Tracking community infection dynamics of COVID-19 by monitoring SARS-CoV-2 RNA in wastewater, counting positive reactions by qPCR

Wastewater-based epidemiology has proved useful for monitoring the COVID-19 infection dynamics in communities. However, in some countries, low concentrations of SARS-CoV-2 RNA in wastewater make this difficult. Getting meaningful information from wastewater-based epidemiology in regions of low prevalence remains a key challenge. Here we used real-time reverse-transcription PCR (RT-qPCR) to monitor SARS-CoV-2 RNA in wastewater from October 2020 to February 2021 during the third wave of the COVID-19 outbreak in Japan. Viral RNA was below the limit of quantification in all samples. However, by counting the positive reactions in repeated qPCR of each sample, we found that the ratio of positive reactions to all tests in wastewater was significantly correlated with the number of clinically confirmed cases by the date of symptom onset during periods of both increasing and decreasing infection. Time-step analysis indicated that COVID-19 patients excreted large amounts of virus in their feces 2 days either side of symptom onset, which wastewater surveillance could detect. The positive count method is thus useful for tracing COVID-19 dynamics in regions of low prevalence.

Risk of SARS-CoV-2 reinfections in children: prospective national surveillance, January 2020 to July 2021, England

BackgroundReinfection after primary SARS-CoV-2 infection is uncommon in adults, but little is known about the risks, characteristics, severity or outcomes of reinfection in children.MethodsWe used national SARS-CoV-2 testing data in England to estimate the risk of reinfection ≥90 days after primary infection from 01 January 2020 to 31 July 2021, which encompassed both the Alpha and Delta waves in England. Disease severity was assessed by linking reinfection cases to national hospitalisation, intensive care admission and death registrations datasets.FindingsReinfection rates closely followed community infection rates, with a small peak during the Alpha wave and a larger peak during the Delta wave. In children aged ≤16 years, there were 688,418 primary infections and 2,343 reinfections. The overall reinfection rate was 66·88/100,000 population, being higher in adults (72.53/100,000) than in children (21·53/100,000). Reinfection rates after primary infection were 0·68% overall, 0·73% in adults and 0·34% in children. Of the 109 reinfections in children admitted to hospital, 78 (72%) had underlying comorbidities. Hospitalisation rates were similar for the first (64/2343, 2·73%) and second episode (57/2343, 2·43%). Intensive care admission was rare after primary infection (n=7) or reinfection (n=4), mainly in children with comorbidities. 44 deaths occurred after primary infection within 28 days of diagnosis (44/688,418, 0·01%), none after possible reinfections.InterpretationThe risk of SARS-CoV-2 reinfection is strongly related to exposure due to community infection rates, especially during the Delta variant wave. Children had a lower risk of reinfection than adults, but reinfections were not associated with more severe disease or fatal outcomes.FundingPHE/UKHSAResearch in ContextEvidence Before this studyWe searched PubMed with the terms “COVID-19” or “SARS-CoV-2” with “reinfection” to identify publications relating to SARS-CoV-2 reinfections from 01 January until 15 November 2021. There were few publications relating to SARS-CoV-2 reinfections, and these primarily related to adults. Published studies reported very low rates of reinfection during the first few months after primary infection in adults. COVID-19 vaccines provide effective immune protection against SARS-CoV-2 infection, but recent studies have reported increasing risk of breakthrough infection with time since primary vaccination due to waning immunity. Several SARS-CoV-2 variants, including the beta, gamma and delta variants have been shown to partially evade immunity after natural infection and vaccination, potentially increasing the risk of reinfections and breakthrough infections, respectively. Data on reinfections in children are lacking and restricted mainly to case reports in immunocompromised children.Added Value of This StudyWe used national SARS-CoV-2 testing data during the first 19 months of the pandemic to estimate the risk of reinfection in children compared to adults during a period that encompassed both the Alpha and the Delta variant waves in England. We found that the risk of reinfection correlated with the risk of SARS-CoV-2 exposure and therefore, closely reflected community infection rates, with most reinfections occurring during the Delta variant wave. Whilst acknowledging the limitation of using national testing data, we found that children had a lower risk of reinfection compared to adults and that the risk of reinfection in children increased with age. Reinfections were not associated with severe disease in terms of hospitalization or intensive care admission and there were no fatalities within 28 days of the reinfection episode in children.Implications of all the Available EvidenceSARS-CoV-2 reinfections are rare in children, especially younger children, and occurred mainly during the Delta wave in England. Reinfections were not associated with more severe disease or fatal outcomes in children. COVID-19 vaccination will provide further protection against primary infections and reinfections in children.

Emergence of the Delta Variant and risk of SARS-CoV-2 infection in secondary school students and staff: prospective surveillance in 18 schools, England

ABSTRACTBackgroundThe role of educational settings on SARS-CoV-2 infection and transmission remains controversial. We investigated SARS-CoV-2 infection, seroprevalence and seroconversions rates in secondary schools during the 2020/21 academic year, which included the emergence of the more transmissible Alpha and Delta variants, in England.MethodsThe UK Health Security Agency (UKHSA) initiated prospective surveillance in 18 urban English secondary schools. Participants had nasal swabs for SARS-CoV-2 RT-PCR and blood sampling for SARS-CoV-2 Nucleoprotein and Spike protein antibodies at the start (Round 1: September-October 2020) and end (Round 2: December 2021) of the autumn term, when schools reopened after national lockdown was imposed in January 2021 (Round 3: March-April) and end of the academic year (Round 4: May-July).FindingsWe enrolled 2,314 participants (1277 students, 1037 staff). In-school testing identified 31 PCR-positive participants (20 students, 11 staff). Another 247 confirmed cases (112 students, 135 staff) were identified after linkage with national surveillance data, giving an overall positivity rate of 12.0% (278/2313; staff [14.1%, 146/1037] vs students [10.3%, 132/1276; p=0.006). Nucleoprotein-antibody seroprevalence increased for students and staff between Rounds 1-3 but changed little in Round 4, when the Delta variant was the dominant circulating strain. Overall, Nucleoprotein-antibody seroconversion was 18.4% (137/744) in staff and 18.8% (146/778) in students, while Spike-antibody seroconversion was higher in staff (72.8% (525/721) than students (21.3%, 163/764) because of vaccination.InterpretationSARS-CoV-2 infection and transmission in secondary schools remained low when community infection rates were low because of national lockdown, even after the emergence of the Delta variantFundingDHSC

Compliance to Community Infection Control Standards during the COVID-19 Pandemic: An Integrative Review

This integrative literature review was conducted to assess the compliance to community infection control standards during the Covid-19 pandemic. As countries struggle to contain Covid-19 and its effects on social and economic aspects of life, non-pharmacologic interventions are seen as a viable option to mitigate the pandemic. This review aims to explore the level and extent to which the community perform health practices as well as the factors that affect compliance to these preventive measures. A systematic search of literatures that was published during 2020 and 2021 that addressed the health practice towards mitigating this pandemic as well as their compliance was included in this literature review. Whittemore and Knafl’s procedure in conducting integrative literature review was utilized. After critical appraisal of these literatures using the Quality Assessment Tool for Qualitative Studies, 4 studies were then included. Overall, studies reveal that health practices to mitigate Covid-19 are highly practiced. This finding is relation to the adequate knowledge of the community towards these preventive measures. However, despite having enough knowledge and awareness on the various information regarding the existence of the Coronavirus disease, the people in the community still need to enhance their knowledge along COVID 19 issues to minimize the risk of having the virus. Key words: Compliance, Community, Infection Control Standards, Covid-19.

Regular testing of asymptomatic healthcare workers identifies cost-efficient SARS-CoV-2 preventive measures

Protecting healthcare professionals is crucial in maintaining a functioning healthcare system. The risk of infection and optimal preventive strategies for healthcare workers during the COVID-19 pandemic remain poorly understood. Here we report the results of a cohort study that included pre- and asymptomatic healthcare workers. A weekly testing regime has been performed in this cohort since the beginning of the COVID-19 pandemic to identify infected healthcare workers. Based on these observations we have developed a mathematical model of SARS-CoV-2 transmission that integrates the sources of infection from inside and outside the hospital. The data were used to study how regular testing and a desynchronisation protocol are effective in preventing transmission of COVID-19 infection at work, and compared both strategies in terms of workforce availability and cost-effectiveness. We showed that case incidence among healthcare workers is higher than would be explained solely by community infection. Furthermore, while testing and desynchronisation protocols are both effective in preventing nosocomial transmission, regular testing maintains work productivity with implementation costs.

384. SARS-CoV-2 Surveillance Testing Patterns among Hospitalized Pediatric Patients in a Single Academic Medical Center

Background Children infected with SARS-CoV-2 often have mild or no symptoms, making symptom screening an ineffective tool for determining isolation precautions. As an infection control measure, universal pre-procedural and admission SARS-CoV-2 testing for pediatric patients was implemented in April and August 2020, respectively. Limited data exist on the utility screening programs in the pediatric population. Methods We performed a retrospective cohort study of pediatric patients (birth to 18 years) admitted to a tertiary care academic medical center from April 2020 to May 2021 that had one or more SARS-CoV-2 point-of-care or polymerase chain reaction tests performed. We describe demographic data, positivity rates and repeat testing trends observed in our cohort. Results A total of 2,579 SARS-CoV-2 tests were performed among 1,027 pediatric inpatients. Of these, 51 tests (2%) from 45 patients (4.3%) resulted positive. Community infection rates ranged from 4.5-60 cases/100,000 persons/day during the study period. Hispanic patients comprised 16% of the total children tested, but were disproportionately overrepresented (40%) among those testing positive (Figure1). Of 654 children with repeated tests, 7 (0.1%) converted to positive from a prior negative result. Median days between repeat tests was 12 (IQR 6-45), not necessarily performed during the same hospital stay. Five of these 7 patients had tests repeated < 3 days from a negative result, of which only 2 had no history of recent infection by testing performed at an outside facility. Pre-procedural tests accounted for 35% of repeat testing, of which 0.9% were positive. Repeated tests were most frequently ordered for patients in hematology/oncology (35%) and solid organ transplant/surgical (33%) wards, each with < 3% positive conversion rate. Notably, no hematopoietic stem cell transplant patients tested positive for SARS-CoV-2 during the study period. Pediatric SARS-CoV-2 Testing Distributed by Race/Ethnicity Conclusion The positivity rate of universal pre-procedural and admission SARS-CoV-2 testing in pediatric patients was low in our inpatient cohort. Tests repeated < 3 days from a negative result were especially low yield, suggesting limited utility of this practice. Diagnostic testing stewardship in certain populations may be useful, especially as community infection rates decline. Disclosures Michael J. Smith, MD, M.S.C.E, Merck (Grant/Research Support)Pfizer (Grant/Research Support) Rebekah W. Moehring, MD, MPH, UpToDate, Inc. (Other Financial or Material Support, Author Royalties)

Wastewater surveillance of SARS-CoV-2 corroborates heightened community infection during the initial peak of COVID-19 in Bexar County, Texas

The purpose of this study was to conduct a preliminary assessment of the levels of SARS-CoV-2 RNA in wastewater at the Salitrillo Wastewater Treatment Plant in Texas during the initial peak of COVID-19 outbreak. Raw wastewater influent (24 h composite, time-based 1 L samples, n = 13) was collected weekly during June-August 2020. We measured SARS-CoV-2 RNA in wastewater by reverse transcription droplet digital PCR (RT-ddPCR) using the same N1 and N2 primer sets employed in COVID-19 clinical testing. Virus RNA copies for positive samples (77%) ranged from 1.4×102 to 4.1×104 copies per liter of wastewater, and exhibited both increasing and decreasing trends, which corresponded well with the COVID-19 weekly infection rate (N1: ρ = 0.558, P = 0.048; and N2: ρ = 0.487, P = 0.092). A sharp increase in virus RNA concentrations was observed during July sampling dates, consistent with highest number of COVID-19 cases reported. This could be attributed to an increase in the spread of COVID-19 infection due to the July 4 holiday week gatherings (outdoor gatherings were limited to 100 people during that time). Our data show that wastewater surveillance is an effective tool to determine trends in infectious disease prevalence, and provide complimentary information to clinical testing.

SARS-CoV-2 Seroprevalence among Healthcare Workers

Background. Monitoring COVID-19 infection risk among health care workers (HCWs) is a public health priority. We examined the seroprevalence of SARS-CoV-2 among HCWs following the fall infection surge in Minnesota, and before and after COVID-19 vaccination. Additionally, we assessed demographic and occupational risk factors for SARS-CoV-2 infection. Methods. We conducted two rounds of seroprevalence testing among a cohort of HCWs: samples in round 1 were collected from 11/22/20 - 02/21/21 and in round 2 from 12/18/20 - 02/15/21. Demographic and occupational exposures assessed with logistic regression were age, sex, healthcare role and setting, and number of children in the household. The primary outcome was SARS-CoV-2 IgG seropositivity. A secondary outcome, SARS-CoV-2 infection, included both seropositivity and self-reported SARS-CoV-2 test positivity. Results. In total, 459 HCWs were tested. 43/454 (9.47%) had a seropositive sample 1 and 75/423 (17.7%) had a seropositive sample 2. By time of sample 2 collection, 54% of participants had received at least one vaccine dose and seroprevalence was 13% among unvaccinated individuals. Relative to physicians, the odds of SARS-CoV-2 infection in other roles were increased (Nurse Practitioner: OR[95%CI] 1.93[0.57,6.53], Physician's Assistant: 1.69[0.38,7.52], Nurse: 2.33[0.94,5.78], Paramedic/EMTs: 3.86[0.78,19.0], other: 1.68[0.58,4.85]). The workplace setting was associated with SARS-CoV-2 infection (p=0.04). SARS-CoV-2 seroprevalence among HCWs reporting duties in the ICU vs. those working in an ambulatory clinic was elevated: OR[95%CI] 2.17[1.01,4.68]. Conclusions. SARS-CoV-2 seroprevalence in HCW increased during our study period which was consistent with community infection rates. HCW role and setting - particularly working in the ICU - is associated with higher risk for SARS-CoV-2 infection.

Infection prevention: coordinating the community response to COVID-19

Sue Rees, Advanced Nurse Practitioner, Community Infection Prevention, Hywel Dda University Health Board ( [email protected] ), was runner up in the Infection Prevention Nurse of the Year category at the BJN Awards 2021

Optimized Post-Vaccination Strategies and Preventative Measures for SARS-CoV-2

Introduction: Since March of 2020, over 210 million SARS-CoV-2 cases have been reported and roughly five billion doses of a SARS-CoV-2 vaccine have been delivered. The rise of the more infectious delta variant has recently indicated the value of reinstating previously relaxed non-pharmacological and test-driven preventative measures. These efforts have been met with resistance, due, in part, to a lack of site-specific quantitative evidence which can justify their value. As vaccination rates continue to increase, a gap in knowledge exists regarding appropriate thresholds for escalation and de-escalation of COVID-19 preventative measures. Methods: We conducted a series of simulation experiments, trialing the spread of SARS-CoV-2 virus in a hypothesized working environment that is subject to COVID-19 infections from the surrounding community. We established cohorts of individuals who would, in simulation, work together for a set period of time. With these cohorts, we tested the rates of workplace and community acquired infections based on applied isolation strategies, community infection rates (CIR), scales of testing, non-pharmaceutical interventions, variant predominance's and testing strategies, vaccination coverages, and vaccination efficacies of the members included. Permuting through each combination of these variables, we estimated expected case counts for 33,462 unique workplace scenarios. Results: When the CIR is 5 new confirmed cases per 100,000 or fewer, and at 50% of the workforce is vaccinated with a 95% efficacious vaccine, then testing daily with an antigen-based or PCR based test in only unvaccinated workers will result in less than one infection through 4,800 person weeks. When the community infection rate per 100,000 persons is less than or equal to 60, and the vaccination coverage of the workforce is 100% with 95% vaccine efficacy then no masking or routine testing + isolation strategies are needed to prevent workplace acquired infections regardless of variant predominance. Identifying and isolating workers with antigen-based SARS-CoV-2 testing methods result in the same or fewer workplace acquired infections than testing with polymerase chain reaction (PCR) methods. Conclusions: Specific scenarios exist in which preventative measures taken to prevent SARS-CoV-2 spread, including masking, and testing plus isolation strategies can safely be relaxed. Further, efficacious testing with quarantine strategies exist for implementation in only unvaccinated cohorts in a workplace. Due to shorter turnaround time, antigen-based testing with lower sensitivity is more effective than PCR testing with higher sensitivities in comparable testing strategies. The general reference interactive heatmap we provide can be used for site specific, immediate, parameter-based case count predictions to inform appropriate institutional policy making.