A multiplex ddPCR assay was used to detect common bacterial pathogens and AMR genes in blood samples of the patients, along with antimicrobial susceptibility testing (AST). The diagnostic performance of the ddPCR assay was evaluated by comparing the results with those obtained through blood culture and clinical diagnosis. Additionally, the ability of ddPCR in detecting bacterial resistance was compared with the AST results.

RESULTS

Of the 200 blood samples collected from 184 patients, 45 (22.5%) were positive using blood culture, while 113 (56.5%) were positive for bacterial targets using the ddPCR assay. The ddPCR assay outperformed blood culture in pathogen detection rate, mixed infection detection rate, and fungal detection rate. Acinetobacter baumannii and Klebsiella pneumoniae were the most commonly detected pathogens in COVID-19 critically ill patients, followed by Enterococcus and Streptococcus. Compared to blood culture, ddPCR achieved a sensitivity of 75.5%, specificity of 51.0%, PPV of 30.9%, and NPV of 87.8%, respectively. However, there were significant differences in sensitivity among different bacterial species, where Gram-negative bacteria have the highest sensitivity of 90.3%. When evaluated on the ground of clinical diagnosis, the sensitivity, specificity, PPV and NPV of ddPCR were 78.1%, 90.5%, 94.7%, and 65.5%, respectively. In addition, the ddPCR assay detected 23 cases of blaKPC, which shown a better consistent with clinical test results than other detected AMR genes. Compared to blaKPC, there were few other AMR genes detected, indicating that the application of other AMR gene detection in the COVID-19 critically ill patients was limited.

CONCLUSION

The multiplex ddPCR assay had a significantly higher pathogen detection positivity than the blood culture, which could be an effective diagnostic tool for BSIs in COVID-19 patients and to improve patient outcomes and reduce the burden of sepsis on the healthcare system, though there is room for optimization of the panels used.- Adjusting the targets to include E. faecalis and E. faecium as well as Candida albicans and Candida glabrata could improve the ddPCR' s effectiveness. However, further research is needed to explore the potential of ddPCR in predicting bacterial resistance through AMR gene detection.

Assessment of the impact of the vaccine pass policy on COVID-19 vaccine hesitancy and uptake among Chinese adults in Hong Kong

BACKGROUND

Recognising the importance of attaining high vaccine coverage to mitigate the COVID-19 impact, a Vaccine Pass scheme was implemented during and after the first large Omicron wave with high mortality in older ages in Hong Kong in early 2022 requiring three doses by June 2022. We did not identify any studies evaluating the policy impact of vaccination mandates with vaccine uptake over whole policy period of time in a Chinese population. We aim to evaluate the impact of the Vaccine Pass policy on COVID-19 vaccine uptake in adults in a Chinese population in Hong Kong.

METHODS

We analysed patterns in vaccine uptake and hesitancy using local data from population vaccine registry and 32 cross-sectional telephone surveys conducted from October 2021 to December 2022. The association of Vaccine Pass phases with vaccine uptake was examined using logistic regression analyses, taking into account covariates including self-risk perception, perceived self-efficacy in preventing COVID-19 and trust in government in pandemic control as well as physical distancing measures and demographics.

RESULTS

The uptake of primary series and third doses was positively significantly associated with the successive stages of Vaccine Pass implementation (adjusted odds ratios ranged from 2.41 to 7.81). Other statistically significant drivers of uptake included age group, chronic condition, higher perceived personal susceptibility to COVID-19, higher trust in government, and higher educational attainment.

CONCLUSION

Vaccine uptake in older adults was observed to have increased by a greater extent after the policy annoucement and implementation, under the contextual changes during and after a large Omicron wave with high mortality in Hong Kong in early 2022. Since the policy withdrawal the uptake of further booster doses has been very low in all ages. We suggest that improving voluntary booster uptake in older adults should be prioritized.

Efficacy and safety of Chinese herbal medicine to prevent and treat COVID-19 household close contacts in Hong Kong: an open-label, randomized controlled trial

Objectives

To evaluate the efficacy and safety of CHM in the prevention of COVID-19 infection and treatment for COVID-19 related symptoms.

Design

Prospective open-label randomized controlled trial.

Setting

Participants' home in Hong Kong.

Participants

Participants who had household close contact with COVID-19-infected family members.

Interventions

Close contacts were stratified into 4 groups (cohort A, B, C, D) based on symptoms and infection status and were randomized in 4:1 ratio to receive CHM granules (9g/sachet, two times daily) or blank control for 7 days with 2 weeks of follow-up.

Main outcome measures

The primary outcome measure was the rate of positive nucleic acid tests. Secondary outcomes were the proportion of developed COVID-19 related symptoms and adverse events during the whole 3-week study period. Subgroup analysis was used to evaluate demographic factors associated with positive infection rates.

Results

A total of 2163 contacts were enrolled and randomly assigned to the CHM group (1720 contacts) and blank control (443 contacts) group. During the 21 days, the rate of PCR-positive cases in cohort A was markedly lower in the CHM group (3.6%) compared to the control group (7.0%) (P=0.036). Overall, the rate of infection in the CHM group was significantly lower than that in the control group (10.69% vs. 6.03%; RR 0.56, 95% CI 0.39-0.82) after 7-day treatment. No serious adverse events were reported during the medication period.

Conclusion

The preliminary findings indicate that CHM may be effective and safe in preventing COVID-19. Future double-blind, randomized controlled trials and long-term follow-up are needed to fully evaluate the efficacy of CHM in a larger contact population.

Clinical trial registration

ClinicalTrials.gov, identifier NCT05269511.

COVID-19 vaccine effectiveness against the Omicron variant of SARS-CoV-2 in multimorbidity: A territory-wide case-control study

Multimorbidity entails a higher risk of SARS-CoV-2 infection and COVID-19 complications. We examined vaccine effectiveness (VE) stratified by multimorbidity using a case-control study of territory-wide electronic health records in Hong Kong. Cases of infection (testing positive), hospitalization, and mortality were identified from January to March 2022. Controls were matched by age, sex, outpatient attendance/hospitalization date, and Charlson Comorbidity Index. We demonstrated a consistently good VE among people with increased multimorbidity burden; even more so than among those with minimal such burden. There was also a significantly greater VE after a third dose of BNT162b2 or CoronaVac against infection. The difference in VE between those with multimorbidity and those without was less pronounced for hospitalization, and such difference for COVID-19-related mortality was negligible. In conclusion, VE of both examined vaccines against SARS-CoV-2 infection among people with more complex multimorbidity burden is significant. Further vaccine roll-out should prioritize people with multimorbidity.

Association of COVID-19 vaccination with duration of hospitalization in older adults in Hong Kong

INTRODUCTION

The association between COVID-19 vaccination and length of hospital stay may provide further insight into vaccination benefits, but few studies have investigated such associations in detail. We aimed to investigate the association between COVID-19 vaccination and length of hospital stay in COVID-19 patients during Omicron waves in Hong Kong, and explore potential predictors.

METHODS

This retrospective cohort study was conducted on local patients aged ≥60 years who were admitted due to COVID-19 infection in Hong Kong in 2022, from 1 February to 22 November, and with 28 days of follow-up since admission. The exposure was either not vaccinated; or having received 2/3/4 doses of CoronaVac (Sinovac); or 2/3/4 doses of BNT162b2 (BioNTech/Fosun Pharma/Pfizer). Length of stay in hospital was the main outcome. Accelerated failure time models were used to quantify variation in hospital stay for vaccinated compared with unvaccinated patients, accounting for age, sex, comorbidity, type of vaccine and number of doses received, care home residence and admission timing; stratified by age groups and epidemic waves.

RESULTS

This study included 32,398 patients aged 60 years and above for main analysis, their median (IQR) age was 79 (71-87) years, 53% were men, and 40% were unvaccinated. The patients were stratified by confirmation prior to or since 23 May 2022, resulting in a sample size of 15,803 and 16,595 in those two waves respectively. Vaccinated patients were found to have 13-39% shorter hospital stay compared to unvaccinated patients. More vaccine doses received were associated with shorter hospital stay, and BNT162b2 recipients had slightly shorter hospital stays than CoronaVac recipients.

CONCLUSION

Vaccination was associated with reduced hospital stay in breakthrough infections. Increased vaccination uptake in older adults may improve hospital bed turnover and public health outcomes especially during large community epidemics.

Vaccine Effectiveness of BNT162b2 and CoronaVac against SARS-CoV-2 Omicron BA.2 in CKD

BACKGROUND

The ongoing coronavirus disease 2019 (COVID-19) pandemic has posed increased risks of hospitalization and mortality in patients with underlying CKD. Current data on vaccine effectiveness of COVID-19 vaccines are limited to patients with CKD on dialysis and seroconversion in the non-dialysis population.

METHODS

A case-control study was conducted of adults with CKD using data extracted from the electronic health record database in Hong Kong. Adults with CKD and COVID-19 confirmed by PCR were included in the study. Each case was matched with up to ten controls attending Hospital Authority services without a diagnosis of COVID-19 on the basis of age, sex, and index date (within three calendar days). The vaccine effectiveness of BNT162b2 and CoronaVac in preventing COVID-19 infection, hospitalizations, and all-cause mortality was estimated using conditional logistic regression adjusted by patients' comorbidities and medication history during the outbreak from January to March 2022.

RESULTS

A total of 20,570 COVID-19 cases, 6604 COVID-19-related hospitalizations, and 2267 all-cause mortality were matched to 81,092, 62,803, and 21,348 controls, respectively. Compared with the unvaccinated group, three doses of BNT162b2 or CoronaVac were associated with a reduced risk of infection (BNT162b2: 64% [95% confidence interval (CI), 60 to 67], CoronaVac: 42% [95% CI, 38 to 47]), hospitalization (BNT162b2: 82% [95% CI, 77 to 85], CoronaVac: 80% [95% CI, 76 to 84]), and mortality (BNT162b2: 94% [95% CI, 88 to 97], CoronaVac: 93% [95% CI, 88 to 96]). Vaccines were less effective in preventing infection and hospitalization in the eGFR <15 and 15-29 ml/min per 1.73 m 2 subgroups as compared with higher GFR subgroups. However, receipt of vaccine, even for one dose, was effective in preventing all-cause mortality, with estimates similar to the higher eGFR subgroups, as compared with unvaccinated.

CONCLUSIONS

A dose-response relationship was observed between the number of BNT162b2 or CoronaVac doses and the effectiveness against COVID-19 infection and related comorbidity in the CKD population.

Clinical characteristics and outcomes of liver transplant recipients infected by Omicron during the opening up of the dynamic zero-coronavirus disease policy in China: A prospective, observational study

We analyzed the characteristics, risk factors, outcomes, and post-coronavirus disease 2019 (COVID-19) symptoms in liver transplant recipients in China's late 2022 COVID-19 wave. Recipients with COVID-19 were enrolled from December 1, 2022, to January 31, 2023, and followed up until May 31, 2023. Baseline and characteristic data were collected. A total of 930 recipients were included, with a vaccination rate (non-mRNA) of 40.0%. Among 726 (78.1%) recipients with COVID-19, 641 (88.3%) patients were treated at home, 81 (11.2%) patients required hospitalization in general wards, 4 (0.6%) patients required intensive care, and 1 (0.1%) patient died because of COVID-19. Severe acute respiratory syndrome coronavirus 2 infection was related to close contact with confirmed cases (P < .001) and the condition of end-stage kidney disease (P < .046). Older age, male sex, less vaccination, and hypertension were independent risk factors for hospitalization. Fatigue (36.9%) was the most common symptom post-COVID-19, followed by memory loss (35.7%) and sleep disturbance (23.9%). Two doses of vaccines had a protective effect against these post-COVID-19 symptoms (P < .05). During this Omicron outbreak, liver transplant recipients were susceptible to COVID-19, with frequent hospitalization but low mortality. Two doses of non-mRNA COVID-19 vaccines could protect against liver transplant recipient hospitalization and post-COVID-19 symptoms.

Comparative epidemiology of outbreaks caused by SARS-CoV-2 Delta and Omicron variants in China

From 2020 to December 2022, China implemented strict measures to contain the spread of severe acute respiratory syndrome coronavirus 2. However, despite these efforts, sustained outbreaks of the Omicron variants occurred in 2022. We extracted COVID-19 case numbers from May 2021 to October 2022 to identify outbreaks of the Delta and Omicron variants in all provinces of mainland China. We found that omicron outbreaks were more frequent (4.3 vs. 1.6 outbreaks per month) and longer-lasting (mean duration: 13 vs. 4 weeks per outbreak) than Delta outbreaks, resulting in a total of 865,100 cases, of which 85% were asymptomatic. Despite the average Government Response Index being 12% higher (95% confidence interval (CI): 9%, 15%) in Omicron outbreaks, the average daily effective reproduction number (Rt) was 0.45 higher (95% CI: 0.38, 0.52, p < 0.001) than in Delta outbreaks. Omicron outbreaks were suppressed in 32 days on average (95% CI: 26, 39), which was substantially longer than Delta outbreaks (14 days; 95% CI: 11, 19; p = 0.004). We concluded that control measures effective against Delta could not contain Omicron outbreaks in China. This highlights the need for continuous evaluation of new variants' epidemiology to inform COVID-19 response decisions.

Risk factors for critical COVID-19 illness during Delta- and Omicron-predominant period in Korea; using K-COV-N cohort in the National health insurance service

BACKGROUND

This study evaluated the clinical characteristics of patients with COVID-19 in Korea, and examined the relationship between severe COVID-19 cases and underlying health conditions during the Delta (September 20, 2021 to December 4, 2021) and the Omicron (February 20, 2022 to March 31, 2022) predominant period.

METHODS

This study assessed the association between critical COVID-19 illness and various risk factors, including a variety of underlying health conditions, using multiple logistic regression models based on the K-COV-N cohort, a nationwide data of confirmed COVID-19 cases linked with COVID-19 vaccination status and the National Health Insurance claim information.

RESULTS

We analyzed 137,532 and 8,294,249 cases of COVID-19 infection during the Delta and the Omicron variant dominant periods, respectively. During the Delta as well as the Omicron period, old age (≥80 years) showed the largest effect size among risk factors for critical COVID-19 illness (aOR = 18.08; 95% confidence interval [CI] = 14.71-22.23 for the Delta; aOR = 24.07; 95% CI = 19.03-30.44 for the Omicron period). We found that patients with solid organ transplant (SOT) recipients, unvaccinated, and interstitial lung disease had more than a two-fold increased risk of critical COVID-19 outcomes between the Delta and Omicron periods. However, risk factors such as urban residence, underweight, and underlying medical conditions, including chronic cardiac diseases, immunodeficiency, and mental disorders, had different effects on the development of critical COVID-19 illness between the Delta and Omicron periods.

CONCLUSION

We found that the severity of COVID-19 infection was much higher for the Delta variant than for the Omicron. Although the Delta and the Omicron variant shared many risk factors for critical illness, several risk factors were found to have different effects on the development of critical COVID-19 illness between those two variants. Close monitoring of a wide range of risk factors for critical illness is warranted as new variants continue to emerge during the pandemic.

Comparison of control and transmission of COVID-19 across epidemic waves in Hong Kong: an observational study

BACKGROUND

Hong Kong contained COVID-19 for two years but experienced a large epidemic of Omicron BA.2 in early 2022 and endemic transmission of Omicron subvariants thereafter. We reflected on pandemic preparedness and responses by assessing COVID-19 transmission and associated disease burden in the context of implementation of various public health and social measures (PHSMs).

METHODS

We examined the use and impact of pandemic controls in Hong Kong by analysing data on more than 1.7 million confirmed COVID-19 cases and characterizing the temporal changes non-pharmaceutical and pharmaceutical interventions implemented from January 2020 through to 30 December 2022. We estimated the daily effective reproductive number (Rt) to track changes in transmissibility and effectiveness of community-based measures against infection over time. We examined the temporal changes of pharmaceutical interventions, mortality rate and case-fatality risks (CFRs), particularly among older adults.

FINDINGS

Hong Kong experienced four local epidemic waves predominated by the ancestral strain in 2020 and early 2021 and prevented multiple SARS-CoV-2 variants from spreading in the community before 2022. Strict travel-related, case-based, and community-based measures were increasingly tightened in Hong Kong over the first two years of the pandemic. However, even very stringent measures were unable to contain the spread of Omicron BA.2 in Hong Kong. Despite high overall vaccination uptake (>70% with at least two doses), high mortality was observed during the Omicron BA.2 wave due to lower vaccine coverage (42%) among adults ≥65 years of age. Increases in antiviral usage and vaccination uptake over time through 2022 was associated with decreased case fatality risks.

INTERPRETATION

Integrated strict measures were able to reduce importation risks and interrupt local transmission to contain COVID-19 transmission and disease burden while awaiting vaccine development and rollout. Increasing coverage of pharmaceutical interventions among high-risk groups reduced infection-related mortality and mitigated the adverse health impact of the pandemic.

FUNDING

Health and Medical Research Fund.

Peripheral Blood CD8+T Cell as a Prognostic Biomarker for Hospitalised COVID-19 Patients Without Antiviral Treatment

Background

The status of T lymphocyte subset counts in patients with COVID-19 remains uncertain. This study aimed to assess alterations in peripheral blood CD3+CD8+T (CD8+T) cells among hospitalized COVID-19 patients who have not received antiviral treatment and to evaluate their prognostic value within this patient population.

Methods

A single-center, retrospective cohort study and a meta-analysis were conducted. The cohort study was performed at Xiangya Hospital from December 5, 2022, to January 31, 2023. We conducted a meta-analysis to explore the association between peripheral blood CD3+CD8+T cells and mortality in COVID-19 patients who did not receive antiviral therapy. All relevant studies in Embase, PubMed, Web of Science databases were systematically searched for meta-analysis.

Results

The retrospective cohort study included 201 patients. A significant decrease in peripheral blood CD8+ T cell count was found to be associated with an increased risk of mortality (adjusted odds ratio [aOR]: 13.88; 95% confidence interval [CI]: 3.15-61.23), after adjusting for gender, age, comorbidities, severity at admission, steroid therapy, and antibiotic therapy. The threshold value for CD8+T cell counts, determined by the receiver operating characteristic (ROC) curve analysis, was 145.5 (area under the curve [AUC]: 0.828, specificity: 90.3%, sensitivity: 72.9%, P<0.001). Additionally, A total of 7 studies with 2765 participants were included in the meta-analysis. The meta-analysis reveals a significant association between lower CD8+ T cell counts and mortality (odds ratio [OR] = 3.543, 95% CI: 1.726 to 7.272; I2=93%).

Conclusion

Peripheral blood CD8+ T cell can serve as a valuable prognostic biomarker for hospitalized patients who do not receive antiviral treatment.

Transmission characteristics and inactivated vaccine effectiveness against transmission of the SARS-CoV-2 Omicron BA.2 variant in Shenzhen, China

We conducted a retrospective cohort study to evaluate the transmission risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 variant and the effectiveness of inactivated COVID-19 vaccine boosters in Shenzhen during a BA.2 outbreak period from 1 February to 21 April 2022. A total of 1,248 individuals were infected with the BA.2 variant, and 7,855 close contacts were carefully investigated. The risk factors for the high secondary attack rate of SARS-CoV-2 infection were household contacts [adjusted odds ratio (aOR): 1.748; 95% confidence interval (CI): 1.448, 2.110], younger individuals aged 0-17 years (aOR: 2.730; 95% CI: 2.118, 3.518), older persons aged ≥60 years (aOR: 1.342; 95% CI: 1.135, 1.588), women (aOR: 1.442; 95% CI: 1.210, 1.718), and the subjects exposed to the post-onset index cases (aOR: 8.546; 95% CI: 6.610, 11.050), respectively. Compared with the unvaccinated and partially vaccinated individuals, a relatively low risk of secondary attack was found for the individuals who received booster vaccination (aOR: 0.871; 95% CI: 0.761, 0.997). Moreover, a high transmission risk was found for the index cases aged ≥60 years (aOR: 1.359; 95% CI: 1.132, 1.632), whereas a relatively low transmission risk was observed for the index cases who received full vaccination (aOR: 0.642; 95% CI: 0.490, 0.841) and booster vaccination (aOR: 0.676; 95% CI: 0.594, 0.770). Compared with full vaccination, booster vaccination of inactivated COVID-19 vaccine showed an effectiveness of 24.0% (95% CI: 7.0%, 37.9%) against BA.2 transmission for the adults ≥18 years and 93.7% (95% CI: 72.4%, 98.6%) for the adults ≥60 years, whereas the effectiveness was 51.0% (95% CI: 21.9%, 69.3%) for the individuals of 14 days to 179 days after booster vaccination and 51.2% (95% CI: 37.5%, 61.9%) for the non-household contacts. The estimated mean values of the generation interval, serial interval, incubation period, latent period, and viral shedding period were 2.7 days, 3.2 days, 2.4 days, 2.1 days, and 17.9 days, respectively. In summary, our results confirmed that the main transmission route of Omicron BA.2 subvariant was household contact, and booster vaccination of the inactivated vaccines was relatively effective against BA.2 subvariant transmission in older people.

Estimating the potential impact and diagnostic requirements for SARS-CoV-2 test-and-treat programs

Oral antivirals have the potential to reduce the public health burden of COVID-19. However, now that we have exited the emergency-phase of the COVID-19 pandemic, declining SARS-CoV-2 clinical testing rates (average testing rates = [Formula: see text]10 tests/100,000 people/day in low-and-middle income countries; <100 tests/100,000 people/day in high-income countries; September 2023) make the development of effective test-and-treat programs challenging. We used an agent-based model to investigate how testing rates and strategies affect the use and effectiveness of oral antiviral test-to-treat programs in four country archetypes of different income levels and demographies. We find that in the post-emergency-phase of the pandemic, in countries where low testing rates are driven by limited testing capacity, significant population-level impact of test-and-treat programs can only be achieved by both increasing testing rates and prioritizing individuals with greater risk of severe disease. However, for all countries, significant reductions in severe cases with antivirals are only possible if testing rates were substantially increased with high willingness of people to seek testing. Comparing the potential population-level reductions in severe disease outcomes of test-to-treat programs and vaccination shows that test-and-treat strategies are likely substantially more resource intensive requiring very high levels of testing (≫100 tests/100,000 people/day) and antiviral use suggesting that vaccination should be a higher priority.

Habitual Mask Wearing as Part of COVID-19 Control in Japan: An Assessment Using the Self-Report Habit Index

Although the Japanese government removed mask-wearing requirements in 2023, relatively high rates of mask wearing have continued in Japan. We aimed to assess psychological reasons and the strength of habitual mask wearing in Japan. An Internet-based cross-sectional survey was conducted with non-random participant recruitment. We explored the frequency of mask usage, investigating psychological reasons for wearing masks. A regression analysis examined the association between psychological reasons and the frequency of mask wearing. The habitual use of masks was assessed in the participant's most frequently visited indoor space and public transport using the self-report habit index. The principal component analysis with varimax rotation revealed distinct habitual characteristics. Among the 2640 participants surveyed from 6 to 9 February 2023, only 4.9% reported not wearing masks at all. Conformity to social norms was the most important reason for masks. Participants exhibited a slightly higher degree of habituation towards mask wearing on public transport compared to indoor spaces. The mask-wearing rate was higher in females than in males, and no significant difference was identified by age group. Daily mask wearing in indoor spaces was characterized by two traits (automaticity and behavioral frequency). A high mask-wearing frequency has been maintained in Japan during the social reopening transition period. Mask wearing has become a part of daily habit, especially on public transport, largely driven by automatic and frequent practice.

Antibiotic use in hospitalized patients with COVID-19: a population-based study in Hong Kong

Background

Hong Kong experienced four epidemic waves caused by the ancestral strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2020-2021 and a large Omicron wave in 2022. Few studies have assessed antibacterial prescribing for coronavirus disease 2019 (COVID-19) inpatients throughout the pandemic.

Objectives

To describe inpatient antibacterial prescribing and explore factors associated with their prescription.

Methods

Electronic health records of patients with COVID-19 admitted to public hospitals in Hong Kong from 21 January 2020 to 30 September 2022 were used to assess the prevalence and rates of inpatient antibacterial drug use (days of therapy/1,000 patient days [DOT/1,000 PD]). We used multivariable logistic regression to investigate potential associations between patients' baseline characteristics and disease severity and prescription of an antibacterial drug during hospital admission.

Results

Among 65,810 inpatients with COVID-19, 54.0% were prescribed antibacterial drugs (550.5 DOT/1,000 PD). Compared to waves 1-2 (46.7%; 246.9 DOT/1,000 PD), the prescriptions were lowest during wave 4 (28.0%; 246.9; odds ratio (OR): 0.39, 95% CI: 0.31-0.49) and peaked in early wave 5 (64.6%; 661.2; 0.82, 0.65-1.03). Older age (≥80 years: OR 2.66, 95% CI, 2.49-2.85; 60-79 years: 1.59, 1.51-1.69, compared with 20-59 years), more severe disease (fatal: 3.64, 3.2-4.16; critical: 2.56, 2.14-3.06, compared with severe), and COVID-19 vaccine doses (two doses: 0.74, 0.69-0.78; three doses: 0.69, 0.64-0.74; four doses: 0.52, 0.44-0.62, compared with unvaccinated) were associated with inpatient antibacterial drug use.

Conclusions

Antibacterial prescribing changed over time for hospitalized patients with confirmed COVID-19 and was potentially related to patients' demographics, medical conditions, and COVID-19 vaccination status as well as healthcare capacity during epidemic waves.

Intrinsic and Effective Severity of Coronavirus Disease 2019 Cases Infected With the Ancestral Strain and Omicron BA.2 Variant in Hong Kong

BACKGROUND

Understanding severity of infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants is crucial to inform public health measures. Here we used coronavirus disease 2019 (COVID-19) patient data from Hong Kong to characterize the severity profile of COVID-19.

METHODS

Time-varying and age-specific effective severity measured by case hospitalization risk and hospitalization fatality risk was estimated with all individual COVID-19 case data collected in Hong Kong from 23 January 2020 through 26 October 2022 over 6 epidemic waves. The intrinsic severity of Omicron BA.2 was compared with the estimate for the ancestral strain with the data from unvaccinated patients without previous infections.

RESULTS

With 32 222 COVID-19 hospitalizations and 9669 deaths confirmed over 6 epidemic waves, the time-varying hospitalization fatality risk dramatically increased from <10% before the largest fifth wave of Omicron BA.2 to 41% during the peak of the fifth wave when hospital resources were severely constrained. The age-specific fatality risk in unvaccinated hospitalized Omicron cases was comparable to the estimates for unvaccinated cases with the ancestral strain. During epidemics predominated by Omicron BA.2, fatality risk was highest among older unvaccinated patients.

CONCLUSIONS

Omicron has comparable intrinsic severity to the ancestral Wuhan strain, although the effective severity is substantially lower in Omicron cases due to vaccination.

Risks of COVID-19-related hospitalisation and mortality among individuals with mental disorders following BNT162b2 and CoronaVac vaccinations: A case-control study

Concerns have been raised regarding potential weaker vaccine immunogenicity with higher immune suppression for individuals with pre-existing mental disorders. Yet, data on the effectiveness of COVID-19 vaccinations among this vulnerable population are limited. A case-control study was conducted to investigate the risks of COVID-19-related hospitalisation and mortality among individuals with mental disorders following one to three doses of BNT162b2 and CoronaVac vaccinations in Hong Kong. Data were extracted from electronic health records, vaccination and COVID-19 confirmed case records. Conditional logistic regression was applied with adjustment for comorbidities and medication history. Subgroup analyses were performed with stratification: by age (< 65 and ≥ 65) and mental disorders diagnosis (depression, schizophrenia, anxiety disorder, and bipolar disorder). Two doses of BNT162b2 and CoronaVac significantly reduced COVID-19-related hospitalisation and mortality. Further protection for both outcomes was provided after three doses of BNT162b2 and CoronaVac. The vaccine effectiveness magnitude of BNT162b2 was generally higher than CoronaVac, but the difference diminished after the third dose. Individuals with mental disorders should be prioritised in future mass vaccination programmes of booster doses or bivalent COVID-19 vaccines. Targeted strategies should be developed to resolve the reasons behind vaccine hesitancy among this population and increase their awareness on the benefits of vaccination.

Integrative proteomics and metabolomics study reveal enhanced immune responses by COVID-19 vaccine booster shot against Omicron SARS-CoV-2 infection

Since its outbreak in late 2021, the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely reported to be able to evade neutralizing antibodies, becoming more transmissible while causing milder symptoms than previous SARS-CoV-2 strains. Understanding the underlying molecular changes of Omicron SARS-CoV-2 infection and corresponding host responses are important to the control of Omicron COVID-19 pandemic. In this study, we report an integrative proteomics and metabolomics investigation of serum samples from 80 COVID-19 patients infected with Omicron SARS-CoV-2, as well as 160 control serum samples from 80 healthy individuals and 80 patients who had flu-like symptoms but were negative for SARS-CoV-2 infection. The multiomics results indicated that Omicron SARS-CoV-2 infection caused significant changes to host serum proteome and metabolome comparing to the healthy controls and patients who had flu-like symptoms without COVID-19. Protein and metabolite changes also pointed to liver dysfunctions and potential damage to other host organs by Omicron SARS-CoV-2 infection. The Omicron COVID-19 patients could be roughly divided into two subgroups based on their proteome differences. Interestingly, the subgroup who mostly had received full vaccination with booster shot had fewer coughing symptom, changed sphingomyelin lipid metabolism, and stronger immune responses including higher numbers of lymphocytes, monocytes, neutrophils, and upregulated proteins related to CD4+ T cells, CD8+ effector memory T cells (Tem), and conventional dendritic cells, revealing beneficial effects of full COVID-19 vaccination against Omicron SARS-CoV-2 infection through molecular changes.

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.

Assessing changes in incubation period, serial interval, and generation time of SARS-CoV-2 variants of concern: a systematic review and meta-analysis

BACKGROUND

After the first COVID-19 wave caused by the ancestral lineage, the pandemic has been fueled from the continuous emergence of new SARS-CoV-2 variants. Understanding key time-to-event periods for each emerging variant of concern is critical as it can provide insights into the future trajectory of the virus and help inform outbreak preparedness and response planning. Here, we aim to examine how the incubation period, serial interval, and generation time have changed from the ancestral SARS-CoV-2 lineage to different variants of concern.

METHODS

We conducted a systematic review and meta-analysis that synthesized the estimates of incubation period, serial interval, and generation time (both realized and intrinsic) for the ancestral lineage, Alpha, Beta, and Omicron variants of SARS-CoV-2.

RESULTS

Our study included 280 records obtained from 147 household studies, contact tracing studies, or studies where epidemiological links were known. With each emerging variant, we found a progressive shortening of each of the analyzed key time-to-event periods, although we did not find statistically significant differences between the Omicron subvariants. We found that Omicron BA.1 had the shortest pooled estimates for the incubation period (3.49 days, 95% CI: 3.13-4.86 days), Omicron BA.5 for the serial interval (2.37 days, 95% CI: 1.71-3.04 days), and Omicron BA.1 for the realized generation time (2.99 days, 95% CI: 2.48-3.49 days). Only one estimate for the intrinsic generation time was available for Omicron subvariants: 6.84 days (95% CrI: 5.72-8.60 days) for Omicron BA.1. The ancestral lineage had the highest pooled estimates for each investigated key time-to-event period. We also observed shorter pooled estimates for the serial interval compared to the incubation period across the virus lineages. When pooling the estimates across different virus lineages, we found considerable heterogeneities (I2 > 80%; I2 refers to the percentage of total variation across studies that is due to heterogeneity rather than chance), possibly resulting from heterogeneities between the different study populations (e.g., deployed interventions, social behavior, demographic characteristics).

CONCLUSIONS

Our study supports the importance of conducting contact tracing and epidemiological investigations to monitor changes in SARS-CoV-2 transmission patterns. Our findings highlight a progressive shortening of the incubation period, serial interval, and generation time, which can lead to epidemics that spread faster, with larger peak incidence, and harder to control. We also consistently found a shorter serial interval than incubation period, suggesting that a key feature of SARS-CoV-2 is the potential for pre-symptomatic transmission. These observations are instrumental to plan for future COVID-19 waves.

Improvements and Persisting Challenges in COVID-19 Response Compared with 1918–19 Influenza Pandemic Response, New Zealand (Aotearoa)

Exploring the results of the COVID-19 response in New Zealand (Aotearoa) is warranted so that insights can inform future pandemic planning. We compared the COVID-19 response in New Zealand to that for the more severe 1918–19 influenza pandemic. Both pandemics were caused by respiratory viruses, but the 1918–19 pandemic was short, intense, and yielded a higher mortality rate. The government and societal responses to COVID-19 were vastly superior; responses had a clear strategic direction and included a highly effective elimination strategy, border restrictions, minimal community spread for 20 months, successful vaccination rollout, and strong central government support. Both pandemics involved a whole-of-government response, community mobilization, and use of public health and social measures. Nevertheless, lessons from 1918–19 on the necessity of action to prevent inequities among different social groups were not fully learned, as demonstrated by the COVID-19 response and its ongoing unequal health outcomes in New Zealand.

Predicting the virulence of future emerging zoonotic viruses

Would you rather kiss a platypus, a hedgehog, or a llama? According to a new study in this issue of PLOS Biology, the virulence of a zoonotic virus in humans depends on its reservoir host. Could physiology be the key to anticipating viral threats lethality?

Viral kinetics of SARS-CoV-2 following onset of COVID-19 in symptomatic patients infected with the ancestral strain and omicron BA.2 in Hong Kong: a retrospective observational study

BACKGROUND

Assessment of viral kinetics of SARS-CoV-2 can inform on host immune responses to the virus and on the viral transmission potential. We aimed to characterise viral shedding kinetics by age, virus type, and clinical outcome, and to examine the potential effect of vaccination on viral shedding.

METHODS

In this retrospective observational study, we analysed longitudinal data on cycle threshold (Ct) values of reverse-transcription quantitative PCR (RT-qPCR) assays of upper respiratory tract samples from symptomatic patients with COVID-19. Patients who were confirmed with COVID-19 with at least one Ct value of the RT-qPCR test available within 28 days after symptom onset, and discharged or died at the time of the analysis, were included in the study. Patients were isolated in hospitals in Hong Kong during three major epidemic waves dominated by the ancestral strain or omicron BA.2. We modelled the temporal trajectories of viral burden in these patients. Electronic medical records of the patients with COVID-19 were retrieved and linked to the patients' epidemiological information obtained from contact tracing. Patients who were infected outside Hong Kong, infected with variants other than the ancestral strain or omicron BA.2, not reporting any COVID-19 related symptoms, still hospitalised at the time of analysis, missing information on age, time of symptom onset, infection severity, vaccination or clinical outcome, infected more than once, or treated with nirmatrelvir-ritonavir or molnupiravir were excluded from analysis. The main outcome of this study is the temporal change of SARS-CoV-2 viral burden measured by Ct values of RT-qPCR tests in symptomatic patients with COVID-19.

FINDINGS

Among 22 461 symptomatic patients with COVID-19 confirmed from July 1, 2020, to May 22, 2022, the estimated viral burden from a random-effects model indicated a longer duration of viral shedding in patients with more severe outcomes of infection (mean difference 13·1 days, 95% CI 12·9-13·3, for fatal vs mild-to-moderate) and in older patients (5·2, 5·0-5·5, for age ≥80 years vs 0-18 years). Vaccinated individuals with a breakthrough infection with the omicron BA.2 variant had a generally lower viral burden and shorter durations of viral shedding (mean difference of 2-4 days) over 4 weeks after onset than unvaccinated individuals infected with omicron BA.2, particularly in patients whose last dose of COVID-19 vaccine was received ≤90 days before symptom onset. Marginal differences in viral burden following symptom onset and the duration of viral shedding were observed between unvaccinated individuals infected with the ancestral strain and omicron BA.2.

INTERPRETATION

The viral kinetics since symptom onset characterised for symptomatic patients with COVID-19 in our study show that previously vaccinated or younger individuals, or those with a milder infection, shed fewer viruses in a shorter period, implying possible transmission dynamics of SARS-CoV-2 and protective mechanisms of vaccination against infection and severe outcomes.

FUNDING

Hong Kong Health and Medical Research Fund and Hong Kong Collaborative Research Fund.

Residential Clustering of Coronavirus Disease 2019 Cases and Efficiency of Building-Wide Compulsory Testing Notices as a Transmission Control Measure in Hong Kong

We described the frequency of residential case clusters and the efficiency of compulsory testing in identifying cases using buildings targeted in compulsory testing and locally infected coronavirus disease 2019 (COVID-19) cases matched by residence in Hong Kong. Most of the buildings (4246 of 7688, 55.2%) with COVID-19 cases identified had only 1 reported case, and 13% of the daily reported cases were detected through compulsory testing. Compulsory testing notices could be essential in attempting to eliminate infections ("zero COVID") and have an impact early in an epidemic, but they appear to be relatively inefficient in response to sustained community transmission.

Modelling the viral dynamics of the SARS-CoV-2 Delta and Omicron variants in different cell types

We use viral kinetic models fitted to viral load data from in vitro studies to explain why the SARS-CoV-2 Omicron variant replicates faster than the Delta variant in nasal cells, but slower than Delta in lung cells, which could explain Omicron's higher transmission potential and lower severity. We find that in both nasal and lung cells, viral infectivity is higher for Omicron but the virus production rate is higher for Delta, with an estimated approximately 200-fold increase in infectivity and 100-fold decrease in virus production when comparing Omicron with Delta in nasal cells. However, the differences are unequal between cell types, and ultimately lead to the basic reproduction number and growth rate being higher for Omicron in nasal cells, and higher for Delta in lung cells. In nasal cells, Omicron alone can enter via a TMPRSS2-independent pathway, but it is primarily increased efficiency of TMPRSS2-dependent entry which accounts for Omicron's increased activity. This work paves the way for using within-host mathematical models to understand the transmission potential and severity of future variants.

Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern

The Alpha, Beta, and Gamma SARS-CoV-2 variants of concern (VOCs) co-circulated globally during 2020 and 2021, fueling waves of infections. They were displaced by Delta during a third wave worldwide in 2021, which, in turn, was displaced by Omicron in late 2021. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of VOCs worldwide. We find that source-sink dynamics varied substantially by VOC and identify countries that acted as global and regional hubs of dissemination. We demonstrate the declining role of presumed origin countries of VOCs in their global dispersal, estimating that India contributed <15% of Delta exports and South Africa <1%-2% of Omicron dispersal. We estimate that >80 countries had received introductions of Omicron within 100 days of its emergence, associated with accelerated passenger air travel and higher transmissibility. Our study highlights the rapid dispersal of highly transmissible variants, with implications for genomic surveillance along the hierarchical airline network.

Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein

The Omicron subvariant BA.2 has become the dominant circulating strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in many countries. Here, we have characterized structural, functional and antigenic properties of the full-length BA.2 spike (S) protein and compared replication of the authentic virus in cell culture and an animal model with previously prevalent variants. BA.2 S can fuse membranes slightly more efficiently than Omicron BA.1, but still less efficiently than other previous variants. Both BA.1 and BA.2 viruses replicated substantially faster in animal lungs than the early G614 (B.1) strain in the absence of pre-existing immunity, possibly explaining the increased transmissibility despite their functionally compromised spikes. As in BA.1, mutations in the BA.2 S remodel its antigenic surfaces, leading to strong resistance to neutralizing antibodies. These results suggest that both immune evasion and replicative advantage may contribute to the heightened transmissibility of the Omicron subvariants.

Rapid review and meta-analysis of serial intervals for SARS-CoV-2 Delta and Omicron variants

BACKGROUND

The serial interval is the period of time between symptom onset in the primary case and symptom onset in the secondary case. Understanding the serial interval is important for determining transmission dynamics of infectious diseases like COVID-19, including the reproduction number and secondary attack rates, which could influence control measures. Early meta-analyses of COVID-19 reported serial intervals of 5.2 days (95% CI: 4.9-5.5) for the original wild-type variant and 5.2 days (95% CI: 4.87-5.47) for Alpha variant. The serial interval has been shown to decrease over the course of an epidemic for other respiratory diseases, which may be due to accumulating viral mutations and implementation of more effective nonpharmaceutical interventions. We therefore aggregated the literature to estimate serial intervals for Delta and Omicron variants.

METHODS

This study followed Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. A systematic literature search was conducted of PubMed, Scopus, Cochrane Library, ScienceDirect, and preprint server medRxiv for articles published from April 4, 2021, through May 23, 2023. Search terms were: ("serial interval" or "generation time"), ("Omicron" or "Delta"), and ("SARS-CoV-2" or "COVID-19"). Meta-analyses were done for Delta and Omicron variants using a restricted maximum-likelihood estimator model with a random effect for each study. Pooled average estimates and 95% confidence intervals (95% CI) are reported.

RESULTS

There were 46,648 primary/secondary case pairs included for the meta-analysis of Delta and 18,324 for Omicron. Mean serial interval for included studies ranged from 2.3-5.8 days for Delta and 2.1-4.8 days for Omicron. The pooled mean serial interval for Delta was 3.9 days (95% CI: 3.4-4.3) (20 studies) and Omicron was 3.2 days (95% CI: 2.9-3.5) (20 studies). Mean estimated serial interval for BA.1 was 3.3 days (95% CI: 2.8-3.7) (11 studies), BA.2 was 2.9 days (95% CI: 2.7-3.1) (six studies), and BA.5 was 2.3 days (95% CI: 1.6-3.1) (three studies).

CONCLUSIONS

Serial interval estimates for Delta and Omicron were shorter than ancestral SARS-CoV-2 variants. More recent Omicron subvariants had even shorter serial intervals suggesting serial intervals may be shortening over time. This suggests more rapid transmission from one generation of cases to the next, consistent with the observed faster growth dynamic of these variants compared to their ancestors. Additional changes to the serial interval may occur as SARS-CoV-2 continues to circulate and evolve. Changes to population immunity (due to infection and/or vaccination) may further modify it.

Analysis of Factors Influencing the Clinical Severity of Omicron and Delta Variants

The Omicron variant is the dominant strain circulating globally, and studies have shown that Omicron cases have milder symptoms than Delta cases. This study aimed to analyze the factors that affect the clinical severity of Omicron and Delta variants, evaluate and compare the effectiveness of COVID-19 vaccines with different technological platforms, and assess the vaccine effectiveness against different variants. We retrospectively collected the basic information of all local COVID-19 cases reported by Hunan Province to the National Notifiable Infectious Disease Reporting System from January 2021 to February 2023, including gender, age, clinical severity, and COVID-19 vaccination history. From 1 January 2021 to 28 February 2023, Hunan Province reported a total of 60,668 local COVID-19 cases, of which, 134 were infected with the Delta variant and 60,534 were infected with the Omicron variant. The results showed that infection with the Omicron variant (adjusted OR (aOR): 0.21, 95% CI: 0.14-0.31), getting vaccinated (booster immunization vs. unvaccinated aOR: 0.30, 95% CI: 0.23-0.39) and being female (aOR: 0.82, 95% CI: 0.79-0.85) were protective factors for pneumonia, while old age (≥60 years vs. <3 years aOR: 4.58, 95% CI: 3.36-6.22) was a risk factor for pneumonia. Being vaccinated (booster immunization vs. unvaccinated aOR: 0.11, 95% CI: 0.09-0.15) and female (aOR: 0.54, 95% CI: 0.50-0.59) were protective factors for severe cases, while older age (≥60 years vs. < 3 years aOR: 4.95, 95% CI: 1.83-13.39) was a risk factor for severe cases. The three types of vaccines had protective effects on both pneumonia and severe cases, and the protective effect on severe cases was better than that on pneumonia. The recombinant subunit vaccine booster immunization had the best protective effect on pneumonia and severe cases, with ORs of 0.29 (95% CI: 0.2-0.44) and 0.06 (95% CI: 0.02-0.17), respectively. The risk of pneumonia from Omicron variant infection was lower than that from Delta. Chinese-produced vaccines had protective effects on both pneumonia and severe cases, with recombinant subunit vaccines having the best protective effect on pneumonia and severe pneumonia cases. Booster immunization should be advocated in COVID-19 pandemic-related control and prevention policies, especially for the elderly, and booster immunization should be accelerated.

SARS-CoV-2 Omicron variants: burden of disease, impact on vaccine effectiveness and need for variant-adapted vaccines

The highly transmissible Omicron (B.1.1.529) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in late 2021. Initial Omicron waves were primarily made up of sub-lineages BA.1 and/or BA.2, BA.4, and BA.5 subsequently became dominant in mid-2022, and several descendants of these sub-lineages have since emerged. Omicron infections have generally caused less severe disease on average than those caused by earlier variants of concern in healthy adult populations, at least, in part, due to increased population immunity. Nevertheless, healthcare systems in many countries, particularly those with low population immunity, have been overwhelmed by unprecedented surges in disease prevalence during Omicron waves. Pediatric admissions were also higher during Omicron waves compared with waves of previous variants of concern. All Omicron sub-lineages exhibit partial escape from wild-type (Wuhan-Hu 1) spike-based vaccine-elicited neutralizing antibodies, with sub-lineages with more enhanced immuno-evasive properties emerging over time. Evaluating vaccine effectiveness (VE) against Omicron sub-lineages has become challenging against a complex background of varying vaccine coverage, vaccine platforms, prior infection rates, and hybrid immunity. Original messenger RNA vaccine booster doses substantially improved VE against BA.1 or BA.2 symptomatic disease. However, protection against symptomatic disease waned, with reductions detected from 2 months after booster administration. While original vaccine-elicited CD8⁺ and CD4⁺ T-cell responses cross-recognize Omicron sub-lineages, thereby retaining protection against severe outcomes, variant-adapted vaccines are required to expand the breadth of B-cell responses and improve durability of protection. Variant-adapted vaccines were rolled out in late 2022 to increase overall protection against symptomatic and severe infections caused by Omicron sub-lineages and antigenically aligned variants with enhanced immune escape mechanisms.

Impacting factors and sources of perceived stress by home-quarantined residents in Shanghai during COVID-19 epidemic

BACKGROUND

Home-quarantine is one of the most common measures implemented to prevent or minimize the transmission of COVID-19 among communities. This study assessed stress levels of the home-quarantined residents in Shanghai during a massive wave of COVID-19 epidemic this year, explored the stress sources perceived by the respondents, and analyzed the association between each of the sociodemographic factors and the stress level.

METHODS

This online survey was launched during April 23 - 30, 2022, the early stage of a massive wave of COVID-19 in Shanghai, China. Participants were quarantined-residents negative for COVID-19. They were asked to list some situations that were their major concerns and perceived stressful, in addition to sociodemographic and COVID-19 related information. Moreover, they were asked to complete the Perceived Stress Scale-14 (PSS-14) for the assessment of stress level.

RESULTS

A total of 488 valid questionnaires were collected from 192 male and 296 female respondents. Overall, 207 persons (42.42%) presented high stress level (PSS-14 score ≥43). The top three concerns perceived stressful by respondents are "not allowed to go outdoors", "uncertain duration of the epidemic", and "lack of food supply". Fewer than 50% of the respondents perceived the other situations stressful. Higher proportions of young adults (≤ 29 years old), males, unemployed, singles, and those with low income (≤ 1999 yuan/month) perceived high stress compared to their counterparts, none of COVID-19 related factors is associated with the stress level, including location of residence, result of nucleic acid test, knowledge about COVID-19, whether vaccinated, and quarantine duration.

CONCLUSION

Home-quarantine applied to people negative for COVID-19 led to a lot of major concerns that may be perceived stressful, whereas the virus-related factors did not show significant impact on mental health of the respondents.

Age-dependent final size equation to anticipate mortality impact of COVID-19 in China

Before reopening society in December 2022, China had not achieved sufficiently high vaccination coverage among people aged 80 years and older, who are vulnerable to severe infection and death owing to COVID-19. Suddenly ending the zero-COVID policy was anticipated to lead to substantial mortality. To investigate the mortality impact of COVID-19, we devised an age-dependent transmission model to derive a final size equation, permitting calculation of the expected cumulative incidence. Using an age-specific contact matrix and published estimates of vaccine effectiveness, final size was computed as a function of the basic reproduction number, R0. We also examined hypothetical scenarios in which third-dose vaccination coverage was increased in advance of the epidemic, and also in which mRNA vaccine was used instead of inactivated vaccines. Without additional vaccination, the final size model indicated that a total of 1.4 million deaths (half of which were among people aged 80 years and older) were anticipated with an assumed R0 of 3.4. A 10% increase in third-dose coverage would prevent 30,948, 24,106, and 16,367 deaths, with an assumed second-dose effectiveness of 0%, 10%, and 20%, respectively. With mRNA vaccine, the mortality impact would have been reduced to 1.1 million deaths. The experience of reopening in China indicates the critical importance of balancing pharmaceutical and non-pharmaceutical interventions. Ensuring sufficiently high vaccination coverage is vital in advance of policy changes.

Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong

Hong Kong experienced a surge of Omicron BA.2 infections in early 2022, resulting in one of the highest per-capita death rates of COVID-19. The outbreak occurred in a dense population with low immunity towards natural SARS-CoV-2 infection, high vaccine hesitancy in vulnerable populations, comprehensive disease surveillance and the capacity for stringent public health and social measures (PHSMs). By analyzing genome sequences and epidemiological data, we reconstructed the epidemic trajectory of BA.2 wave and found that the initial BA.2 community transmission emerged from cross-infection within hotel quarantine. The rapid implementation of PHSMs suppressed early epidemic growth but the effective reproduction number (Re) increased again during the Spring festival in early February and remained around 1 until early April. Independent estimates of point prevalence and incidence using phylodynamics also showed extensive superspreading at this time, which likely contributed to the rapid expansion of the epidemic. Discordant inferences based on genomic and epidemiological data underscore the need for research to improve near real-time epidemic growth estimates by combining multiple disparate data sources to better inform outbreak response policy.

Trends in Cases, Hospitalizations, and Mortality Related to the Omicron BA.4/BA.5 Subvariants in South Africa

BACKGROUND

In this study, we compared admission incidence risk and the risk of mortality in the Omicron BA.4/BA.5 wave to previous waves.

METHODS

Data from South Africa's SARS-CoV-2 case linelist, national COVID-19 hospital surveillance system, and Electronic Vaccine Data System were linked and analyzed. Wave periods were defined when the country passed a weekly incidence of 30 cases/100 000 population. In-hospital case fatality ratios (CFRs) during the Delta, Omicron BA.1/BA.2, and Omicron BA.4/BA.5 waves were compared using post-imputation random effect multivariable logistic regression models.

RESULTS

The CFR was 25.9% (N = 37 538 of 144 778), 10.9% (N = 6123 of 56 384), and 8.2% (N = 1212 of 14 879) in the Delta, Omicron BA.1/BA.2, and Omicron BA.4/BA.5 waves, respectively. After adjusting for age, sex, race, comorbidities, health sector, and province, compared with the Omicron BA.4/BA.5 wave, patients had higher risk of mortality in the Omicron BA.1/BA.2 wave (adjusted odds ratio [aOR], 1.3; 95% confidence interval [CI]: 1.2-1.4) and Delta wave (aOR, 3.0; 95% CI: 2.8-3.2). Being partially vaccinated (aOR, 0.9; 95% CI: .9-.9), fully vaccinated (aOR, 0.6; 95% CI: .6-.7), and boosted (aOR, 0.4; 95% CI: .4-.5) and having prior laboratory-confirmed infection (aOR, 0.4; 95% CI: .3-.4) were associated with reduced risks of mortality.

CONCLUSIONS

Overall, admission incidence risk and in-hospital mortality, which had increased progressively in South Africa's first 3 waves, decreased in the fourth Omicron BA.1/BA.2 wave and declined even further in the fifth Omicron BA.4/BA.5 wave. Mortality risk was lower in those with natural infection and vaccination, declining further as the number of vaccine doses increased.

Risk of within-hotel transmission of SARS-CoV-2 during on-arrival quarantine in Hong Kong: an epidemiological and phylogenomic investigation

Background

On-arrival quarantine has been one of the primary measures to prevent the introduction of SARS-CoV-2 into Hong Kong since the start of the pandemic. Most on-arrival quarantines have been done in hotels, with the duration of quarantine and testing frequency during quarantine modified over time along with other pandemic control measures. However, hotels are not designed with infection control in mind. We aimed to systematically study the potential risk of acquisition of SARS-CoV-2 infection among individuals undergoing hotel quarantine.

Methods

We examined data on each laboratory-confirmed COVID-19 case identified in on-arrival quarantine in a hotel in Hong Kong between 1 May 2020 and 31 January 2022. We sequenced the whole genomes of viruses from cases that overlapped with other confirmed cases in terms of the hotel of stay, date of arrival and date of testing positive. By combining multiple sources of evidence, we identify probable and plausible transmission events and calculate the overall risk of transmission.

Findings

Among 221 imported cases that overlapped with other cases detected during hotel quarantine with available sequence data, phylogenomic analyses identified five probable and two plausible clusters of within-hotel transmission. Only two of these clusters were recognised at the time. Including other clusters reported in Hong Kong, we estimate that 8-11 per 1000 cases identified in hotel quarantine may be infected by another unlinked case during quarantine, or 2-3 per 100,000 overseas arrivals.

Interpretation

We have identified additional undetected occurrences of COVID-19 transmission within hotel quarantine in Hong Kong. Although hotels provide suboptimal infection control as improvised quarantine facilities, the risk of contracting infection whilst in quarantine is low. However, these unlikely events could have high consequences by allowing the virus to spread into immunologically naïve communities. Additional vigilance should be taken in the absence of improved controls to identify such events. If on-arrival quarantine is expected to be used for a long time, quarantine facilities could be purpose-built to minimise the risk of transmission.

Funding

Health and Medical Research Fund, Hong Kong.

Serial Intervals and Incubation Periods of SARS-CoV-2 Omicron and Delta Variants, Singapore

We compared serial intervals and incubation periods for SARS-CoV-2 Omicron BA.1 and BA.2 subvariants and Delta variants in Singapore. Median incubation period was 3 days for BA.1 versus 4 days for Delta. Serial interval was 2 days for BA.1 and 3 days for BA.2 but 4 days for Delta.

Evolution of long-term vaccine-induced and hybrid immunity in healthcare workers after different COVID-19 vaccine regimens

BACKGROUND

Both infection and vaccination, alone or in combination, generate antibody and T cell responses against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the maintenance of such responses-and hence protection from disease-requires careful characterization. In a large prospective study of UK healthcare workers (HCWs) (Protective Immunity from T Cells in Healthcare Workers [PITCH], within the larger SARS-CoV-2 Immunity and Reinfection Evaluation [SIREN] study), we previously observed that prior infection strongly affected subsequent cellular and humoral immunity induced after long and short dosing intervals of BNT162b2 (Pfizer/BioNTech) vaccination.

METHODS

Here, we report longer follow-up of 684 HCWs in this cohort over 6-9 months following two doses of BNT162b2 or AZD1222 (Oxford/AstraZeneca) vaccination and up to 6 months following a subsequent mRNA booster vaccination.

FINDINGS

We make three observations: first, the dynamics of humoral and cellular responses differ; binding and neutralizing antibodies declined, whereas T and memory B cell responses were maintained after the second vaccine dose. Second, vaccine boosting restored immunoglobulin (Ig) G levels; broadened neutralizing activity against variants of concern, including Omicron BA.1, BA.2, and BA.5; and boosted T cell responses above the 6-month level after dose 2. Third, prior infection maintained its impact driving larger and broader T cell responses compared with never-infected people, a feature maintained until 6 months after the third dose.

CONCLUSIONS

Broadly cross-reactive T cell responses are well maintained over time-especially in those with combined vaccine and infection-induced immunity ("hybrid" immunity)-and may contribute to continued protection against severe disease.

FUNDING

Department for Health and Social Care, Medical Research Council.

Three-dose vaccination-induced immune responses protect against SARS-CoV-2 Omicron BA.2: a population-based study in Hong Kong

Background

The ongoing outbreak of SARS-CoV-2 Omicron BA.2 infections in Hong Kong, the model city of universal masking of the world, has resulted in a major public health crisis. Although the third vaccination resulted in strong boosting of neutralization antibody, vaccine efficacy and correlate of immune protection against the major circulating Omicron BA.2 remain to be investigated.

Methods

We investigated the vaccine efficacy against the Omicron BA.2 breakthrough infection among 470 public servants who had received different SARS-CoV-2 vaccine regimens including two-dose BNT162b2 (2 × BNT, n = 169), three-dose BNT162b2 (3 × BNT, n = 168), two-dose CoronaVac (2 × CorV, n = 34), three-dose CoronaVac (3 × CorV, n = 67) and third-dose BNT162b2 following 2 × CorV (2 × CorV+1BNT, n = 32). Humoral and cellular immune responses after three-dose vaccination were further characterized and correlated with clinical characteristics of BA.2 infection.

Findings

During the BA.2 outbreak, 27.7% vaccinees were infected. The timely third-dose vaccination provided significant protection with lower incidence rates of breakthrough infections (2 × BNT 46.2% vs 3 × BNT 13.1%, p < 0.0001; 2 × CorV 44.1% vs 3 × CorV 19.4%, p = 0.003). Investigation of immune responses on blood samples derived from 90 subjects in three-dose vaccination cohorts collected before the BA.2 outbreak revealed that the third-dose vaccination activated spike (S)-specific memory B cells and Omicron cross-reactive T cell responses, which correlated with reduced frequencies of breakthrough infections and disease severity rather than with types of vaccines. Moreover, the frequency of S-specific activated memory B cells was significantly lower in infected vaccinees than uninfected vaccinees before vaccine-breakthrough infection whereas IFN-γ+ CD4 T cells were negatively associated with age and viral clearance time. Critically, BA.2 breakthrough infection boosted cross-reactive memory B cells with enhanced cross-neutralizing antibodies to Omicron sublineages, including BA.2.12.1 and BA.4/5, in all vaccinees tested.

Interpretation

Our results imply that the timely third vaccination and immune responses are likely required for vaccine-mediated protection against Omicron BA.2 pandemic. Although BA.2 conferred the highest neutralization resistance compared with variants of concern tested before the emergence of BA.2.12.1 and BA.4/5, the third dose vaccination-activated S-specific memory B cells and Omicron cross-reactive T cell responses contributed to reduced frequencies of breakthrough infection and disease severity. Neutralizing antibody potency enhanced by BA.2 breakthrough infection in vaccinees with prior 3 doses of CoronaVac or BNT162b2 may reduce the risk of infection against ongoing BA.2.12.1 and BA.4/5.

Funding

Hong Kong Research Grants Council Collaborative Research Fund, Health and Medical Research Fund, Wellcome Trust, Shenzhen Science and Technology Program, the Health@InnoHK, Innovation and Technology Commission of Hong Kong, China, National Program on Key Research Project, Emergency Key Program of Guangzhou Laboratory, donations from the Friends of Hope Education Fund and the Hong Kong Theme-Based Research Scheme.