Clustering and multiple-spreading events of nosocomial severe acute respiratory syndrome coronavirus 2 infection

Whole-genome sequencing to investigate transmission of SARS-CoV-2 in the acute healthcare setting: a systematic review

BACKGROUND

Whole-genome sequencing (WGS) has been used widely to elucidate transmission of SARS-CoV-2 in acute healthcare settings, and to guide infection, prevention, and control (IPC) responses.

AIM

To systematically appraise available literature, published between January 1st, 2020 and June 30th, 2022, describing the implementation of WGS in acute healthcare settings to characterize nosocomial SARS-CoV-2 transmission.

METHODS

Searches of the PubMed, Embase, Ovid MEDLINE, EBSCO MEDLINE, and Cochrane Library databases identified studies in English reporting the use of WGS to investigate SARS-CoV-2 transmission in acute healthcare environments. Publications involved data collected up to December 31st, 2021, and findings were reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement.

FINDINGS

In all, 3088 non-duplicate records were retrieved; 97 met inclusion criteria, involving 62 outbreak analyses and 35 genomic surveillance studies. No publications from low-income countries were identified. In 87/97 (90%), WGS supported hypotheses for nosocomial transmission, while in 46 out of 97 (47%) suspected transmission events were excluded. An IPC intervention was attributed to the use of WGS in 18 out of 97 (18%); however, only three (3%) studies reported turnaround times ≤7 days facilitating near real-time IPC action, and none reported an impact on the incidence of nosocomial COVID-19 attributable to WGS.

CONCLUSION

WGS can elucidate transmission of SARS-CoV-2 in acute healthcare settings to enhance epidemiological investigations. However, evidence was not identified to support sequencing as an intervention to reduce the incidence of SARS-CoV-2 in hospital or to alter the trajectory of active outbreaks.

Comparison of secondary attack rate and viable virus shedding between patients with SARS-CoV-2 Delta and Omicron variants: A prospective cohort study

There are limited data comparing the transmission rates and kinetics of viable virus shedding of the Omicron variant to those of the Delta variant. We compared these rates in hospitalized patients infected with Delta and Omicron variants. We prospectively enrolled adult patients with COVID-19 admitted to a tertiary care hospital in South Korea between September 2021 and May 2022. Secondary attack rates were calculated by epidemiologic investigation, and daily saliva samples were collected to evaluate viral shedding kinetics. Genomic and subgenomic SARS-CoV-2 RNA was measured by PCR, and virus culture was performed from daily saliva samples. A total of 88 patients with COVID-19 who agreed to daily sampling and were interviewed, were included. Of the 88 patients, 48 (59%) were infected with Delta, and 34 (41%) with Omicron; a further 5 patients gave undetectable or inconclusive RNA PCR results and 1 was suspected of being coinfected with both variants. Omicron group had a higher secondary attack rate (31% [38/124] vs. 7% [34/456], p < 0.001). Survival analysis revealed that shorter viable virus shedding period was observed in Omicron variant compared with Delta variant (median 4, IQR [1-7], vs. 8.5 days, IQR [5-12 days], p < 0.001). Multivariable analysis revealed that moderate-to-critical disease severity (HR: 1.96), and immunocompromised status (HR: 2.17) were independent predictors of prolonged viral shedding, whereas completion of initial vaccine series or first booster-vaccinated status (HR: 0.49), and Omicron infection (HR: 0.44) were independently associated with shorter viable virus shedding. Patients with Omicron infections had higher transmission rates but shorter periods of transmissible virus shedding than those with Delta infections.

Control of an outbreak of COVID-19 at a tertiary hospital in Taiwan

BACKGROUND

Coronavirus disease 2019 (COVID-19) has circulated in Taiwan since late 2019. Healthcare facilities are vulnerable to COVID-19 outbreaks due to clusters of symptomatic patients and susceptible hosts. Prompt control of outbreaks is crucial. In May 2021, an index case of COVID-19 was detected at Far Eastern Memorial Hospital (FEMH) in New Taipei City, Taiwan, 3 days after hospital admission, spreading to 26 patients and staff. Herein we evaluate control of this COVID-1 outbreak.

METHODS

To control the outbreak, the index case ward was closed, and large-scale COVID-19 testing (RT PCR) was performed for all inpatients, caregivers and healthcare workers (HCWs). All exposed persons were quarantined. Thorough investigation was conducted to analyze the transmission route.

RESULTS

The outbreak comprised 12 patients, 12 caregivers, and 3 HCWs. Seven patients expired and the remaining cases recovered. Overall, 456 patients/caregivers and 169 HCWs were quarantined. Analysis showed that longer exposure time was the main cause of HCW infection; all three infected HCWs were primary-care nurses related to the index case. To diminish hidden cases, all hospitalized patients/caregivers received PCR examinations and all results were negative. Thereafter, all patients/caregivers routinely received PCR examination on admission. Hospital-wide PCR screening for HCW detected 4 positive HCWs unrelated to this outbreak, and a second-round of screening detected 2 more cases, with no additional cases during the following 6 months.

CONCLUSION

Prompt infection control measures and large-scale PCR screening can control a COVID-19 outbreak within 2 weeks. Exposure time is the major risk factor for HCW infection.

Usefulness of universal SARS-CoV-2 PCR testing for inpatients and their caregivers during the omicron era

Background

Since January 2022, the Omicron variant has become the dominant strain in South Korea, and COVID-19 cases among hospitalized patients and their guardians or caregivers have increased. We evaluated the usefulness of universal periodic screening for SARS-CoV-2 in patients and resident caregivers in a South Korean tertiary care hospital.

Methods

We evaluated the reason for testing in COVID-19 confirmed patients and resident caregivers during their hospitalization from March 3 to 31, 2022. The rate of positive PCR universal testing in hospital (or residency) (HD) on days 3 and 7 in asymptomatic patients and caregivers were evaluated. The test for SARS-CoV-2 was done by RT-PCR.

Results

During the study period, 677 patients were diagnosed with COVID-19. The reasons for testing were the symptoms (226 (33%)), pre-admission test (183 (27%)), exposure to COVID-19 (124 (18%)), universal testing on HD 3 (94 (14%)), and that on HD 7 (34 (5%)). Caregivers (n = 340) were tested during their residency due to exposure to COVID-19 cases, 103 (30%); universal testing on HD 3, 90 (26%); symptom development, 46 (14%); pre-stay, 39 (11%); and universal testing on HD 7, 29 (9%). The positive test rates of inpatients and caregivers on HD 3 and HD 7 were as follows: 1.4% (93/6553) and 2.1% (55/2646) in inpatients, and 1.3% (79/5989) and 1.7% (35/2106) in caregivers, respectively.

Conclusions

Universal testing, regardless of symptom or epidemiologic link, is useful for detecting pre-symptomatic and asymptomatic COVID-19 cases among hospitalized patients and caregivers and preventing a nosocomial outbreak during the Omicron era.

Evaluation of In-Hospital Cluster of COVID-19 Associated With a Patient With Prolonged Viral Shedding Using Whole-Genome Sequencing

BACKGROUND

Patients with hematologic malignancies may produce replication-competent virus beyond 20 days of SARS-CoV-2 infection. However, data regarding the transmission of SARS-CoV-2 from patients with prolonged viral shedding is limited.

METHODS

In May 2022, four additional cases of COVID-19 were reported in a hematologic ward at a tertiary care hospital in South Korea, after an 8-week isolation of a patient with prolonged viral shedding. We performed whole-genome sequencing (WGS) of SARS-CoV-2 to evaluate the possibility of post-isolation transmission from this prolonged viral shedding.

RESULTS

A patient (case 1) with acute myeloid leukemia was released from isolation 54 days after the diagnosis of COVID-19 based on rising Ct value of up to 29.3, and moved to a six-patient room. On days 10 and 11 post-isolation, his doctor (case 2) and 2 patients who were his roommates (case 3, 4) had positive SARS-CoV-2 PCR results. Additionally, 16 days post-isolation, another patient (case 5) in a remote room had positive SARS-CoV-2 PCR result. All the three patients were hospitalized for ≥ 14 days when they were diagnosed with SARS-CoV-2 infection. Except for case 3, the remaining 4 cases were available for WGS, which revealed that case 1 exhibited a 7 nucleotides difference in comparison to cases 4 and 5 and case 2 displayed a 20 nucleotides difference compared with case 1, while sequences of cases 4 and 5 were identical.

CONCLUSIONS

Despite the possibility of transmission from the patient with prolonged viral shedding, no evidence of the transmission of SARS-CoV-2 from the patient with prolonged positive RT-PCR using WGS was found.

A SARS-CoV-2 outbreak associated with vaccine breakthrough in an acute care hospital

BACKGROUND

We aimed to analyze an outbreak caused by a vaccine breakthrough infection in a hospital with an active infection control program where 91.9% of health care workers were vaccinated.

METHODS

We investigated a SARS-CoV-2 outbreak between September 9 and October 2, 2021, in a referral teaching hospital in Korea. We retrospectively collected data on demographics, vaccination history, transmission, and clinical features of confirmed coronavirus disease 2019 (COVID-19) in patients, health care workers, and caregivers.

RESULTS

During the outbreak, 94 individuals tested positive for SARS-CoV-2 using reverse transcription-polymerase chain reaction testing. There were infections in 61 health care workers, 18 patients, and 15 caregivers; 74.5% (70/94) were vaccine breakthrough infections. Most transmissions appeared to be caused by three index cases, which accounted for 86.2% (81/94) of transmissions. Forty-seven (58.0%, 47/81) cases were associated with the hospital staff cafeteria and offices located in the basement. Among health care workers and caregivers, only one required oxygen supplementation. In contrast, among patients, there were four fatal cases (22.2%, 4/18), 3 of which were unvaccinated.

CONCLUSIONS

Superspreading infection among fully vaccinated individuals occurred in an acute care hospital while the delta variant was dominant. Given the potential for severe complications, as this outbreak demonstrated, preventive measures including adequate ventilation should be emphasized to minimize transmission in hospitals.

Nosocomial Outbreak by Delta Variant From a Fully Vaccinated Patient

BACKGROUND

The potential for a nosocomial outbreak of coronavirus disease 2019 (COVID-19) from a fully vaccinated individual is largely unknown.

METHODS

In October 2021, during the time when the delta variant was dominant, a nosocomial outbreak of COVID-19 occurred in two wards in a tertiary care hospital in Seoul, Korea. We performed airflow investigations and whole-genome sequencing (WGS) of the virus.

RESULTS

The index patient developed symptoms 1 day after admission, and was diagnosed with COVID-19 on day 4 post-admission. He was fully vaccinated (ChAdOx1 nCoV-19) 2 months before the diagnosis. Three inpatients and a caregiver in the same room, two inpatients in an adjacent room, two inpatients in rooms remote from the index room, and one nurse on the ward tested positive. Also, two resident doctors who stayed in an on-call room located on the same ward tested positive (although they had no close contact), as well as a caregiver who stayed on an adjacent ward, and a healthcare worker who had casual contact with this caregiver. Samples from five individuals were available for WGS, and all showed ≤ 1 single-nucleotide polymorphism difference. CCTV footage showed that the index case walked frequently in the corridors of two wards. An airflow study showed that the air from the corridor flowed into the resident on-call room, driven by an air circulator that was always turned on.

CONCLUSION

Transmission of severe acute respiratory syndrome coronavirus 2 from a fully vaccinated index occurred rapidly via the wards and on-call room. Care must be taken to not use equipment that can change the airflow.

Transmission and Infectious SARS-CoV-2 Shedding Kinetics in Vaccinated and Unvaccinated Individuals

IMPORTANCE

Data are limited on whether patients with breakthrough COVID-19 infection have the potential to significantly contribute to the spread of SARS-CoV-2.

OBJECTIVE

To compare the secondary attack rate and infectious viral shedding kinetics of SARS-CoV-2 between fully vaccinated individuals (breakthrough infection group) and partially or unvaccinated individuals (nonbreakthrough infection group).

DESIGN, SETTING, AND PARTICIPANTS

This cohort study assessed secondary transmission by analyzing the epidemiologic data of health care workers, inpatients, and caregivers diagnosed with COVID-19 during hospitalization or residence in a tertiary care hospital between March 1, 2020, and November 6, 2021. To evaluate viral shedding kinetics, the genomic RNA of SARS-CoV-2 was measured using polymerase chain reaction and performed virus culture from daily saliva samples of individuals with mild COVID-19 infected with the Delta variant who were isolated in a community facility in Seoul, South Korea, between July 20 and August 20, 2021.

EXPOSURES

COVID-19 vaccination.

MAIN OUTCOMES AND MEASURES

The secondary attack rate and infectious viral shedding kinetics according to COVID-19 vaccination status.

RESULTS

A total of 173 individuals (median [IQR] age, 47 [32-59] years; 100 female [58%]) with COVID-19 were included in the secondary transmission study, of whom 50 (29%) had a breakthrough infection. Secondary transmission was significantly less common in the breakthrough infection group than in the nonbreakthrough infection group (3 of 43 [7%] vs 29 of 110 [26%]; P = .008). In the viral shedding kinetics study, 45 patients (median age, 37 years [IQR, 25-49 years]; 14 female [31%]) infected with the Delta variant were included, of whom 6 (13%) were fully vaccinated and 39 (87%) were partially or unvaccinated. Although the initial genomic viral load was comparable between the 2 groups, viable virus in cell culture was detected for a notably longer duration in partially vaccinated (8 days after symptom onset) or unvaccinated (10 days after symptom onset) individuals compared with fully vaccinated individuals (4 days after symptom onset).

CONCLUSIONS AND RELEVANCE

In this cohort study, although the initial genomic viral load was similar between vaccinated and unvaccinated individuals, fully vaccinated individuals had a shorter duration of viable viral shedding and a lower secondary attack rate than partially vaccinated or unvaccinated individuals. Data from this study provide important evidence that despite the possibility of breakthrough infections, COVID-19 vaccinations remain critically useful for controlling the spread of SARS-CoV-2.

Risk of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Among Healthcare Workers Dining in Hospital Staff Cafeterias

BACKGROUND

Preventive measures are needed to reduce the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among healthcare workers (HCWs). Notably, hospital staff are usually exposed when they are unmasked. There are limited data on the risk of transmission during mealtimes at hospital staff cafeterias. We aimed to evaluate the risk of transmission in cafeterias.

METHODS

From January 2020 through September 2021, we analyzed the risk of SARS-CoV-2 transmission through closed-circuit television and radio-frequency identification tracking and follow-up testing when 33 HCWs, who were eventually diagnosed as coronavirus disease 2019 (COVID-19), ate in staff cafeterias during the infectious period. The seats were arranged so the HCWs would sit on either side without facing each other. There were no plastic barriers installed, and HCWs were encouraged not to talk during meals.

RESULTS

Three of the 119 individuals who ate at seats next (about 30 cm) to index during the period of transmission and underwent follow-up SARS-CoV-2 polymerase chain reaction tests were diagnosed with COVID-19 (2.5%; 95% confidence interval, 0.5-7.4%). Among the 98 HCWs who were investigated about talking during meals, there was a higher attack rate among those who spoke with each other than among those who did not (12.5% [3/24] vs. 0% [0/74], P = 0.013).

CONCLUSION

The risk of transmission in a hospital's employee cafeterias is not high with side-by-side seating, especially in the absence of conversation.

Experience of a COVID-19 outbreak response in a general hospital in Gyeonggi Province, Korea

OBJECTIVES

Coronavirus disease 2019 (COVID-19) outbreaks in general hospitals are particularly risky because they not only overburden the regional healthcare delivery system, but also increase the possibility of community transmission. This study shares an experience of a COVID-19 outbreak response in a general hospital in Gyeonggi Province, Korea.

METHODS

Since the first COVID-19 confirmed case was recognized in Hospital A on March 29, 2020, the Immediate Response Team of Gyeonggi Province and Korea Disease Control and Prevention Agency devised a plan to conduct an epidemiological investigation and minimize the paralysis of hospital functions. Apart from the epidemiological investigation, a risk assessment of the hospital and management of contacts, including patients and workers, were also undertaken.

RESULTS

In total, 72 confirmed cases were identified, including 26 hospitalized patients, 16 healthcare personnel, 7 visitors, and 22 cases identified externally. The majority of the confirmed cases were exposed in Ward B or were contacts of people exposed in Ward A (58.3% of 72 cases). Among healthcare personnel, caregivers were found to be the most vulnerable to COVID-19 in this outbreak.

CONCLUSIONS

Preparation for all possible situations in medical facilities is important because it is difficult to find alternative resources. The findings of this study provide information on controlling the further transmission of COVID-19 and furnish evidence of the importance of ordinary management skills to be prepared for COVID-19.