Effectively monitoring COVID-19 in reopened educational institutions: the San Diego model

*Important notice: medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

An interesting new study from the University of California San Diego (UCSD) shows that using preventive measures to block viral transmission, coupled with repeated testing and rapid turnaround times for the results, can successfully prevent outbreaks associated with the reopening of educational institutions.

A preprint version of the study is available on the medRxiv* server, while the article undergoes peer review.


The ongoing coronavirus disease 2019 (COVID-19) pandemic – due to the global outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – continues to affect huge swathes of the global population. To date, over 181.5 million cases have been over 2.995 million deaths have been confirmed.

Since the pandemic's onset in early 2020, governments worldwide have resorted to closing down international borders, business and school closures, implementing face mask-wearing, physical distancing and even national or state-level lockdowns.

Many of these measures have slowed down viral spread in places where they have been consistently observed, but have brought with them a high social and economic cost. As schools and businesses reopen, the experts recommend that mask use be maintained, along with physical distancing, frequent handwashing, and above all, a case identification-isolation-contact tracing policy to nip outbreaks in the bud.

The practicality of these measures is yet to be assessed in Western communities, often less accustomed to giving up individual liberties for the sake of the family or community at large compared to Eastern societies.

The danger of symptom-led testing

Even now, testing is not universally available when required unless the individual is symptomatic or a known contact of a confirmed case. This limitation allows asymptomatic and presymptomatic individuals infected by SARS-CoV-2, who make up, indeed, at least 40-45% of all infections, to spread the virus freely.

Routine testing of asymptomatic individuals in a context of potential contact, as in the neighborhood of a cluster of infections, is essential to cut the outbreak short. The need for a reliable, high-capacity system that can deliver rapid results at an affordable cost is obvious.

How was the study conducted?

The researchers in this study built such as system and tested it on 5,000 healthcare workers in San Diego County and 1,160 first responders from the San Diego Fire and Rescue force. Over 21,000 students and staff from UCSD were also screened, as well as more than 6,000 staff and students from San Diego preschool-grade 12 schools that had not completely closed down during the pandemic.

The testing pipeline used the reverse transcriptase quantitative polymerase chain reaction (RT qPCR) test, which is the gold standard for viral RNA detection in this pandemic, applied through a miniaturized kit that has received Emergency Use Authorization by the U.S. Food and Drug Administration.

A clinical laboratory called the Expedited COVID-351 19 Identification Environment (EXCITE) lab was set up around this testing protocol, conforming to Clinical Laboratory Improvement Amendments (CLIA) norms, at UCSD. The capacity was scaled up to 6,000 samples a day, with the results available the following day. They also tested and validated the use of anterior nares swabs rather than nasopharyngeal swabs, since the former could be collected by the patient.

The shortage of nasopharyngeal swabs prompted them to make their own from rayon using 3D printing. These swabs are used universally for COVID-19 testing. However, they must be collected by a qualified or experienced person at close range, putting the provider and patient at risk of infection.

The discomfort and risk associated with this type of testing reduce testing rates, and thus it is unsuited for large-scale screening. On the other hand, anterior nares swabs are collected by the patient without any pain but with comparable accuracy.

The researchers also explored the use of a different medium for the swabs that instantly inactivates the virus, making it easier to handle. They used two rooms next to each other to carry out the testing.

The samples came as part of two sets: the SEARCH study between April 17 and June 30, 2020, which was an initial proof-of-concept study, and for the EXCITE lab between September 15, 2020, and February 5, 2021.

Low test positivity rates

With the first set, only 0.27% of samples were positive, but with the second cohort, testing began with low positivity in the fall of 2020, rose from the end of November 2020 for a time, then peaked again in January 2021. This is similar to San Diego County testing data. However, where the county had a positivity rate between 2-7%, the EXCITE lab results showed <2% positivity.

The lower positivity results in this study could be due to the different populations being tested. While county testing focused chiefly on symptomatic individuals or known contacts, the EXCITE lab results came from asymptomatic cohorts who were repeatedly tested for the sake of screening for the disease.

The reduction in cases in San Diego County in January 2021 is attributable to the return home of most people following the holidays, with a fall in social mixing coupled with a smaller contribution from rising vaccination rates.

The researchers failed to find any association between viral load as assessed by the cycle threshold (Ct) value, and the individual's age. Neither was there any link between viral load and the individual's sex. Most positives came from the age group 20-39 years, probably because the EXCITE lab-tested mostly the university staff and students. Again, people aged 10-19 made up a larger proportion of the cases in this set for the same reason.

Risk factors for transmission

The RT PCR test typically fails to amplify the spike gene in infections caused by the alpha variant (B.1.1.7) because of the characteristic mutations in this genetic region. This gene 'dropout' is seen in about a tenth of positive cases. However, the other two genes were tested. Namely, the Nucleocapsid (N) gene and the open reading frame 1 (ORF1) gene, show dropout in only 1-2%.

In the case of the alpha variant, the spike gene dropout is coupled with low Ct values, below 30, for the other two genes. Conversely, other samples showing dropouts for any gene have a higher Ct value, indicating a lower viral load. The mean value for such samples was 32, compared to 23 for those without dropouts. For the alpha variant, the mean Ct value was 22.

Symptomatic individuals showed a correlation with a higher viral load, that is, a lower Ct value for amplification of all three of the target genes. Moreover, a dropout was found in only one of 19 positive tests associated with symptomatic infection. Since dropouts other than with the alpha variant are associated with higher Ct values, the above findings suggest the viral load is higher when symptoms are present.

The median age of test-positive individuals was 36 years in San Diego County, while in the current study, it was 35 years. This matches earlier reports of a reduction in median age over time, from over 40 years to below 36 years. Another scientist attributes this to altered testing patterns with heavier testing of asymptomatic younger patients than before, rather than a change in the actual spreading patterns of the virus.

School screening

Among staff and students on UCSD and at schools, test-positives had a mean age of 25 and 26 years, respectively. Adults were more frequently positive than children at private schools, at 2% and 1% respectively. At public schools, children between 11 and 13 years were most likely to have the infection.

The reasons could be related to the voluntary testing scheme at public schools vs. the mandatory testing at private schools. The former was also meant for asymptomatic screening, with those who fell sick being encouraged to test at county sites or their own doctors rather than at school.

The picture obtained from the school testing results is thus very patchy. However, it is clear that, as reported earlier, schools are not hotbeds of virus spread, and adults at school are more likely to transmit the infection than students. None of the schools in this study had an outbreak traceable to the students.

What are the implications?

The current study reports the development of a "high-throughput semi-automated pipeline for RT-qPCR detection of SARS-CoV-2, with scalable capacity and rapid turnaround times."

This was incorporated into a CLIA-conforming lab, used to screen asymptomatic populations for COVID-19. So far, they were able to cover over 150,000 anterior nares swabs from over 28,000 individuals.

The importance of asymptomatic testing was obvious because this group contributed over half the test positives. However, symptomatic cases likely had a higher viral load, as shown by lower Ct values.

Non-White ethnicities had higher test positivity rates, confirming the pattern seen throughout the pandemic.

In private schools, adults were more often positive than students. Conversely, students were more likely to test positive on UCSD campus and in public schools, though the rate is still low. "The low positivity among school-aged children provides an argument for opening P-12 schools for in-person learning."

These findings came from a period when vaccination coverage was below 10%.  This argument is modulated because most schools were closed during this time, limiting contact between children. Yet, it seems that with the use of mitigation measures to reduce transmission risk, educational institutions may reopen without unduly raising the risk of an outbreak.

*Important notice: medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Dr. Liji Thomas

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.


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