Genomic epidemiology of SARS- CoV-2 Omicron variants in the Republic of Korea

Impact of COVID-19 Infection and Its Association With Previous Vaccination in Patients With Myasthenia Gravis in Korea: A Multicenter Retrospective Study

BACKGROUND

During the coronavirus disease 2019 (COVID-19) pandemic, patients with myasthenia gravis (MG) were more susceptible to poor outcomes owing to respiratory muscle weakness and immunotherapy. Several studies conducted in the early stages of the COVID-19 pandemic reported higher mortality in patients with MG compared to the general population. This study aimed to investigate the clinical course and prognosis of COVID-19 in patients with MG and to compare these parameters between vaccinated and unvaccinated patients in South Korea.

METHODS

This multicenter, retrospective study, which was conducted at 14 tertiary hospitals in South Korea, reviewed the medical records and identified MG patients who contracted COVID-19 between February 2022 and April 2022. The demographic and clinical characteristics associated with MG and vaccination status were collected. The clinical outcomes of COVID-19 infection and MG were investigated and compared between the vaccinated and unvaccinated patients.

RESULTS

Ninety-two patients with MG contracted COVID-19 during the study. Nine (9.8%) patients required hospitalization, 4 (4.3%) of whom were admitted to the intensive care unit. Seventy-five of 92 patients were vaccinated before contracting COVID-19 infection, and 17 were not. During the COVID-19 infection, 6 of 17 (35.3%) unvaccinated patients were hospitalized, whereas 3 of 75 (4.0%) vaccinated patients were hospitalized (P < 0.001). The frequencies of ICU admission and mechanical ventilation were significantly lower in the vaccinated patients than in the unvaccinated patients (P = 0.019 and P = 0.032, respectively). The rate of MG deterioration was significantly lower in the vaccinated patients than in the unvaccinated patients (P = 0.041). Logistic regression after weighting revealed that the risk of hospitalization and MG deterioration after COVID-19 infection was significantly lower in the vaccinated patients than in the unvaccinated patients.

CONCLUSION

This study suggests that the clinical course and prognosis of patients with MG who contracted COVID-19 during the dominance of the omicron variant of COVID-19 may be milder than those at the early phase of the COVID-19 pandemic when vaccination was unavailable. Vaccination may reduce the morbidity of COVID-19 in patients with MG and effectively prevent MG deterioration induced by COVID-19 infection.

Worsening of health disparities across COVID-19 pandemic stages in Korea

OBJECTIVES

With the end of the coronavirus disease 2019 (COVID-19) pandemic, the health outcomes of this disease in Korea must be examined. We aimed to investigate health outcomes and disparities linked to socioeconomic status during the COVID-19 pandemic in Korea and to identify risk factors for hospitalization and mortality.

METHODS

This nationwide retrospective study incorporated an analysis of individuals with and without COVID-19 in Korea between January 1, 2020 and December 31, 2022. The study period was divided into 4 stages. Prevalence, hospitalization, mortality, and case-fatality rates were calculated per 100,000 population. Multivariate logistic regression was performed to identify risk factors for COVID-19 hospitalization and mortality.

RESULTS

Overall, the incidence rate was 40,601 per 100,000 population, the mortality rate was 105 per 100,000 population, and the case-fatality rate was 259 per 100,000 cases. A total of 12,577,367 new cases (24.5%) were recorded in stage 3 and 8,979,635 cases (17.5%) in stage 4. Medical Aid recipients displayed the lowest 3-year cumulative incidence rate (32,737 per 100,000) but the highest hospitalization (5,663 cases per 100,000), mortality (498 per 100,000), and case-fatality (1,521 per 100,000) rates. Male sex, older age, lower economic status, non-metropolitan area of residence, high Charlson comorbidity index, and disability were associated with higher risk of hospitalization and death. Vaccination was found to reduce mortality risk.

CONCLUSIONS

As the pandemic progressed, surges were observed in incidence, hospitalization, and mortality, exacerbating disparities associated with economic status and disability. Nevertheless, Korea has maintained a low case-fatality rate across all economic groups.

Analytical performance of the Abbott ID NOW 2.0 assay for SARS-CoV-2 detection in clinical samples from symptomatic patients

We evaluated the analytical performance of ID NOW™ COVID-19 2.0 assay versus conventional real-time reverse transcription-polymerase chain reaction (RT-PCR) using a total of 792 clinical samples from nasopharyngeal and oropharyngeal swabs, stored in frozen universal transport medium samples. Positive percent agreement (PPA) and negative percent agreement of ID NOW were 97.6 % and 100 %, respectively. The overall percent agreement between ID NOW and RT-PCR was 99.5 %. The PPA of ID NOW in detecting SARS-CoV-2 in 164 RT-PCR positive patients, all of whom had symptoms related COVID-19, was 97.1 % within 8 days since symptom onset, 97.9 % from 8 to 14 days since symptom onset, and 97.6 % after 14 days since symptom onset, with no significant difference between the days since symptom onset. The ID NOW assay demonstrated good performance, providing a rapid and randomly accessible alternative to conventional RT-PCR for timely SARS-CoV-2 detection, particularly in situations requiring rapid results for patient care.

Mortality Rate and Outcomes of Omicron Variant Positive Patients with Osteoporotic Fractures: A Retrospective Study

BACKGROUND

During the lockdown period associated with the coronavirus disease 2019 (COVID-19) pandemic, increased mortality rates among patients with COVID-19 have been reported. This study aimed to analyze the mortality rate of osteoporotic hip fractures in patients who were COVID-19-positive after the lockdown during the Omicron period.

METHODS

A retrospective study was performed with 194 patients who were aged 70 years or more and diagnosed with osteoporotic hip fracture. The patients were divided into two groups according to their COVID-19 diagnoses. Surgery was performed within 10 days of diagnosis. Age, sex, past medical history, time until surgery, postoperative complications, and the primary outcome of mortality rate at 30 and 90 days were analyzed.

RESULTS

Among the 194 patients, 13 and 181 were in the COVID-19-positive and negative group, respectively. The total, 30-day, and 90-day mortality rates in the control and COVID-positive group were 11% and 0% (P=0.368), 1.7% and 0% (P=1.000), and 5.0% and 0% (P=1.000), respectively. No significant differences were observed in age, sex, history, time to surgery, postoperative complications, or postoperative mortality. In 1:1 propensity score matching, the time to surgery was 5.34 days in patients who were COVID-19-positive, and 3.00 days in patients who were COVID-19 negative, with no statistical significance (P=0.09). Age, sex, medical history, postoperative complications, and postoperative mortality were not significantly different between the groups.

CONCLUSIONS

Regardless of the COVID-19 diagnosis, surgical treatment without delay is believed to result in positive outcomes in older patients with osteoporotic hip fractures, as no significant differences in mortality rate and respiratory complications were observed between patients who were COVID-19-positive and those who were COVID-19 negative.

Development and Validation of a Robust and Interpretable Early Triaging Support System for Patients Hospitalized With COVID-19: Predictive Algorithm Modeling and Interpretation Study

BACKGROUND

Robust and accurate prediction of severity for patients with COVID-19 is crucial for patient triaging decisions. Many proposed models were prone to either high bias risk or low-to-moderate discrimination. Some also suffered from a lack of clinical interpretability and were developed based on early pandemic period data. Hence, there has been a compelling need for advancements in prediction models for better clinical applicability.

OBJECTIVE

The primary objective of this study was to develop and validate a machine learning-based Robust and Interpretable Early Triaging Support (RIETS) system that predicts severity progression (involving any of the following events: intensive care unit admission, in-hospital death, mechanical ventilation required, or extracorporeal membrane oxygenation required) within 15 days upon hospitalization based on routinely available clinical and laboratory biomarkers.

METHODS

We included data from 5945 hospitalized patients with COVID-19 from 19 hospitals in South Korea collected between January 2020 and August 2022. For model development and external validation, the whole data set was partitioned into 2 independent cohorts by stratified random cluster sampling according to hospital type (general and tertiary care) and geographical location (metropolitan and nonmetropolitan). Machine learning models were trained and internally validated through a cross-validation technique on the development cohort. They were externally validated using a bootstrapped sampling technique on the external validation cohort. The best-performing model was selected primarily based on the area under the receiver operating characteristic curve (AUROC), and its robustness was evaluated using bias risk assessment. For model interpretability, we used Shapley and patient clustering methods.

RESULTS

Our final model, RIETS, was developed based on a deep neural network of 11 clinical and laboratory biomarkers that are readily available within the first day of hospitalization. The features predictive of severity included lactate dehydrogenase, age, absolute lymphocyte count, dyspnea, respiratory rate, diabetes mellitus, c-reactive protein, absolute neutrophil count, platelet count, white blood cell count, and saturation of peripheral oxygen. RIETS demonstrated excellent discrimination (AUROC=0.937; 95% CI 0.935-0.938) with high calibration (integrated calibration index=0.041), satisfied all the criteria of low bias risk in a risk assessment tool, and provided detailed interpretations of model parameters and patient clusters. In addition, RIETS showed potential for transportability across variant periods with its sustainable prediction on Omicron cases (AUROC=0.903, 95% CI 0.897-0.910).

CONCLUSIONS

RIETS was developed and validated to assist early triaging by promptly predicting the severity of hospitalized patients with COVID-19. Its high performance with low bias risk ensures considerably reliable prediction. The use of a nationwide multicenter cohort in the model development and validation implicates generalizability. The use of routinely collected features may enable wide adaptability. Interpretations of model parameters and patients can promote clinical applicability. Together, we anticipate that RIETS will facilitate the patient triaging workflow and efficient resource allocation when incorporated into a routine clinical practice.

Extracorporeal Membrane Oxygenation Support and Critically Ill COVID-19 Patient Outcomes: A Population-Based Cohort Study

We selected critically ill patients with coronavirus disease 2019 (COVID-19) who were receiving extracorporeal membrane oxygenation (ECMO) support and had been transferred to experienced centers. Thus, we aimed to evaluate factors that were associated with receiving ECMO support and factors that were associated with patient mortality. Using data from the National Health Insurance Service and Korea Disease Control and Prevention Agency in South Korea, adult patients admitted to an intensive care unit from October 8, 2020, to December 31, 2021, with a main diagnosis of COVID-19 were included. They were divided into two groups: ECMO group (n = 455) and non-ECMO group (n = 12,648). Receiving ECMO support was less associated with old age [odds ratio (OR), 0.95; 95% confidence interval (CI), 0.94-0.96; p  < 0.001], underlying severe disabilities (OR, 0.49; 95% CI, 0.29-0.83; p  = 0.008), and booster vaccination status (second: OR, 0.61; 95% CI, 0.39-0.94; p  = 0.024; third: OR, 0.40; 95% CI, 0.25-0.65; p  < 0.001). In addition, after adjusting for various variables, low mortality in patients with ECMO support was associated with having previously received a second booster vaccination (OR, 0.33; 95% CI, 0.14-0.77; p  = 0.010). Vaccination and booster therapy may lower the need for ECMO support and lower mortality among critically ill patients with COVID-19 with ECMO support.

One-year antibody durability induced by EuCorVac-19, a liposome-displayed COVID-19 receptor binding domain subunit vaccine, in healthy Korean subjects

OBJECTIVE

EuCorVac-19 (ECV-19), an adjuvanted liposome-displayed receptor binding domain (RBD) COVID-19 vaccine, previously reported interim Phase 2 trial results showing induction of neutralizing antibodies 3 weeks after prime-boost immunization. The objective of this study was to determine the longer-term antibody response of the vaccine.

METHODS

To assess immunogenicity 6 and 12 months after vaccination, participants in the Phase 2 trial (NCT04783311) were excluded if they: 1) withdrew, 2) reported COVID-19 infection or additional vaccination, or 3) exhibited increasing Spike (S) antibodies (representing possible non-reported infection). Following exclusions, of the 197 initial subjects, anti-S IgG antibodies and neutralizing antibodies were further assessed in 124 subjects at the 6-month timepoint, and 36 subjects at the 12-month timepoint.

RESULTS

Median anti-S antibody half-life was 52 days (interquartile range [IQR]:42-70), in the "early" period from 3 weeks to 6 months, and 130 days (IQR:97-169) in the "late" period from 6 to 12 months. There was a negative correlation between initial antibody titer and half-life. Anti-S and neutralizing antibody responses were correlated. Neutralizing antibody responses showed longer half-lives; the early period had a median half-life of 120 days (IQR:81-207), and the late period had a median half-life of 214 days (IQR:140-550).

CONCLUSION

These data establish antibody durability of ECV-19, using a framework to analyze COVID-19 vaccine-induced antibodies during periods of high infection.

COVID-19 infection and efficacy of vaccination in patients with rheumatic diseases during Omicron outbreak in South Korea: a prospective cohort study

OBJECTIVES

This study aims to investigate COVID-19 epidemiological data in patients with autoimmune inflammatory rheumatic diseases (AIRDs) during Omicron wave and to identify clinical factors associated with infection, including COVID-19 vaccination.

METHODS

This prospective longitudinal study was performed between January and October 2022 in South Korea. Patients were classified into AIRD and non-AIRD groups according to their underlying diseases. COVID-19 status, date of confirmed infection and vaccination status were captured from the patient survey and national database. The COVID-19 incidence during the study period was examined and compared between the two groups. The effect of clinical factors on the infection rate was analysed in the AIRD group.

RESULTS

A total of 1814 patients (1535 and 279 in the AIRD and non-AIRD groups, respectively) were analysed. During the study period, 857 COVID-19 cases were reported in 834 patients (46.0%). The infection rates in the AIRD and non-AIRD groups were comparable. In the AIRD group, older age (≥70 years) and glucocorticoid use were significantly associated with a lower rate of COVID-19 infection. The third booster vaccination significantly lowered the incidence of COVID-19 (adjusted HR 0.85 (95% CI 0.73 to 0.99)), and the prophylactic effect was more evident in patients aged <70 years (0.81 (95% CI 0.69 to 0.95), p value for interaction 0.036).

CONCLUSION

The risk of SARS-CoV-2 infection with the Omicron variant did not increase in patients with AIRDs. The third booster vaccination regimen decreased the infection rate in patients aged <70 years.

Genomic epidemiology of SARS-CoV-2 variants in South Korea between January 2020 and February 2023

The Korea Disease Control and Prevention Agency (KDCA) has been conducting national genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2). To monitor and characterize circulating SARS-CoV-2 variants in South Korea, 102,873 oropharyngeal/nasopharyngeal swab samples collected from patients with confirmed COVID-19 were sequenced, assigned lineages, and phylogenetically analyzed. Each wave followed a pattern of variants emerging first abroad and then spreading domestically. In 2020, B.41 lineage led the first wave, and B.1.497 dominated the second and third waves. In 2021, the fourth wave was driven by Delta (AY.69 and AY.122.5). In 2022, the fifth to seventh waves were dominated by Omicron sub-lineages BA.1/BA.1.1 and BA.2/BA.2.3, BA.5/BA.5.2, and BN.1, sequentially. The KDCA detected and monitored increasing variants in advance prior to large-scale epidemics, but the repeated emergence of new variants could threaten public health again. Therefore, it is important to continue to monitor and characterize emerging and circulating variants through national genomic surveillance.

Effectiveness of Bivalent Omicron-Containing Booster Vaccines against SARS-CoV-2 Omicron Variant among Individuals with and without Prior SARS-CoV-2 Infection

In this study, we evaluated the effectiveness of the bivalent mRNA COVID-19 vaccines against the Omicron variant in individuals with or without prior SARS-CoV-2 infection history. We assessed the SARS-CoV-2-specific neutralizing antibody in serum samples by surrogate virus neutralizing assay (sVNT) and determined the serum's neutralizing capacity against the Omicron BA.5 by a plaque reduction neutralizing test (PRNT50). The results of the sVNT assay demonstrate a higher percentage of inhibition of the serum samples from the infected group than from the uninfected group (p = 0.01) before the bivalent vaccination but a similarly high percentage of inhibition after the vaccination. Furthermore, the results of the PRNT50 assay demonstrate a higher neutralizing capacity of the serum samples against Omicron BA.5 in the infected group compared to the uninfected group, both before and after the bivalent vaccine administration (p < 0.01 and p = 0.02 for samples collected before and after the bivalent vaccination, respectively). A higher neutralizing capacity of the serum samples against BA.5 following bivalent vaccination compared to those before vaccination suggests the efficacy of bivalent mRNA COVID-19 vaccines in triggering an immune response against the Omicron variant, particularly BA.5, regardless of infection history.

Clinical Characteristics of Post-COVID-19 Persistent Cough in the Omicron Era

Cough is one of the most common symptoms of acute coronavirus disease 2019, but cough may persist for weeks or months. This study aimed to examine the clinical characteristics of patients with post-coronavirus disease (COVID) persistent cough in the Omicron era. We conducted a pooled analysis comparing 3 different groups: 1) a prospective cohort of post-COVID cough (> 3 weeks; n = 55), 2) a retrospective cohort of post-COVID cough (> 3 weeks; n = 66), and 3) a prospective cohort of non-COVID chronic cough (CC) (> 8 weeks; n = 100). Cough and health status was assessed using patient-reported outcomes (PROs). Outcomes, including PROs and systemic symptoms, were longitudinally evaluated in the prospective post-COVID cough registry participants receiving usual care. A total of 121 patients with post-COVID cough and 100 with non-COVID CC were studied. Baseline cough-specific PRO scores did not significantly differ between post-COVID cough and non-COVID CC groups. There were no significant differences in chest imaging abnormality or lung function between groups. However, the proportions of patients with fractional exhaled nitric oxide (FeNO) ≥ 25 ppb were 44.7% in those with post-COVID cough and 22.7% in those with non-COVID CC, which were significantly different. In longitudinal assessment of the post-COVID registry (n = 43), cough-specific PROs, such as cough severity or Leicester Cough Questionnaire (LCQ) scores, significantly improved between visits 1 and 2 (visit interval: median 35 [interquartile range, IQR: 23-58] days). In the LCQ score, 83.3% of the patients showed improvement (change ≥ +1.3), but 7.1% had worsened (≤ -1.3). The number of systemic symptoms was median 4 (IQR: 2-7) at visit 1 but decreased to median 2 (IQR: 0-4) at visit 2. In summary, post-COVID persistent cough was similar in overall clinical characteristics to CC. Current cough guideline-based approaches may be effective in most patients with post-COVID cough. Measurement of FeNO levels may also be useful for cough management.

Exploring the vaccine-induced immunity against severe acute respiratory syndrome coronavirus 2 in healthcare workers

We aimed to analyze the kinetics of T-cell-mediated and B-cell-mediated humoral immune responses against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) before and after booster vaccination, as well as the impacts of the in vitro test results the type of vaccination on the prediction of SARS-CoV-2 infection. A total of 240 healthcare workers vaccinated twice were serially tested using an interferon gamma release assay (IGRA) and a neutralizing antibody (nAb). At the end of the study, we investigated the history of SARS-CoV-2 infection of all the enrolled participants to analyze the effects of the test results and the type of vaccination on SARS-CoV-2 infection. Overall, the positive rates were 52.3% and 80.0% for IGRA and 84.6% and 100% for the nAb test before and after booster vaccination, respectively. However, the positive rates were 52.8% for IGRA and 100% for nAb 3 months after booster vaccination. The in vitro test results and the type of vaccination were not associated with SARS-CoV-2 infection. The antibody response caused by the SARS-CoV-2 vaccination lasted more than 6 months, although the response of the T-cells disappeared rapidly after 3 months. However, these in vitro results and the type of vaccination cannot be used for predicting the risk of SARS-CoV-2 infection.

Association of Physical Activity With SARS-CoV-2 Infection and Severe Clinical Outcomes Among Patients in South Korea

Importance

The association of moderate to vigorous physical activity (MVPA) with COVID-19 outcomes is unclear and needs to be investigated.

Objective

To identify the association of longitudinal changes in MVPA with SARS-CoV-2 infection and severe COVID-19 outcomes.

Design, Setting, and Participants

This nested case-control study used data from 6 396 500 adult patients in South Korean who participated in National Health Insurance Service (NHIS) biennial health screenings from period 1 (2017-2018) to period 2 (2019-2020). Patients were followed from October 8, 2020, until the diagnosis of COVID-19 or December 31, 2021.

Exposure

Moderate to vigorous physical activity was measured by self-report on questionnaires during both NHIS health screenings and calculated by adding the frequency (times per week) of each moderate (≥30 minutes per day) and vigorous (≥20 minutes per day) physical activity.

Main Outcomes and Measures

The main outcomes were a positive diagnosis of SARS-CoV-2 infection and severe COVID-19 clinical events. Adjusted odds ratio (aORs) and 99% CIs were calculated using multivariable logistic regression analysis.

Results

A total of 183 350 patients with COVID-19 (mean [SD] age, 51.9 [13.8] years; female, 89 369 [48.7%]; male, 93 981 [51.3%]) among 2 110 268 participants were identified. For participants with vs without COVID-19, the proportion of MVPA frequency at period 2 was 35.8% vs 35.9% for physically inactive, 18.9% vs 18.9% for 1 to 2 times per week, 17.7% vs 17.7% for 3 to 4 times per week, and 27.5% vs 27.4% for 5 or more times per week. Among unvaccinated, physically inactive patients at period 1, the odds for infection increased when engaged in MVPA 1 to 2 times per week (aOR, 1.08; 99% CI, 1.01-1.15), 3 to 4 times per week (aOR, 1.09; 99% CI, 1.03-1.16), or 5 or more times per week (aOR, 1.10; 99% CI, 1.04-1.17) at period 2. Conversely, among unvaccinated patients with MVPA of 5 or more times per week at period 1, the odds for infection decreased when engaged 1 to 2 times per week (aOR, 0.90; 99% CI, 0.81-0.98) or physically inactive (aOR, 0.80; 99% CI, 0.73-0.87) at period 2. The trend of MVPA and incident infection was mitigated when participants were fully vaccinated. Furthermore, the odds for severe COVID-19 showed significant but limited associations with MVPA.

Conclusions and Relevance

The findings of this nested case-control study show a direct association of MVPA with risk of SARS-CoV-2 infection, which was mitigated after completion of the COVID-19 vaccination primary series. In addition, higher levels of MVPA were associated with a lower risk of severe COVID-19 outcomes to limited proportions.