Results from a systematic programme of evaluating COVID-19 reinfection cases in the early phase of the pandemic, Singapore.

OBJECTIVES: The objectives of this study were to describe the coronavirus disease caused by SARS-CoV-2 (COVID-19) reinfection evaluation algorithm used in the early phase of the pandemic in Singapore and analyze the clinical and laboratory characteristics of the cases evaluated. METHODS: We performed a retrospective case-control analysis including all COVID-19 cases evaluated for possible reinfection under the local COVID-19 reinfection evaluation programme between 1 June 2020-30 June 2021. Whole genome sequencing (WGS) was used as confirmatory testing. We compared all reinfection ("RI") cases against those who were evaluated but eventually assessed not to be reinfection ("non-RI"). RESULTS: There were 74 possible reinfection cases evaluated through the programme, of which 32 were subsequently classified as RI. There was strong statistical evidence that RI cases had a longer interval between 1st and 2nd episode (mean 297 days; 95%-confidence interval (CI) 267-327) compared to non-RI cases (mean 186 days; 95%-CI 144-228). The cycle threshold (Ct) value of initial polymerase chain rection (PCR) at 2nd episode was also found to be significantly lower in RI cases (mean 23; 95%-CI 20-26) compared to non-RI cases (mean 34; 95%-CI 32-36). There was no significant difference in the proportion of individuals who had fever, acute respiratory symptoms or asymptomatic in both groups. Delta and beta variants were most commonly identified from WGS and provide indication of re-infection as these were not 'wild-type' and were not circulating during the time period of the index infection. CONCLUSIONS: Using a combination of serologic, microbiologic and genomic criteria to evaluate possible reinfection cases is useful and can provide a framework for evaluation that may be modified for future similar situations.

Comparison of the clinical features, viral shedding and immune response in vaccine breakthrough infection by the Omicron and Delta variants (preprint)

BackgroundOn 26 November 2021, the World Health Organization designated the B.1.1.529 lineage of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as the fifth variant of concern, Omicron. Infections have quickly spread worldwide, but understanding of the viral dynamics and the cytokine and cellular immunological response during infection remain limited.MethodsDetailed patient-level data from 174 age-matched patients with sequence confirmed Omicron or Delta infection admitted to the National Centre for Infectious Diseases, Singapore were analyzed in an observational cohort study. Peripheral blood samples for measurement of SARS-CoV-2 immunological parameters were obtained from a subset. Respiratory samples were collected for viral cultures and correlated to corresponding PCR cycle threshold (Ct) values. ResultsOmicron and Delta variant infections in this hospitalized cohort were mild with only 3 (3%) and 14 (16%) developing pneumonia respectively. Omicron infections were more likely to present with sore throat (46.0 vs x23.0%, p=0.005). Neutrophil counts and C-reactive protein (CRP) were significantly lower among the Omicron cohort (Median neutrophil 2.95 [IQR 2.16 – 3.96] vs 4.60 [IQR 3.76 – 6.10] x 109/L , p<0.001; Median CRP 5.7 [IQR 2.0 – 10.0] vs 12.0 [IQR 6.1 – 22.0] mg/L, p<0.001). Trough polymerase chain reaction (PCR) cycle threshold (Ct) values were significantly higher with Omicron infection (17.6 [IQR 16.3 – 19.3] vs 14.9 [IQR 13.9 – 19.0], p=0.001). The pattern and rate of rise in Ct values was similar between Omicron and Delta. At the time of infection, Omicron infected patients had lower levels of pro-inflammatory cytokines Vaccine breakthrough infections with the Omicron variant had a low concentration of proinflammatory cytokines, chemokines, and growth factors at the acute phase of infection, but a more robust IFN-γ response. Less dysregulated immune cell profiles were also observed, including a lower immature neutrophil cell count in Omicron breakthrough casesConclusionsOmicron infections resulted in mild vaccine breakthrough illness in the majority of patients. Compared with Delta, Omicron infections were more frequently associated with upper respiratory tract infections, had lower viral loads, lower levels of pro-inflammatory cytokines and less dysregulated immune cell profiles.

COVID-19 Quarantine is a Risk Factor for Poor Pregnancy Outcomes in GDM Patients: A Retrospective Study (preprint)

Aims: : T his study was to evaluate the effects of the home quarantine on pregnancy outcomes of gestational diabetes mellitus (GDM) patients during the COVID-19 outbreak. Methods: : Thecomplete electronic medical records of GDM patients with home quarantine history were collected and classified into the home quarantine group from 24 February 2020 to 24 November 2020. The same period of GDM patients without home quarantine historywas included in the control group from 2018 and 2019. Results: : A total of 1358 GDM patients were included in the analysis, including 484 in 2018, 468 in 2019, and 406 in 2020. GDM patients with home quarantine in 2020 had higher glycemic levels and worse pregnancy outcomes than 2018 and 2019, including higher cesarean section rate,lower Apgar scores, and higher incidence of macrosomia and nuchal cord. More importantly, the second trimester of home quarantine had brought a broader impactto pregnant women and fetuses. Conclusion: Home quarantine has aggravated the condition of GDM pregnant women and brought more adverse pregnancy outcomes during the COVID-19 outbreak. Therefore, we suggested that governments and hospitals should strengthen lifestyle guidance, glucose management, and antenatal care for GDM patients with home quarantine during public health emergencies.

Virological and serological kinetics of SARS-CoV-2 Delta variant vaccine-breakthrough infections: a multi-center cohort study (preprint)

Objectives Highly effective vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed but variants of concerns (VOCs) with mutations in the spike protein are worrisome, especially B.1.617.2 (Delta) which has rapidly spread across the world. We aim to study if vaccination alters virological and serological kinetics in breakthrough infections. Methods We conducted a multi-centre retrospective cohort study of patients in Singapore who had received a licensed mRNA vaccine and been admitted to hospital with B.1.617.2 SARS-CoV-2 infection. We compared the clinical features, virological and serological kinetics (anti-nucleocapsid, anti-spike and surrogate virus neutralization titres) between fully vaccinated and unvaccinated individuals. Results Of 218 individuals with B.1.617.2 infection, 84 had received a mRNA vaccine of which 71 were fully vaccinated, 130 were unvaccinated and 4 received a non-mRNA. Despite significantly older age in the vaccine breakthrough group, the odds of severe COVID-19 requiring oxygen supplementation was significantly lower following vaccination (adjusted odds ratio 0.07 95%CI: 0.015-0.335, p=0.001). PCR cycle threshold (Ct) values were similar between both vaccinated and unvaccinated groups at diagnosis, but viral loads decreased faster in vaccinated individuals. Early, robust boosting of anti-spike protein antibodies was observed in vaccinated patients, however, these titers were significantly lower against B.1.617.2 as compared with the wildtype vaccine strain. Conclusion The mRNA vaccines are highly effective at preventing symptomatic and severe COVID-19 associated with B.1.617.2 infection. Vaccination is associated with faster decline in viral RNA load and a robust serological response. Vaccination remains a key strategy for control of COVID-19 pandemic.

Clinical and Virological Features of SARS-CoV-2 Variants of Concern: A Retrospective Cohort Study Comparing B.1.1.7 (Alpha), B.1.315 (Beta), and B.1.617.2 (Delta) (preprint)

Background: The impact of SARS-CoV-2 variants of concern (VOCs) on disease severity is unclear. In this retrospective cohort study, we compared outcomes of patients infected with B.1.1.7, B.1.351, and B.1.617.2 with those with wild-type strains from early 2020.Methods: National surveillance data from 1-January-2021 to 22-May-2021 were obtained from the Ministry of Health, and outcomes in relation to VOC were explored. Detailed patient level data from all SARS-CoV-2 patients with VOC infection admitted to our centre between 20-December-2020 and 12-May-2021 were analysed. Outcomes were compared with a cohort of 846 patients admitted January-April 2020.Findings: There were 838 VOC infections in Singapore in the study period. After adjusting for age and gender, B.1.617.2 infection was associated with higher odds of oxygen requirement, ICU admission, or death (adjusted odds ratio (aOR) 4·90, [95% CI 1·43-30·78]. 157 patients with VOCs were admitted to our centre. After adjusting for age, gender, comorbidities, and vaccination, aOR for pneumonia with B.1.617.2 was 1·88 [95% CI 0·95-3·76]) compared with wild-type. B.1.617.2 was associated with significantly lower PCR Ct values and significantly longer duration of Ct value ≤30 (estimated median duration 18 days for B.1.617.2, 13 days for wild-type). Vaccine breakthrough cases were less severe.Interpretation: There was a signal toward increased severity associated with B.1.617.2. The association of B.1.617.2 with lower Ct value and longer viral shedding provides a potential mechanism for increased transmissibility. These findings provide a strong impetus for the rapid implementation of vaccination programmes.Funding Information: National Medical Research Council grants COVID19RF-001 and COVID19RF-008.Declaration of Interests: BEY reports personal fees from Roche and Sanofi, outside the submitted work. All other authors declare no competing interests.Ethics Approval Statement: Informed consent for retrospective data collection was waived as approved by the institutional review board (NHG-DSRB reference number 2020/01122).

The use of methylprednisolone in COVID-19 patients: A propensity score matched retrospective cohort study.

PURPOSE: To evaluate the efficacy and safety of methylprednisolone in treating the coronavirus disease 2019 (COVID-19) patients. METHODS: A retrospective cohort study was conducted, and all COVID-19 patients were recruited who were admitted to the Yichang Third People's Hospital from February 1st to March 31st, 2020. One-to-one propensity score matching (PSM) was used for minimizing confounding effects. The primary outcome was hospital mortality, with the secondary outcomes being the time needed for a positive SARS-CoV-2 nucleic acid test to turn negative and the length of hospital stay. RESULTS: Totaling 367 patients with COVID-19 hospitalized at the Yichang Third People's Hospital were identified, of whom 276 were mild or stable COVID-19, and 67 were serious or critically ill. Among them, 255 patients were treated using methylprednisolone, and 188 did not receive any corticosteroid-related treatment. After PSM, no statistically significant difference was found in the baseline characteristics between the two groups. Regarding the outcomes, there also were no statistically significant difference between the two groups. Patients without the use of methylprednisolone were more quickly to obtain negative results of their nasopharyngeal swab tests of SARS-CoV-2 nucleic acid after treatment, compared to those receiving methylprednisolone. CONCLUSION: Methylprednisolone could not improve the prognosis of patients with COVID-19, and the efficacy and safety of the use of methylprednisolone in patients with COVID-19 still remain uncertain, thus the use of corticosteroids clinically in patients with COVID-19 should be with cautions.

A COVID-19 Nursing Home Cluster Linked to a Household Transmission: An Epidemiological, Clinical and Phylogenetic Investigation (preprint)

Background: Residents in nursing homes are at risk of high morbidity and mortality due to coronavirus disease 2019 (COVID-19). We report the first nursing home COVID-19 outbreak linked to a nursing staff’s household transmission through clinical, epidemiological, laboratory and phylogenetic investigations.Methods: Serial point prevalence testing was conducted among the residents and staff following identification of the index case (a symptomatic resident) with SARS-CoV-2 infection. Active contact tracing, screening of close contacts, whole genome sequencing and phylogenetic analysis were conducted to identify the source and extent of the outbreak.Results: Among the 108 residents and 56 healthcare workers (HCW) in the nursing home, 14 (13%) residents and two (3.6%) HCW were diagnosed with COVID-19, with case fatality rate of 28.6% (4/14) among the residents. Five residents were symptomatic (35.7%) and the others were asymptomatic (64.3%) before the point prevalence survey. The genomic virus typing in this nursing home outbreak was lineage B.6 which is rare among other GISAID clades globally but common regionally. Among the family contacts of the two infected healthcare workers, only one member was infected and had recent travel history.Interpretation: Nursing staffs can be a potential source of infection in nursing home. Through prompt active case finding, and infection prevention and control measures, the outbreak can be contained. Minimising community and household contacts among nursing care staffs may reduce the risk of SARS-CoV-2 introduction into nursing home.Funding: None.Conflict of Interest: The authors declared no conflict of interest.Ethical Approval: Data were collected under the Infectious Disease Act for outbreak investigation and approved by Ministry of Health, Singapore.

A COVID-19 Nursing Home Cluster Linked to a Household Transmission: An Epidemiological, Clinical and Phylogenetic Investigation (preprint)

Backgroun:d Residents in nursing homes are at risk of high morbidity and mortality due to coronavirus disease 2019 (COVID-19). We report the first nursing home COVID-19 outbreak in Singapore and its clinical, epidemiological, laboratory and phylogenetic investigations.Methods: Serial point prevalence testing was conducted among the residents and staff following identification of the index case (a symptomatic resident) with SARS-CoV-2 infection. Active contact tracing, screening of close contacts, whole genome sequencing and phylogenetic analysis were conducted to identify the source and extent of the outbreak.Results: Among the 108 residents and 56 healthcare workers (HCW) in the nursing home, 14 (13%) residents and two (3.6%) HCW were diagnosed with COVID-19, with case fatality rate of 28.6% (4/14) among the residents. Five residents were symptomatic (35.7%) and the others were asymptomatic (64.3%) before the point prevalence survey. The genomic virus typing in this nursing home outbreak was lineage B.6 which is rare among other GISAID clades globally but common regionally. Among the family contacts of the two infected healthcare workers, only one member was infected and had recent travel history.Conclusion: The COVID-19 outbreak in a nursing home in Singapore was contained through prompt epidemiological investigations, active case finding and containment, and infection prevention and control measures.Funding Statement: None.Declaration of Interests: The authors declared no conflict of interest.Ethics Approval Statement: Data were collected under the Infectious Disease Act for outbreak investigation and approved by Ministry of Health, Singapore.

Dynamic changes of liver function parameters in patients with coronavirus disease 2019: A multicenter, retrospective study (preprint)

Background: Liver injuries in patients with coronavirus disease 2019 (COVID-19) have been reported, however, the clinical role played by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is obscure.  Methods: In this multicenter, retrospective study, the parameters of liver function tests in COVID-19 inpatients were compared between various timepoints referred to SARS-CoV-2 shedding, and 3 to 7 days before first detection of viral shedding was regarded as reference baseline.Results: Totally, 70 COVID-19 inpatients were enrolled. Twenty-two (31.4%) cases had self-medications history after illness. At baseline, 10 (14.3%), 7 (10%), 9 (12.9%), 2 (2.9%), 15 (21.4%), and 4 (5.7%) patients already had abnormal rates of alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma-glutamyl transferase (GGT), alkaline phosphatase (ALP), albumin, and total bilirubin (TBIL), respectively. ALT and AST abnormal rates and levels did not show any significantly dynamic change during the full period of viral shedding (all P > 0.05). GGT abnormal rate (P = 0.008) and level (P = 0.033) significantly increased on day 10 of viral shedding. Meanwhile, no simultaneously significant increases of ALP abnormal rates and levels were observed. TBIL abnormal rates and levels significantly increased on day 1 and 5 of viral shedding (all P < 0.05). Albumin abnormal decrease rates increased and levels decreased consistently from baseline to SARS-CoV-2 clearance day (all P < 0.05). Thirteen (18.6%) patients had chronic liver diseases, two of them died. The ALT and AST abnormal rates and levels did not increase in patients with chronic liver diseases during SARS-CoV-2 shedding.Conclusions: The SARS-CoV-2 does not directly lead to elevations of ALT and AST, but may result in elevations of GGT and TBIL, the albumin decreased extraordinarily even SARS-CoV-2 shedding discontinued.

Epidemiological characteristics of respiratory viruses in patients with acute respiratory infections during 2009-2018 in southern China.

BACKGROUND: Acute respiratory infections (ARIs) remain a significant public threat with high morbidity and mortality worldwide; viruses are significant pathogens that cause ARIs. This study was conducted to better understand the epidemiological characteristics of respiratory viruses circulating in southern China. METHODS: We collected 22,680 respiratory samples from ARI patients in 18 hospitals in southern China during 2009-2018; seven common respiratory viruses including Flu, RSV, PIV, hMPV, ADV, HCoV, and HBoV were screened using in-house real-time PCR. RESULTS: Of all samples, 9760 ARI cases (9760/22680, 43.03%) tested positive for the seven common respiratory viruses. The most detected virus was Flu (14.15%), followed by RSV (10.33%) and PIV (5.43%); Flu-A, PIV3, and HCoV-OC43 were the predominant subtypes. Although most of the viruses were detected in male inpatients, Flu was more likely detected in female outpatients. Flu infection was more likely to cause URTI (upper respiratory tract infection), whereas RSV infection was more likely to cause pneumonia and bronchitis. The prevalence of Flu was particularly high in 2009. The epidemic level was found notably high in 2014-2018 for RSV, in 2016-2018 for PIV, in the summer of 2018 for ADV, in the summer of 2016 and winter of 2018 for HCoV, and in the summer of 2011 and autumn of 2018 for HBoV. The co-detection rate of the seven viruses was 4.70%; RSV, PIV, and Flu were the most commonly co-detected viruses. CONCLUSIONS: This work demonstrates the epidemiological characteristics of seven common respiratory viruses in ARI patients in southern China.