Identification and Analysis of SARS-CoV-2 Alpha Variants in the Largest Taiwan COVID-19 Outbreak in 2021

Co-detection of various viruses in SARS-CoV-2 in children with respiratory infections

The co-detection of SARS-CoV-2 variant with other respiratory virus has been extensively investigated. However, conclusive evidence remains elusive and conflicted. This study investigated the source- and age-dependent prevalence, incidence, and co-detection of multiple viral infections in children younger than 18 years old who presented with clinical symptoms indicative of respiratory infections during SARS-CoV-2 pandemic. We retrospectively obtained and analyzed pediatric patients admitted to the institution and underwent Film Array Respiratory Panel (BIOFIRE® RP2.1) testing between January 2021 and December 2022. This encompassed pre-Delta, Delta and omicron periods, evaluating Film Array results for singular and co-detections. The overall detection rate was 84.2% (1670/1983) among 1,983 pediatric patients. Of these, 106 were SARS-CoV-2 positive. Notably, 45 patients (42%) harbored SARS-CoV-2 as the sole pathogen. Co-detection was significant; 32 cases (30.2%) involved Human Rhinovirus/Enterovirus, 29 (24.5%) involved parainfluenza 3, and 26 (24.5%) involved Respiratory syncytial virus. Peaks of co-detected parainfluenza 3 and Respiratory syncytial virus were evident in the winter of 2022 and absent in 2021. The top three viral strain for co-detection was HRV/EV, PIV-3, and RSV. The emergence order of co-detection strain was HRV/EV ◊PIV-3◊ RSV during the Omicron period in Taiwan. We identified characteristic patterns of SARS-CoV-2-associated co-detections, with a notable emphasis on the co-detection of HRV/EV, PIV3, and RSV alongside SARS-CoV-2. This association appears to hold heightened significance during the Omicron variant era compared to earlier SARS-CoV-2 variants, which contrast with previous studies. The simultaneous circulation of different variants may contribute to variations in viral co-detection, particularly in young children, warranting further investigation.

The Mediating Role of Human Mobility in Temporal-Lagged Relationships Between Risk Perception and COVID-19 Dynamics in Taiwan: Statistical Modeling for Comparing the Pre-Omicron and Omicron Eras

Background

The COVID-19 pandemic has profoundly impacted all aspects of human life for over 3 years. Understanding the evolution of public risk perception during these periods is crucial. Few studies explore the mechanisms for reducing disease transmission due to risk perception. Thus, we hypothesize that changes in human mobility play a mediating role between risk perception and the progression of the pandemic.

Objective

The study aims to explore how various forms of human mobility, including essential, nonessential, and job-related behaviors, mediate the temporal relationships between risk perception and pandemic dynamics.

Methods

We used distributed-lag linear structural equation models to compare the mediating impact of human mobility across different virus variant periods. These models examined the temporal dynamics and time-lagged effects among risk perception, changes in mobility, and virus transmission in Taiwan, focusing on two distinct periods: (1) April-August 2021 (pre-Omicron era) and (2) February-September 2022 (Omicron era).

Results

In the pre-Omicron era, our findings showed that an increase in public risk perception correlated with significant reductions in COVID-19 cases across various types of mobility within specific time frames. Specifically, we observed a decrease of 5.59 (95% CI -4.35 to -6.83) COVID-19 cases per million individuals after 7 weeks in nonessential mobility, while essential mobility demonstrated a reduction of 10.73 (95% CI -9.6030 to -11.8615) cases after 8 weeks. Additionally, job-related mobility resulted in a decrease of 3.96 (95% CI -3.5039 to -4.4254) cases after 11 weeks. However, during the Omicron era, these effects notably diminished. A reduction of 0.85 (95% CI -1.0046 to -0.6953) cases through nonessential mobility after 10 weeks and a decrease of 0.69 (95% CI -0.7827 to -0.6054) cases through essential mobility after 12 weeks were observed.

Conclusions

This study confirms that changes in mobility serve as a mediating factor between heightened risk perception and pandemic mitigation in both pre-Omicron and Omicron periods. This suggests that elevating risk perception is notably effective in impeding virus progression, especially when vaccines are unavailable or their coverage remains limited. Our findings provide significant value for health authorities in devising policies to address the global threats posed by emerging infectious diseases.

Impact of COVID-19 pandemic on neurodevelopmental outcomes of premature infants: a retrospective national cohort study

OBJECTIVE

To compare the neurodevelopmental outcomes of preterm infants before and during the COVID-19 pandemic.

DESIGN

Premature infants born in 2018 were assigned to the pre-pandemic group, while those born in 2019 were assigned to the during-pandemic group.

SETTING

Nationwide cohort study.

PATIENTS

Very low birthweight premature infants registered in the Taiwan Premature Infant Follow-up Network database.

INTERVENTIONS

Anti-epidemic measures, including quarantine and isolation protocols, social distancing, the closure of public spaces and restrictions on travel and gatherings during COVID-19 pandemic.

MAIN OUTCOME MEASURES

Outcomes were measured by Bayley Scales of Infant and Toddler Development Third Edition at corrected ages of 6, 12 and 24 months old. Generalised estimating equation (GEE) was applied to incorporate all measurements into a single model.

RESULTS

Among the 1939 premature infants who were enrolled, 985 developed before the pandemic, while 954 developed during the pandemic. Premature infants whose development occurred during the pandemic exhibited better cognitive composite at the corrected age of 6 months (beta=2.358; 95% CI, 1.07 to 3.65; p<0.001), and motor composite at corrected ages of 12 months (beta=1.680; 95% CI, 0.34 to 3.02; p=0.014). GEE analysis showed that infants who had grown during the pandemic achieved higher scores in cognitive composite (beta=1.416; 95% CI, 0.36 to 2.48; p=0.009).

CONCLUSION

Premature infants in Taiwan who developed during the pandemic showed better neurodevelopment compared with those born before the pandemic.

Prognostic factors for poor outcomes in patients with severe COVID-19 treated with remdesivir plus dexamethasone in Taiwan

BACKGROUND

Coronavirus disease-2019 (COVID-19) remains a global public health concern, and remdesivir plus dexamethasone combination therapy is suggested for patients with severe disease. However, the factors associated with poor outcomes in these patients remain unclear. We identified the factors associated with poor outcomes in Taiwanese patients with severe COVID-19 treated with remdesivir plus dexamethasone.

METHODS

Adults with severe COVID-19 (oxygen saturation <94% on room air or requiring supplemental oxygen) treated with remdesivir and dexamethasone were identified between 1 May and 31 July 2021. The main outcomes were 14-day non-recovery, 28-day mortality, and progression to respiratory failure requiring invasive mechanical ventilation or death in initially non-ventilated patients. The prognostic factors associated with poor outcomes were analyzed by multivariate logistic regression and Cox regression.

RESULTS

Of the 110 patients treated with remdesivir and dexamethasone, 57 (51.8%) recovered within 14 days and 6 (5.5%) died within 28 days. Of the 89 initially non-ventilated patients, 12 (13.5%) progressed to respiratory failure or death. Charlson Comorbidity Index, SOFA score, and admission to remdesivir treatment interval were associated with 14-day non-recovery. C-reactive protein level was associated with 28-day mortality. Pneumonia Severity Index and admission to remdesivir treatment interval were associated with progression to respiratory failure requiring invasive mechanical ventilation or death in initially non-ventilated patients.

CONCLUSION

High disease severity on admission and delayed initiation of remdesivir therapy were associated with poor outcomes in COVID-19 patients treated with remdesivir and dexamethasone.

Dengue virus serotype did not contribute to clinical severity or mortality in Taiwan's largest dengue outbreak in 2015

BACKGROUND

Dengue virus serotype 2 (DENV-2) was the major serotype in the 2015 dengue outbreak in Taiwan, while DENV-1 and DENV-3 were dominant between 2005 and 2014. We aimed to investigate whether DENV-2 contributed to disease severity and mortality in the outbreak in Kaohsiung city, Taiwan.

METHODS

We collected serum samples from dengue patients to detect the presence of DENV and determine the serotypes by using quantitative reverse transcription-polymerase chain reaction. Our cohorts comprised 105 DENV-1-infected cases and 1,550 DENV-2-infected cases. Demographic data, DENV serotype, and comorbidities were covariates for univariate and multivariate analyses to explore the association with severity and mortality.

RESULTS

The results suggested that DENV-1 persisted and circulated, while DENV-2 was dominant during the dengue outbreak that occurred between September and December 2015. However, DENV-2 did not directly contribute to either severity or mortality. Aged patients and patients with diabetes mellitus (DM) or moderate to severe chronic kidney disease (CKD) had a higher risk of developing severe dengue. The mortality of dengue patients was related to a higher Charlson comorbidity index score and severe dengue. Among DENV-2-infected patients and older patients, preexisting anti-dengue IgG, DM, and moderate to severe CKD were associated with severe dengue. Moreover, female sex and severe dengue were associated with a significantly higher risk of death.

CONCLUSIONS

Our findings highlight the importance of timely serological testing in elderly patients to identify potential secondary infections and focus on the meticulous management of elderly patients with DM or moderate to severe CKD to reduce dengue-related death.

Epidemiology and analysis of SARS-CoV-2 Omicron subvariants BA.1 and 2 in Taiwan

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first detected in October 2021, possessed many mutations compared to previous variants. We aimed to identify and analyze SARS-CoV-2 Omicron subvariants among coronavirus disease 2019 (COVID-19) patients between January 2022 and September 2022 in Taiwan. The results revealed that BA.2.3.7, featuring K97E and G1251V in the spike protein compared with BA.2, emerged in March 2022 and persistently dominated between April 2022 and August 2022, resulting in the largest COVID-19 outbreak since 2020. The accumulation of amino acid (AA) variations, mainly AA substitution, in the spike protein was accompanied by increasing severity in Omicron-related COVID-19 between April 2022 and January 2023. Older patients were more likely to have severe COVID-19, and comorbidity was a risk factor for COVID-19-related mortality. The accumulated case fatality rate (CFR) dropped drastically after Omicron variants, mainly BA.2.3.7, entered Taiwan after April 2022, and the CFR was 0.16% in Taiwan, which was lower than that worldwide (0.31%) between April 2021 and January 2023. The relatively low CFR in Omicron-related COVID-19 patients can be attributed to adjustments to public health policies, promotion of vaccination programs, effective antiviral drugs, and the lower severity of the Omicron variant.

The identification and phylogenetic analysis of SARS-CoV-2 delta variants in Taiwan

In Taiwan, coronavirus disease 2019 (COVID-19) involving the delta variant occurred after that involving the alpha variant in 2021. In this study, we aimed to analyze the Delta variant. A total of 318 patients in Taiwan infected with delta variants were identified. The case fatality rate (CFR) of patients infected with delta variants was 0.94% in Taiwan compared with that of those infected with alpha variants (5.95%). The possible reasons for the low CFR might be hybrid immunity due to infection and rapid promotion of the COVID-19 vaccination program during the alpha variant outbreak. We identified three 21J delta variants. Two long gene deletions were detected in these severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) isolates: ORF7aΔ91 in KMUH-8 and SpikeΔ30 in KMUH-9. Protein structure prediction indicates that ORF7aΔ91 results in malfunction of NS7a as an interferon antagonist and that SpikeΔ30 results in a truncated spike protein (N679-A688del), resulting in a lower infection rate compared with the delta variant without these deletions. The impact of these two deletions on SARS-CoV-2-associated pathogenesis deserves further investigation. Delta variants still exist in many regions in the omicron era, and the backbone of the delta variant genome possibly spread worldwide in the form of delta-omicron hybrids (deltacron; e.g., XBC.1 and XAY.2), which casts a potential threat to public health. Our study further highlighted the importance of more understanding of the delta variants.

Analysis of the effect of cytomegalovirus infection in clinical outcomes and prolonged duration of SARS-CoV-2 shedding in intensive care unit patients with COVID-19 pneumonia

BACKGROUND

Coronavirus disease 2019 (COVID-19) is a global outbreak disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Cytomegalovirus (CMV) infection can occur in critical COVID-19 patients and is associated with adverse clinical outcomes.

OBJECTIVE

The aim of this study was to explore the clinical characteristics and outcome of CMV infection in critical COVID-19 patients.

DESIGN

This was a retrospective cohort study.

METHODS

From May to September 2021, SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR)-confirmed COVID-19 patients with intensive care unit (ICU) admission were enrolled. CMV infection was confirmed by PCR. Baseline characteristics, critical illness data and clinical outcomes were recorded and analyzed.

RESULTS

Seventy-two RT-PCR-confirmed COVID-19 patients with ICU admission were included during the study period and 48 (66.7%) patients required mechanical ventilation (MV). Overall, in-hospital mortality was 19.4%. Twenty-one (29.2%) patients developed CMV infection. Patients with CMV infection had a higher likelihood of diabetes, higher lactate dehydrogenase and lactate levels, and higher proportions of MV, anticoagulant, and steroid use. Patients with CMV infection were associated with longer duration of SARS-CoV-2 shedding, longer ICU and hospital stay, and fewer ventilator-free days. The independent risk factor for development of CMV infection was a higher accumulative steroid dose.

CONCLUSION

CMV infection adversely impacted the outcomes of critical COVID-19 patients, resulting in longer ICU stays, longer mechanical ventilation uses and prolonged shedding of SARS-CoV-2.

Comparison of clinical outcomes in critically ill COVID-19 patients on mechanical ventilation with nosocomial pneumonia between Alpha and Omicron variants

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a pandemic that has resulted in millions of deaths worldwide. Critically ill COVID-19 patients who require intubation and develop nosocomial pneumonia, commonly caused by gram-negative bacilli, have a higher mortality rate than those without nosocomial pneumonia.

OBJECTIVES

The aim of this study is to compare the clinical characteristics and outcomes and associated risk factors of Alpha and Omicron SARS-CoV-2 variants in critically ill patients on mechanical ventilation (MV) with nosocomial pneumonia.

DESIGN

This is a retrospective single-center cohort study.

METHODS

This observational study was conducted at Taipei Veterans General Hospital, Taiwan from May 2021 to September 2022. Critically ill patients who had confirmed SARS-CoV-2 infection and intubated on a MV with bacterial pneumonia were enrolled. Demographic data, laboratory results, and treatment information were collected and analyzed. In addition, clinical outcomes among different SARS-CoV-2 variants were examined.

RESULTS

This study included 94 critically ill COVID-19 patients who required intubation and intensive care unit (ICU) admission. The Alpha group had a longer duration of SARS-CoV-2 viral shedding, MV days, and ICU stay, while the Omicron group had older age, more comorbidities, higher APACHE II scores, and higher in-hospital mortality (47.0% versus 25.0%, p = 0.047). However, independent risk factors for in-hospital mortality included malignancy, lower serum albumin levels, and lack of Remdesivir treatment, except for the SARS-CoV-2 variant.

CONCLUSION

Our study discovered a higher in-hospital mortality rate in severe COVID-19 patients with MV and secondary pneumonia infected with the Omicron variant compared to the Alpha variant; however, real independent risk factors for in-hospital mortality are malignancy, lower serum albumin level, and lack of Remdesivir treatment.

Rhabdomyolysis in Pediatric Patients with SARS-CoV-2 Infection

Background: Rhabdomyolysis is a rare but severe complication in adult patients with Coronavirus disease 2019 (COVID-19), which can result in acute kidney injury and death; however, it is rarely reported in pediatric patients. Methods: In this study, we retrospectively reviewed the clinical features and outcomes of rhabdomyolysis in pediatric patients aged 0–18 years with COVID-19 who were hospitalized at Taipei Tzu Chi Hospital, an epicenter of COVID-19 in northern Taiwan. Results: We treated eight patients with rhabdomyolysis during the omicron variant-Severe acute respiratory syndrome coronavirus 2 (omicron variant-SARS-CoV-2) community outbreak and none during the alpha variant endemic. These eight patients shared stereotypical presentations, including the presence of bilateral calf pain after defervescence. The creatinine kinase (CK) levels were between 1346 and 6937 U/L on admission, and clinical course was uneventful after aggressive saline hydration. Conclusion: Rhabdomyolysis is not a rare complication in pediatric patients with the omicron-SARS-CoV-2 infection, and reassurance of a good prognosis is important to alleviate family anxiety.