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1.
mBio ; : e0378821, 2022 Feb 08.
Article in English | MEDLINE | ID: covidwho-1673352

ABSTRACT

The severe acute respiratory coronavirus-2 (SARS-CoV-2) is the cause of the global outbreak of COVID-19. Evidence suggests that the virus is evolving to allow efficient spread through the human population, including vaccinated individuals. Here, we report a study of viral variants from surveillance of the Delaware Valley, including the city of Philadelphia, and variants infecting vaccinated subjects. We sequenced and analyzed complete viral genomes from 2621 surveillance samples from March 2020 to September 2021 and compared them to genome sequences from 159 vaccine breakthroughs. In the early spring of 2020, all detected variants were of the B.1 and closely related lineages. A mixture of lineages followed, notably including B.1.243 followed by B.1.1.7 (alpha), with other lineages present at lower levels. Later isolations were dominated by B.1.617.2 (delta) and other delta lineages; delta was the exclusive variant present by the last time sampled. To investigate whether any variants appeared preferentially in vaccine breakthroughs, we devised a model based on Bayesian autoregressive moving average logistic multinomial regression to allow rigorous comparison. This revealed that B.1.617.2 (delta) showed 3-fold enrichment in vaccine breakthrough cases (odds ratio of 3; 95% credible interval 0.89-11). Viral point substitutions could also be associated with vaccine breakthroughs, notably the N501Y substitution found in the alpha, beta and gamma variants (odds ratio 2.04; 95% credible interval of1.25-3.18). This study thus overviews viral evolution and vaccine breakthroughs in the Delaware Valley and introduces a rigorous statistical approach to interrogating enrichment of breakthrough variants against a changing background. IMPORTANCE SARS-CoV-2 vaccination is highly effective at reducing viral infection, hospitalization and death. However, vaccine breakthrough infections have been widely observed, raising the question of whether particular viral variants or viral mutations are associated with breakthrough. Here, we report analysis of 2621 surveillance isolates from people diagnosed with COVID-19 in the Delaware Valley in southeastern Pennsylvania, allowing rigorous comparison to 159 vaccine breakthrough case specimens. Our best estimate is a 3-fold enrichment for some lineages of delta among breakthroughs, and enrichment of a notable spike substitution, N501Y. We introduce statistical methods that should be widely useful for evaluating vaccine breakthroughs and other viral phenotypes.

2.
Am J Infect Control ; 50(4): 462-464, 2022 04.
Article in English | MEDLINE | ID: covidwho-1653967

ABSTRACT

We evaluated the effect of terminal cleaning on SARS-CoV-2 RNA contamination of COVID-19 isolation rooms in an acute care hospital. SARS-CoV-2 RNA was detected on 32.1% of room surfaces after cleaning; the odds of contamination increased with month. The prevalence of elevated high-touch surface contamination was lower in terminally cleaned rooms than patient-occupied rooms.


Subject(s)
COVID-19 , Disinfection , COVID-19/prevention & control , Hospitals , Humans , Patients' Rooms , RNA, Viral/genetics , SARS-CoV-2
3.
Infect Control Hosp Epidemiol ; : 1-6, 2021 Dec 27.
Article in English | MEDLINE | ID: covidwho-1627722

ABSTRACT

BACKGROUND: The spatial and temporal extent of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) environmental contamination has not been precisely defined. We sought to elucidate contamination of different surface types and how contamination changes over time. METHODS: We sampled surfaces longitudinally within COVID-19 patient rooms, performed quantitative RT-PCR for the detection of SARS-CoV-2 RNA, and modeled distance, time, and severity of illness on the probability of detecting SARS-CoV-2 using a mixed-effects binomial model. RESULTS: The probability of detecting SARS-CoV-2 RNA in a patient room did not vary with distance. However, we found that surface type predicted probability of detection, with floors and high-touch surfaces having the highest probability of detection: floors (odds ratio [OR], 67.8; 95% credible interval [CrI], 36.3-131) and high-touch elevated surfaces (OR, 7.39; 95% CrI, 4.31-13.1). Increased surface contamination was observed in room where patients required high-flow oxygen, positive airway pressure, or mechanical ventilation (OR, 1.6; 95% CrI, 1.03-2.53). The probability of elevated surface contamination decayed with prolonged hospitalization, but the probability of floor detection increased with the duration of the local pandemic wave. CONCLUSIONS: Distance from a patient's bed did not predict SARS-CoV-2 RNA deposition in patient rooms, but surface type, severity of illness, and time from local pandemic wave predicted surface deposition.

5.
Open forum infectious diseases ; 8(Suppl 1):310-310, 2021.
Article in English | EuropePMC | ID: covidwho-1565055

ABSTRACT

Background There are limited data regarding SARS-CoV-2 (SC2) environmental contamination in staff areas of healthcare settings. We performed environmental sampling of staff areas in wards where coronavirus disease 19 (COVID-19) patients received care and compared findings to surfaces within COVID-19 patient rooms. Methods The study was conducted at the Hospital of the University of Pennsylvania (Philadelphia, PA) from 9/15/20-1/26/21. Sampling of 20cm2 surfaces in staff common areas (breakroom high-touch surfaces comprising tables and microwave/refrigerator handles;bathroom surfaces comprising toilet, sink, and doorknob;and floors), nurse workstations (computer mice and floors), and COVID-19 patient rooms (high-touch surfaces comprising bedrail, computer mice/keyboards, and doorknobs;bathroom surfaces;and floors) was performed using flocked swabs one or more times per week. Specimens underwent RNA extraction and quantitative real-time polymerase chain reaction to detect the SC2 N1 region. Median comparisons were performed using Wilcoxon rank sum test. Trends in odds were evaluated using Score test. Results Proportions of surface specimens with detectable SC2 RNA are summarized in Table 1. Median copy numbers were lower among staff toilets compared to COVID-19 patient toilets (135.6 vs. 503.8 copies/specimen, p=0.02), lower among staff breakroom compared to patient room high-touch surfaces (104.3 vs. 220.3 copies/specimen, p=0.007), and similar between staff and patient room samples from sinks and floors. At nurse workstations, SC2 RNA was detected among 22/177 (12.4%) computer mouse and 147/178 (82.6%) floor samples. Odds of SC2 detection increased by study week among common area (p< 0.001) and nurse workstation samples (p< 0.001) (Figures 1 and 2). Table 1. SARS-CoV-2 (SC2) RNA detection on staff common area and coronavirus disease 19 (COVID-19) patient room surfaces at the Hospital of the University of Pennsylvania, 9/15/20-1/26/21. Figure 1. Proportion of environmental surface specimens with detectable SARS-CoV-2 RNA from a) staff common areas and b) nurse workstations of inpatient wards where coronavirus disease-19 patients received care at the Hospital of the University of Pennsylvania, 9/15/20-1/26/21. Figure 2. Proportion of environmental surface specimens with detectable SARS-CoV-2 RNA in staff common areas of inpatient wards where coronavirus disease-19 patients received care at the Hospital of the University of Pennsylvania, 9/15/20-1/26/21, by surface type: a) staff breakroom surfaces, b) staff bathroom surfaces, c) staff common area floors. Conclusion A low prevalence of detectable SC2 RNA was observed among staff area high-touch surfaces;however, the likelihood of detection increased over time. Environmental SC2 RNA detection may reflect primary contamination from infected healthcare workers or secondary contamination from contact with infected patients, though a direct relationship between surface SC2 RNA viral detection and transmission risk has not been established. Disclosures Michael Z. David, MD PhD, GSK (Board Member) Ebbing Lautenbach, MD, MPH, MSCE, Merck (Other Financial or Material Support, Member of Data and Safety Monitoring Board (DSMB))

6.
Infect Control Hosp Epidemiol ; : 1-4, 2021 Nov 15.
Article in English | MEDLINE | ID: covidwho-1545552

ABSTRACT

We prospectively surveyed SARS-CoV-2 RNA contamination in staff common areas within an acute-care hospital. An increasing prevalence of surface contamination was detected over time. Adjusting for patient census or community incidence of coronavirus disease 2019 (COVID-19), the proportion of contaminated surfaces did not predict healthcare worker COVID-19 infection on study units.

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