Relative role of community transmission and campus contagion in driving the spread of SARS-CoV-2: Lessons from Princeton University

Mathematical models have played a crucial role in exploring and guiding pandemic responses. University campuses present a particularly well-documented case for institutional outbreaks, thereby providing a unique opportunity to understand detailed patterns of pathogen spread. Here, we present descriptive and modeling analyses of SARS-CoV-2 transmission on the Princeton University (PU) campus-this model was used throughout the pandemic to inform policy decisions and operational guidelines for the university campus. Epidemic patterns between the university campus and surrounding communities exhibit strong spatiotemporal correlations. Mathematical modeling analysis further suggests that the amount of on-campus transmission was likely limited during much of the wider pandemic until the end of 2021. Finally, we find that a superspreading event likely played a major role in driving the Omicron variant outbreak on the PU campus during the spring semester of the 2021-2022 academic year. Despite large numbers of cases on campus in this period, case levels in surrounding communities remained low, suggesting that there was little spillover transmission from campus to the local community.

1890. Molecular Biology of SARS-CoV-2 and its Evolution within the Princeton University Campus Community

Background

SARS-CoV-2, a novel and highly pathogenic coronavirus, has caused unprecedented global disruption following its introduction into the human population. Beginning in January 2021, a NJ university invited all students to campus and initiated an asymptomatic testing protocol using weekly to twice-weekly PCR-based detection of human saliva samples. RNA extracted from PCR-positive human saliva samples was sequenced for surveillance purposes.

Methods

Positive samples were submitted for RNA-Seq analysis (ARTIC amplicon sequencing protocol, Illumina MiSeq) and analyzed using Nextclade and USHER (comparison data from GISAID). Using sequencing data, the evolution, transmission, and emergence of SARS-CoV-2 variants were monitored over time in the campus community. Using sequencing data from NY, PA, and NJ in combination with University data, we performed an IQ-TREE based phylogenetic analysis.

Results

Analyzing sequencing data of 1,011 University positive samples we demonstrate that SARS-CoV-2 variants Delta (B.1.617.2) and Omicron (BA.1 and BA.2) were first to emerge following widespread vaccination and, quickly, became predominant. These trends witnessed on campus preceded those same variants emerging in New Jersey, providing evidence of local campus spread distinct from the state-wide pandemic. The analysis of 2,359 total sequences from NY, PA, and NJ in combination with University data, provided evidence of the SARS-CoV-2 transmission chain on campus evolving from out-of-state (January 2021) to local (January 2022) spread over one year of the virus circulating within the community at large. Upon performing a Ct value analysis of 2,822 Princeton University sequences, no significant differences were discovered between N gene Ct values when grouped by age or vaccination status. However, there were significant differences in Ct values between strains.

The Emergence of SARS-CoV-2 Variants at Princeton University

This plot represents the emergence of SARS-CoV-2 clades at Princeton University, organized by Nextstrain clade and displayed as a proportion out of one. Dates of sample collection range from January 25, 2021, to March 1, 2022. X-axis represents SARS-CoV-2 sample test date (grouped by month); Y-axis represents the count per day organized by Nextstrain clade.

Conclusion

Sequencing of positive SARS-CoV-2 samples from population screening of a highly vaccinated University campus community allowed the detection of emergence of new variants that became predominant on campus irrespective of the circulation of variants in the surrounding area.

Disclosures

All Authors: No reported disclosures.

1881. Detection of SARS-CoV-2 Transmission on a College Campus using a Combined Contact Tracing and Molecular Strategy

Background

SARS-CoV-2 has caused unprecedented global disruption following its introduction into the human population. Beginning in August 2021, a residential college initiated an asymptomatic testing protocol using PCR-based detection of human saliva samples (Thermofisher, TaqPath SARS-CoV-2 Assay; QuantStudio v1.3). In January 2021 all students were invited to campus and were required to test once or twice weekly in an effort to isolate those positive (cases) as early as possible and minimize transmission.

Methods

Cases were contacted within 12 hours by trained clinical staff and interviewed with a standardized questionnaire to determine contacts and exposures. Positive samples were submitted for RNA-Seq analysis (ARTIC amplicon sequencing protocol, Illumina MiSeq) and analyzed using Nextclade and USHER (comparison data from GISAID). Using this sequence data, we monitored the evolution, transmission, and emergence of variants over time in the campus community.

Results

In March 2022 a one-week break and the activities preceding it were followed by an outbreak of COVID among campus members. All cases were attributed to the Omicron variant. Based on traditional contact tracing 10 presumed clusters of transmission were identified (34 students). Sequence data from these 34 samples were assembled to identify phylogenetic and molecular patterns of similarity. Several molecular signatures were identified. In a group of 5 cases, all were Omicron BA.2.9; these individuals comprised a clinical cluster of students who had travelled together. Other lineages were BA.2 (N=26), BA.1(N=2), BA.2.12. (N=3), BA.2.3 (N=1) and an Omicron Clade 21M variant that appeared to be a BA.1/BA.2 recombinant (N=2). The BA.2.12 samples were contributed over 2 days; they were found in two different clusters (a social club and an artistic group), demonstrating likely transmission between members. The BA.2 samples were distributed across a wide number of student groups, and while not identical with one another, did not fall into the clusters identified by contact tracing, suggesting endemic transmission across our campus.

Conclusion

This analysis demonstrates that molecular analysis of SARS-CoV-2 transmission can supplement and inform the data provided by clinical/epidemiological analysis of cases.

Disclosures

All Authors: No reported disclosures.

Multistate Outbreak of Burkholderia cepacia Complex Bloodstream Infections After Exposure to Contaminated Saline Flush Syringes: United States, 2016-2017

BACKGROUND

Burkholderia cepacia complex (Bcc) has caused healthcare-associated outbreaks, often in association with contaminated products. The identification of 4 Bcc bloodstream infections in patients residing at a single skilled nursing facility (SNF) within 1 week led to an epidemiological investigation to identify additional cases and the outbreak source.

METHODS

A case was initially defined via a blood culture yielding Bcc in a SNF resident receiving intravenous therapy after 1 August 2016. Multistate notifications were issued to identify additional cases. Public health authorities performed site visits at facilities with cases to conduct chart reviews and identify possible sources. Pulsed-field gel electrophoresis (PFGE) was performed on isolates from cases and suspect products. Facilities involved in manufacturing suspect products were inspected to assess possible root causes.

RESULTS

An outbreak of 162 Bcc bloodstream infections across 59 nursing facilities in 5 states occurred during September 2016-January 2017. Isolates from patients and pre-filled saline flush syringes were closely related by PFGE, identifying contaminated flushes as the outbreak source and prompting a nationwide recall. Inspections of facilities at the saline flush manufacturer identified deficiencies that might have led to the failure to sterilize a specific case containing a partial lot of the product.

CONCLUSIONS

Communication and coordination among key stakeholders, including healthcare facilities, public health authorities, and state and federal agencies, led to the rapid identification of an outbreak source and likely prevented many additional infections. Effective processes to ensure the sterilization of injectable products are essential to prevent similar outbreaks in the future.

1611. Interventions to Decrease the Absolute Number of Individuals Not Immune to Measles at Princeton University (PU)

Background

PU’s dormitories house ~100% of undergraduate and ~70% of graduate students. MMR is required for all students by NJ law, allowing for medical and religious exemptions (RE). Information on immunization requirements is widely available and accessible. If a student is found not compliant, measures include monetary fines, class registration holds, and contact by residential staff. Visiting short-term students should submit immunization records, but, due to rolling matriculation dates, enforcement measures may not be applicable. In the fall of 2018, a measles outbreak was reported close to campus. We sought to engage all students not immune to measles with proactive messaging.

Methods

Starting on December 3, 2018, the electronic health record (EHR) was used to generate a weekly report of active students not immune to measles following the CDC’s immunity criteria. Notifications and education material were sent via secure messaging and/or email. Students with no immunization data were provided instructions on record submission. Reminders were sent to those due for second MMR. Students with RE were offered blood tests for measles immunity. Alerts were placed in the EHR of all non-immune students so every encounter would serve as reminder. Student travelers on PU sponsored trips were informed about measles outbreaks and, often, MMR became a trip requirement.

Results

On December 3, 2018, 84 students were measles non-immune: 2 with medical and 23 with RE; 59 lacking second MMR or with no immunization data.The 23 RE became 24 when a student in absentia returned. Since, 3 of the students with RE had blood tests revealing measles immunity; 2 received MMR to travel; 3 decided that their RE was not current. On 4/22/19, there were 18 students lacking second MMR or with no immunization data, most of them new visiting students. Overall, 57% reduction of absolute number of measles nonimmune students.

Conclusion

This community intervention shows that students who remained measles non-immune despite the regular immunization compliance activities, could become compliant through active messaging, education and continued engagement. Importantly, 8 of 24 students with RE, when engaged and provided with information and potential consequences of unimmunized status, were found either already immunized or not opposed to receiving immunizations.

Disclosures

All authors: No reported disclosures.

Varicella Vaccine Effectiveness in Preventing Community Transmission in the 2-Dose Era

OBJECTIVES

We examined overall and incremental effectiveness of 2-dose varicella vaccination in preventing community transmission of varicella among children aged 4 to 18 years in 2 active surveillance sites. One-dose varicella vaccine effectiveness (VE) was examined in those aged 1 to 18 years.

METHODS

From May 2009 through June 2011, varicella cases identified during active surveillance in Antelope Valley, CA and Philadelphia, PA were enrolled into a matched case-control study. Matched controls within 2 years of the patient's age were selected from immunization registries. A standardized questionnaire was administered to participants' parents, and varicella vaccination history was obtained from health care provider, immunization registry, or parent records. We used conditional logistic regression to estimate varicella VE against clinically diagnosed and laboratory-confirmed varicella.

RESULTS

A total of 125 clinically diagnosed varicella cases and 408 matched controls were enrolled. Twenty-nine cases were laboratory confirmed. One-dose VE (1-dose versus unvaccinated) was 75.6% (95% confidence interval [CI], 38.7%-90.3%) in preventing any clinically diagnosed varicella and 78.1% (95% CI, 12.7%-94.5%) against moderate or severe, clinically diagnosed disease (≥50 lesions). Among subjects aged ≥4 years, 2-dose VE (2-dose versus unvaccinated) was 93.6% (95% CI, 75.6%-98.3%) against any varicella and 97.9% (95% CI, 83.0%-99.7%) against moderate or severe varicella. Incremental effectiveness (2-dose versus 1-dose) was 87.5% against clinically diagnosed varicella and 97.3% against laboratory-confirmed varicella.

CONCLUSIONS

Two-dose varicella vaccination offered better protection against varicella from community transmission among school-aged children compared with 1-dose vaccination.

Knowledge, attitudes, and practices for diagnosing breakthrough varicella in the outpatient setting

OBJECTIVES

We assessed provider knowledge, attitudes, and practices for the management of breakthrough varicella and identified barriers to implementation of laboratory testing and reporting.

METHODS

We surveyed 145 health-care providers (HCPs) from 30 pediatric practices in Philadelphia who did not have a history of laboratory testing for breakthrough varicella. The self-administered survey instrument collected information on clinicians' practices for management of children presenting with rash, infection-control strategies, reporting to public health agencies, and laboratory testing.

RESULTS

Among the 144 HCPs who completed the survey, 73 (51%) had practiced for more than 10 years. While 115 HCPs (80%) would elect to evaluate a child with rash in the office, only 19 (13%) would submit diagnostics. When patients had a known recent exposure to varicella, 84 HCPs (58%) would use laboratory tests: 40% would use direct fluorescent antibody staining on a specimen from a cutaneous lesion, 24% would use polymerase chain reaction on a lesion specimen, 21% would use acute and convalescent serology, and 10% would use other tests. While waiting for test results, 82 HCPs (57%) would advise that the child be kept at home, 39 (27%) would notify the local health department, and 33 (23%) would inform the school nurse.

CONCLUSION

As varicella becomes increasingly uncommon, laboratory confirmation becomes more critical for appropriate diagnosis, similar to poliomyelitis and measles. Our findings suggest that HCPs need further education regarding laboratory confirmation, containment, and reporting of breakthrough varicella.

Implementation of rotavirus immunization in Philadelphia, Pennsylvania: high levels of vaccine ineligibility and off-label use

OBJECTIVE

Our goal was to predict, using delayed diphtheria-tetanus-acellular pertussis vaccination as an indicator, whether the current narrowly defined age limits for pentavalent rotavirus vaccine exclude a substantial proportion of children from complete immunization against rotavirus and to assess adherence of providers to recommended age limits by examining the first 6 months of use of pentavalent rotavirus vaccine in Philadelphia, Pennsylvania.

PATIENTS AND METHODS

Data from a computerized children's immunization registry in Philadelphia were analyzed. Demographics and age at immunization with first 3 diphtheria-tetanus-acellular pertussis doses were examined from 2001 to 2005. Similar characteristics were evaluated for children who received pentavalent rotavirus vaccine doses during the first 6 months of its availability (August 2006 through January 2007).

RESULTS

During the 5-year period, 24 403 of 103 967 recipients of first diphtheria-tetanus-acellular pertussis vaccine were >12 weeks of age; only 56 411 of 79 564 first diphtheria-tetanus-acellular pertussis recipients <or=12 weeks of age received the first 3 doses at ages that they could have completed the pentavalent rotavirus vaccine series if vaccines were given at the same visit. Children using public providers were more likely to have delayed immunization. During the first 6 months of pentavalent rotavirus vaccine implementation, 5566 pentavalent rotavirus vaccine doses were recorded in the Kids Immunization Database/Tracking System: 3912 first doses, 1419 second doses, and 235 third doses. Of 3912 first-dose pentavalent rotavirus vaccine recipients, 770 were >12 weeks of age. Hospital-based providers were less likely to administer pentavalent rotavirus vaccine off-label.

CONCLUSIONS

With the current level of vaccine implementation and current pentavalent rotavirus vaccine recommendations for series initiation, a substantial proportion of children are expected to be excluded from receiving any pentavalent rotavirus vaccine or completing the series. In the first 6 months of availability, pentavalent rotavirus vaccine frequently was used off-label for age, underscoring the importance of education of immunization providers. Current outreach programs for finding 10-month-old toddlers delinquent for immunizations will not improve the possibility of protection against rotavirus.

Routine laboratory testing data for surveillance of rotavirus hospitalizations to evaluate the impact of vaccination

OBJECTIVE

The recent implementation of a rotavirus vaccination program in the United States makes it imperative to assess the impact of immunization on the incidence of severe rotavirus disease leading to hospitalization. Active surveillance for laboratory-confirmed rotavirus hospitalizations is the ideal approach for surveillance, but requires substantial resources to implement. We examined laboratory and hospital discharge data for 2 tertiary care pediatric hospitals to assess the utility of routine laboratory testing data for surveillance of rotavirus gastroenteritis and to estimate rotavirus disease burden.

DESIGN

We obtained all discharge records of hospitalizations for acute gastroenteritis among children <5 years of age at Children's Mercy Hospital (CMH), Kansas City, from July 2000 to June 2005 and at Children's Hospital of Philadelphia (CHOP) from July 2004 to June 2006. We linked these discharge records to laboratory results of rotavirus testing to evaluate epidemiologic differences in children who were tested and not tested for rotavirus and to estimate overall rotavirus burden by extrapolating clinical testing results to the untested group.

RESULTS

At CMH, of the 3702 children with acute gastroenteritis, 69% (n = 2552) were discharged during the winter (January through May) months, when rotavirus is most common. Similarly, at CHOP, 62% (n = 779) of the 1261 gastroenteritis discharges occurred during the winter months. During these months, 47% (n = 1197 of 2552) of the discharges at CMH and 56% (n = 438 of 779) of the discharges at CHOP were tested for rotavirus and of those tested, 71% (n = 853 of 1197) and 55% (n = 242 of 438) were positive, respectively. At both hospitals, children with and without rotavirus testing had similar gender and race/ethnicity, but the rate of testing differed by age at CHOP and by month of admission at CMH. After adjusting for these differences, we estimate that 56%-70% of winter and 34%-48% of year-round gastroenteritis in children <5 years can be attributable to rotavirus. Overall, 3%-5% of all hospitalizations in children <5 years of age were caused by rotavirus.

CONCLUSIONS

Sentinel hospitals where a large proportion of children hospitalized for gastroenteritis are routinely tested for rotavirus could provide a useful and cost-efficient platform to complement ongoing active surveillance efforts to evaluate the impact of rotavirus vaccination. The data reaffirm the substantial burden of rotavirus hospitalizations in US children and the potential health benefits of vaccination.

Resource consumption in the infection control management of pertussis exposure among healthcare workers in pediatrics

OBJECTIVE

To assess consumption of resources in the infection control management of healthcare workers (HCWs) exposed to pertussis and to assess avoidability of exposure.

SETTING

Tertiary care children's medical center.

METHODS

Analysis of the extent of and reasons for HCW exposure to pertussis during contact with children with the disease, whether exposures were avoidable (because of the failure to recognize a case or to order or adhere to isolation precautions) or unavoidable (because the case was not recognizable or because another diagnosis was confirmed), and the cost of implementing exposure management.

INTERVENTIONS

Interventions consisted of an investigation of every HCW encounter with any patient who was confirmed later to have pertussis from the time of hospital admission of the patient, use of azithromycin as postexposure prophylaxis (PEP) for exposed HCWs, performance of 21-day surveillance for cough illness, testing of symptomatic exposed HCWs for Bordetella pertussis, and enhanced preexposure education of HCWs.

RESULTS

From September 2003 through April 2005, pertussis was confirmed in 28 patients (median age, 62 days); 24 patients were admitted. For 11 patients, pertussis was suspected, appropriate precautions were taken, and no HCW was exposed. Inadequate precautions for 17 patients led to 355 HCW exposures. The median number of HCWs exposed per exposing patient was 9 (range, 1-86 HCWs; first quartile mean, 2; fourth quartile mean, 61). Exposure was definitely avoidable for only 61 (17%) of 355 HCWs and was probably unavoidable for 294 HCWs (83%). The cost of 20-month infection control management of HCWs exposed to pertussis was $69,770. The entire cohort of HCWs involved in direct patient care at the facility could be immunized for approximately $60,000.

CONCLUSIONS

Exposure of HCWs to pertussis during contact with children who have the disease is largely unavoidable, and management of this exposure is resource intensive. Universal preexposure vaccination of HCWs is a better utilization of resources than is case-based postexposure management.