Linking sporadic hospital clusters during a community surge of the severe acute respiratory coronavirus virus 2 (SARS-CoV-2) B.1.617.2 delta variant: The utility of whole-genome sequencing.

Sporadic clusters of healthcare-associated coronavirus disease 2019 (COVID-19) occurred despite intense rostered routine surveillance and a highly vaccinated healthcare worker (HCW) population, during a community surge of the severe acute respiratory coronavirus virus 2 (SARS-CoV-2) B.1.617.2 δ (delta) variant. Genomic analysis facilitated timely cluster detection and uncovered additional linkages via HCWs moving between clinical areas and among HCWs sharing a common lunch area, enabling early intervention.

Three-Dimensional Disease Outbreak Surveillance System in a Tertiary Hospital in Singapore: A Proof of Concept

Objective To develop an electronic surveillance system that provides prompt in-depth situational infectious disease risk and linkage analysis for inpatients in a tertiary hospital. Patients and Methods All patients admitted to Singapore General Hospital (SGH), a 1900-bedded tertiary care hospital, are included in routine surveillance. The 3-Dimensional Disease Outbreak Surveillance System (3D-DOSS) was developed to spatiotemporally represent inpatient surveillance data on a "digital twin” of SGH and evaluated for performance in surveillance, contact tracing, and outbreak investigations. This study was conducted over a 12 month period (October 1, 2020 to September 30, 2021). Results The 3D-DOSS surveillance module identified an influenza cluster of 10 inpatients in November 2018, mapping retrospective data between September 2018 and December 2018. Seventy-six clusters of 2 or more linked patients with health care–associated Klebsiella pneumoniae carbapenemase–type carbapenemase-producing Enterobacteriaceae were detected in SGH in 2 years (2018 and 2019). The 3D-DOSS contact tracing module promptly identified 44 primary and 162 secondary inpatient contacts, after exposure to a health care worker with coronavirus disease 2019 in April 2021. For outbreak mapping, 24 patients with OXA-48 were mapped on October 22, 2020, using 3D-DOSS to determine their spatiotemporal distribution. Conclusion The integration of health care data and representation on a virtual hospital digital twin is a useful tool in an outbreak alert and response framework. Infectious disease surveillance systems, which are syndrome-based, that can access real-time data, and can incorporate movement networks, can potentially enhance health care–associated infection prevention and preparedness for disease X.

SG-APSIC1098: Impact of the COVID-19 pandemic on influenza vaccination uptake among healthcare workers

Objectives: Influenza vaccination is encouraged for all healthcare workers (HCWs) to reduce the risk of acquiring the infection and onward transmission to colleagues and patients during the influenza season. Thus, vaccination was introduced at Singapore General Hospital (SGH) in 2007 and has been offered to all HCWs at no cost. The HCW influenza vaccination program is conducted annually in October and biannually during years with vaccine mismatch. However, influenza vaccine uptake remained low among HCWs. We sought to determine the impact of the coronavirus disease 2019 (COVID-19) pandemic on influenza vaccine uptake among HCWs. Methods: At SGH, 2 methods of vaccine delivery are offered: centralized (1-month drop-in system during office hours) and decentralized (administered by vaccination teams in offices or ward staff in inpatient locations). In the 4-year study period between 2018 and 2021, 6 influenza vaccination exercise campaigns were conducted during 8 influenza seasons. During each exercise, ~9,000 HCWs were eligible for vaccination. Results: Prior to the COVID-19 pandemic, vaccine uptake in the Southern Hemisphere was 77.6% (6,964 of 8,977) in 2018 and 84.2% (7,296 of 8,670) in 2019. During the COVID-19 pandemic in 2020, vaccine uptake in the Southern Hemisphere increased by 10% to 94.1% (8,361 of 8,889). In the Northern Hemisphere, vaccine uptake was 79.2% (7,114 of 8,977) in 2018, and this increased by 17.9% to 97.1% (8,926 of 9,194) during the COVID-19 pandemic in 2020. During the 2021 Southern Hemisphere influenza season, no vaccination program was conducted because the risk of influenza was considered low due to the closure of international borders and the implementation of public health measures. In addition, priority was given to COVID-19 vaccination efforts. Conclusions: Increased uptake of the influenza vaccination was observed during the COVID-19 pandemic. Anxiety created by the respiratory disease pandemic and debate surrounding vaccines likely contributed to increased awareness and uptake in influenza vaccine among HCWs.

Nosocomial SARS-CoV-2 transmission in multi-bedded hospital cubicles over successive pandemic waves: Lower mortality but wider spread with Omicron despite enhanced infection-prevention measures.

BACKGROUND: Increased transmissibility of severe-acute-respiratory-syndrome-coronavirus-2(SARS-CoV-2) variants, such as the Omicron-variant, presents an infection-control challenge. We contrasted nosocomial transmission amongst hospitalized inpatients across successive pandemic waves attributed to the Delta- and Omicron variants, over a 9-month period in which enhanced-infection-prevention-measures were constantly maintained. METHODS: Enhanced-infection-prevention-measures in-place at a large tertiary hospital included universal N95-usage, routine-rostered-testing (RRT) for all inpatient/healthcare-workers (HCWs), rapid-antigen-testing (RAT) for visitors, and outbreak-investigation coupled with enhanced-surveillance (daily-testing) of exposed patients. The study-period lasted from 21st June 2021-21st March 2022. Chi-square test and multivariate-logistic-regression was utilized to identify factors associated with onward transmission and 28d-mortality amongst inpatient cases of hospital-onset COVID-19. RESULTS: During the Delta-wave, hospital-onset cases formed 2.7% (47/1727) of all COVID-19 cases requiring hospitalisation; in contrast, hospital onset-cases formed a greater proportion (17.7%, 265/1483; odds-ratio, OR = 7.78, 95%CI = 5.65-10.70) during the Omicron-wave, despite universal N95-usage and other enhanced infection-prevention measures that remained unchanged. The odds of 28d-mortality were higher during the Delta-wave compared to the Omicron-wave (27.7%, 13/47, vs. 10.6%, 28/265, adjusted-odds-ratio, aOR = 2.78, 95%CI = 1.02-7.69). Onward-transmission occurred in 21.2% (66/312) of hospital-onset cases; being on enhanced-surveillance (daily-testing) was independently associated with lower odds of onward-transmission (aOR = 0.18, 95%CI = 0.09-0.38). Costs amounted to $USD7141 per-hospital-onset COVID-19 case. CONCLUSION: A surge of hospital-onset COVID-19 cases was encountered during the Omicron-wave, despite continuation of enhanced infection-prevention measures; mortality amongst hospital-onset cases was reduced. The Omicron variant poses an infection-control challenge in contrast to Delta; surveillance is important especially in settings where infrastructural limitations make room-sharing unavoidable, despite the high risk of transmission.

Environmental contamination and evaluation of healthcare-associated SARS-CoV-2 transmission risk in temporary isolation wards during the COVID-19 pandemic.

BACKGROUND: Temporary isolation wards have been introduced to meet demands for airborne-infection-isolation-rooms (AIIRs) during the COVID-19 pandemic. Environmental sampling and outbreak investigation was conducted in temporary isolation wards converted from general wards and/or prefabricated containers, in order to evaluate the ability of such temporary isolation wards to safely manage COVID-19 cases over a period of sustained use. METHODS: Environmental sampling for SARS-CoV-2 RNA was conducted in temporary isolation ward rooms constructed from pre-fabricated containers (N = 20) or converted from normal-pressure general wards (N = 47). Whole genome sequencing (WGS) was utilized to ascertain health care-associated transmission when clusters were reported amongst HCWs working in isolation areas from July 2020 to December 2021. RESULTS: A total of 355 environmental swabs were collected; 22.4% (15/67) of patients had at least one positive environmental sample. Patients housed in temporary isolation ward rooms constructed from pre-fabricated containers (adjusted-odds-ratio, aOR = 10.46, 95% CI = 3.89-58.91, P = .008) had greater odds of detectable environmental contamination, with positive environmental samples obtained from the toilet area (60.0%, 12/20) and patient equipment, including electronic devices used for patient communication (8/20, 40.0%). A single HCW cluster was reported amongst staff working in the temporary isolation ward constructed from pre-fabricated containers; however, health care-associated transmission was deemed unlikely based on WGS and/or epidemiological investigations. CONCLUSION: Environmental contamination with SARS-CoV-2 RNA was observed in temporary isolation wards, particularly from the toilet area and smartphones used for patient communication. However, despite intensive surveillance, no healthcare-associated transmission was detected in temporary isolation wards over 18 months of prolonged usage, demonstrating their capacity for sustained use during succeeding pandemic waves.

Favorable outcomes of COVID-19 in vaccinated hematopoietic stem cell transplant recipients: A single-center experience.

INTRODUCTION: A high incidence of mortality and severe COVID-19 infection was reported in hematopoietic stem cell transplant (HSCT) recipients during the early phases of the COVID-19 pandemic; however, outcomes with subsequent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, such as the omicron variant, have yet to be reported. Additionally, rollout of COVID-19 vaccinations in subsequent pandemic waves may modify COVID-19 disease severity and mortality in this immunocompromised population. We describe COVID-19 outcomes among a highly vaccinated population of HSCT recipients at a single center during successive waves of community transmission arising from the SARS-CoV-2 delta and omicron variants. METHODS: We retrospectively reviewed medical records of all HSCT recipients at our institution who tested positive for SARS-CoV-2 from May 2021 to May 2022. Descriptive statistics were reported; the chi-square test was utilized to identify factors associated with 90-day all-cause mortality and severity of COVID-19 infection. RESULTS: Over the 1-year study period, 77 HSCT recipients at our center contracted COVID-19 (43 allogenic; 34 autologous). Twenty-six (33.8%) patients were infected with the SARS-CoV-2 delta variant, while 51 (66.2%) had the SARS-CoV-2 omicron variant. Thirty-nine (50.6%) patients required hospitalization. More than 80% had received prior COVID-19 vaccination (57.1% with two doses, 27.3% with three doses). The majority (90.9%) had mild disease; only one (1.3%) patient required mechanical ventilation. Active hematological disease at time of COVID-19 infection was associated with increased odds of mortality [odds ratio (OR) = 6.90, 95% confidence interval (CI) = 1.20-40]. The 90-day all-cause mortality was 7.8% (six patients). Infection with the omicron variant (vs. delta) was associated with less severe illness (OR = 0.05, 95% CI = 0.01-0.47) and decreased odds of mortality (OR = 0.08, 95% CI = 0.01-0.76). Being on immunosuppression (OR = 5.10, 95% CI = 1.10-23.60) and being unvaccinated at disease onset (OR = 14.76, 95% CI = 2.89-75.4) were associated with greater severity of COVID-19 infection. CONCLUSION: We observed favorable outcomes with COVID-19 infection in a cohort of vaccinated HSCT patients. The SARS-CoV-2 omicron variant was associated with both less severe illness and decreased odds of mortality. As COVID-19 moves toward endemicity, early access to treatment and encouraging vaccination uptake is crucial in mitigating the challenge of COVID-19 management among HSCT recipients. Surveillance and assessment of clinical outcomes with new SARS-CoV-2 variants also remains important in this immunocompromised population.

COVID-19 among healthcare workers of a tertiary-care hospital in Singapore

Background: Singapore General Hospital (SGH) is the largest acute tertiary-care hospital in Singapore. Healthcare workers (HCWs) are at risk of acquiring COVID-19 in both the community and workplaces. SGH has a robust exposure management process including prompt contact tracing, immediate ring fencing, lock down of affected cubicles or single room isolation for patient contacts, and home isolation orders for staff contacts of COVID-19 cases during the containment phase of the pandemic. Contacts were also placed on enhanced surveillance with PCR testing on days 1 and 4 as well as daily antigen rapid tests (ARTs) for 10 days after exposure. Here, we describe the characteristic of HCWs with COVID-19 during the third wave of the COVID-19 pandemic. Methods: This retrospective observational study included all SGH HCWs who acquired COVID-19 during the third wave (ie, the 18-week period from September 1 to December 31, 2021) of the COVID-19 pandemic. Univariate analysis was used to compare characteristics of work-associated infection (WAI) and community-acquired infection (CAI) among HCWs. Results: Among a workforce of >10,000 at SGH, 335 HCWs acquired COVID-19 during study period. CAI (exposure to known clusters or household contact) accounted for 111 HCW infections (33.1%). Also, 48 HCWs (14.3%) had a WAI (ie, acquired at their work places where there was no patient contact). Among WAsI, only 5 HCWs had hospital-acquired infection (confirmed by phylogenetic analysis). The sources of exposure for the remaining 176 HCWs were unknown. Weekly incidence of COVID-19 among HCWs was comparable to the epidemiology curve of all cases in Singapore (Fig. 1 and 2). The mean age of HCWs with COVID-19 was 39.6 years, and most were women. At the time of positive SARS-CoV-2 PCR test, 223 HCWs were symptomatic, and 67 (20.0%) of them had comorbidities. Only 16 HCWs (4.8%) required hospitalization, and all recovered fully with no mortality (Table 1). Being female was associated with community COVID-19 acquisition (OR, 4.6, P Conclusions: During the thrid wave of the COVID-19 pandemic, a higher percentage of HCWs at SGH acquired the infection from the community than from the workplace. Safe management measures, such as universal masking, social distancing, and robust exposure management processes including prompt contact tracing and environmental disinfection, can reduce the risk of COVID-19 in the hospital work environment.Funding: NoneDisclosures: None

Respiratory surveillance wards as a strategy to reduce nosocomial transmission of COVID-19 through early detection: The experience of a tertiary-care hospital in Singapore.

OBJECTIVES: Patients with COVID-19 may present with respiratory syndromes indistinguishable from those caused by common viruses. Early isolation and containment is challenging. Although screening all patients with respiratory symptoms for COVID-19 has been recommended, the practicality of such an effort has yet to be assessed. METHODS: Over a 6-week period during a SARS-CoV-2 outbreak, our institution introduced a "respiratory surveillance ward" (RSW) to segregate all patients with respiratory symptoms in designated areas, where appropriate personal protective equipment (PPE) could be utilized until SARS-CoV-2 testing was done. Patients could be transferred when SARS-CoV-2 tests were negative on 2 consecutive occasions, 24 hours apart. RESULTS: Over the study period, 1,178 patients were admitted to the RSWs. The mean length-of-stay (LOS) was 1.89 days (SD, 1.23). Among confirmed cases of pneumonia admitted to the RSW, 5 of 310 patients (1.61%) tested positive for SARS-CoV-2. This finding was comparable to the pickup rate from our isolation ward. In total, 126 HCWs were potentially exposed to these cases; however, only 3 (2.38%) required quarantine because most used appropriate PPE. In addition, 13 inpatients overlapped with the index cases during their stay in the RSW; of these 13 exposed inpatients, 1 patient subsequently developed COVID-19 after exposure. No patient-HCW transmission was detected despite intensive surveillance. CONCLUSIONS: Our institution successfully utilized the strategy of an RSW over a 6-week period to contain a cluster of COVID-19 cases and to prevent patient-HCW transmission. However, this method was resource-intensive in terms of testing and bed capacity.

Detection of viable SARS-CoV-2 in deep respiratory specimens despite negative nasopharyngeal SARS-CoV-2 RT-PCR: Occult COVID-19 as an unsuspected cause of pulmonary infiltrates in immunocompromised patients.

Background: Prolonged shedding/relapse of COVID-19 infection has been reported, particularly in patients who received anti-CD20 agents (eg. rituximab). However, cases of occult COVID-19, in which SARS-CoV-2 persistence in lung parenchyma is diagnosed despite clearance from nasopharyngeal (NP) specimens, are uncommon. Case summary: We describe two cases of occult COVID-19 in immunocompromised patients. Both patients had received rituximab previously. Both cases initially presented as ground-glass infiltrates on lung imaging; the diagnosis was originally not suspected due to repeated demonstration of negative SARS-CoV-2 from NP specimens, and alternative etiologies were originally considered. Persistence of SARS-CoV-2 in lung parenchyma, however, was demonstrated on bronchoalveolar lavage (BAL) specimens; additionally, isolation of viable SARS-CoV-2 virus and detection of SARS-CoV-2 nucleocapsid and spike-protein antigen in lung tissue on immunohistochemistry close to 3-months from primary infection strongly suggested ongoing viral persistence and replication as a driver of the lung parenchymal changes, which resolved after antiviral treatment. Discussion: Occult COVID-19 can be a cause of unexplained ground-glass infiltrates on lung imaging; negative NP samples do not rule out SARS-CoV-2 persistence and invasive sampling must be considered. The unsuspected presence of viable virus on BAL, however, highlights that procedurists perfoming aerosol-generating-procedures during an ongoing pandemic wave must also practise appropriate infection-prevention precautions to limit potential exposure.

Dengue and COVID-19: Managing Undifferentiated Febrile Illness during a "Twindemic".

BACKGROUND: During the COVID-19 pandemic, distinguishing dengue from COVID-19 in endemic areas can be difficult, as both may present as undifferentiated febrile illness. COVID-19 cases may also present with false-positive dengue serology. Hospitalisation protocols for managing undifferentiated febrile illness are essential in mitigating the risk from both COVID-19 and dengue. METHODS: At a tertiary hospital contending with COVID-19 during a dengue epidemic, a triage strategy of routine COVID-19 testing for febrile patients with viral prodromes was used. All febrile patients with viral prodromes and no epidemiologic risk for COVID-19 were first admitted to a designated ward for COVID-19 testing, from January 2020 to December 2021. RESULTS: A total of 6103 cases of COVID-19 and 1251 cases of dengue were managed at our institution, comprising a total of 3.9% (6103/155,452) and 0.8% (1251/155,452) of admissions, respectively. A surge in dengue hospitalisations in mid-2020 corresponded closely with the imposition of a community-wide lockdown. A total of 23 cases of PCR-proven COVID-19 infection with positive dengue serology were identified, of whom only two were true co-infections; both had been appropriately isolated upon admission. Average length-of-stay for dengue cases initially admitted to isolation during the pandemic was 8.35 days (S.D. = 6.53), compared with 6.91 days (S.D. = 8.61) for cases admitted outside isolation (1.44 days, 95%CI = 0.58-2.30, p = 0.001). Pre-pandemic, only 1.6% (9/580) of dengue cases were admitted initially to isolation-areas; in contrast, during the pandemic period, 66.6% (833/1251) of dengue cases were initially admitted to isolation-areas while awaiting the results of SARS-CoV-2 testing. CONCLUSIONS: During successive COVID-19 pandemic waves in a dengue-endemic country, coinfection with dengue and COVID-19 was uncommon. Routine COVID-19 testing for febrile patients with viral prodromes mitigated the potential infection-prevention risk from COVID-19 cases, albeit with an increased length-of-stay for dengue hospitalizations admitted initially to isolation.

Sporadic outbreaks of healthcare-associated COVID-19 infection in a highly-vaccinated inpatient population during a community outbreak of the B.1.617.2 variant: The role of enhanced infection-prevention measures.

Sporadic clusters of health care-associated COVID-19 infection occurred in a highly vaccinated health care-workers and patient population, over a 3-month period during ongoing community transmission of the B.1.617.2 variant. Enhanced infection-prevention measures and robust surveillance systems, including routine-rostered-testing of all inpatients and staff and usage of N95-respirators in all clinical areas, were insufficient in achieving zero health care-associated transmission. The unvaccinated and immunocompromised remain at-risk and should be prioritized for enhanced surveillance.

Utilisation of SARS-CoV-2 rapid antigen assays in screening asymptomatic hospital visitors: mitigating the risk in low-incidence settings.

Retrospective contact tracing, enabled by the use of automated visitor-management systems and digital contact tracing, together with rapid antigen detection (RAD) for SARS-CoV-2 among visitors staying ≥ 30 minutes, identified COVID-19 cases in < 0.01% (6/72 605) of hospital visitors to a large hospital campus over an 8-week study period. The potential for nosocomial transmission of SARS-CoV-2 from hospital visitors was thus very low, and could be further mitigated by universal mask-wearing among staff and visitors.