The scourge of COVID-19 is currently a world-wide pandemic. It is apparent that a substantial amount of virus dissemination is through undocumented infections in asymptomatic individuals, as well as through contact with known COVID-19 cases. Large, representative community-based samples must be collected and tested to understand the spread of infection and impact on human health. Our study goals are to: 1) better understand the short- and long-term prevalence and the spread of COVID-19 in East Bay Area communities through a longitudinal study; 2) examine health and social outcomes that have resulted from the pandemic; and 3) identify factors that affect risk of infection and/or modify disease manifestation. Our initial results are described here.
We invited >300,000 households in 12 East Bay cities to participate in the study via postcards in English and Spanish mailed to all households in the census records. We pursued various means of community outreach: contacted numerous community-based organizations and mayors/city officials for social media; utilized Spanish-language flyers, twitter, and radio; created a website and study materials in Spanish; enlisted the help of East Bay artists; and conducted outreach to local school districts. More than 16,000 individuals responded, randomized within the household by the person with the next birthday, and ~14,500 completed the screening questionnaire. Biospecimen collection kits were developed, optimized, and prepared. Detailed instructions in print and video in both English and Spanish were generated and enhanced with feedback from study participants and study personnel. We then selected a random sample of ~7,200 screening respondents, first emphasizing individuals who self-identified as a racial or ethnic minority, for in-home testing and additional data collection. Of these participants, ~5,500 completed the study questionnaire and ~5,200 returned biospecimen kits including dried blood spots, nasal/nares swabs and saliva samples.
A sensitive, quantitative reverse-transcriptase PCR test for SARS-CoV-2 was performed using the nasal/nares swabs with our partner laboratory at the University of Minnesota. A commercial total antibody test (Ortho Clinical Diagnostics) was performed on participant’s dried blood spots, following assay optimization and validation, in collaboration with Creative Testing Solutions testing facilities (Phoenix, AZ) and Vitalant Research Institute (San Francisco, CA). See below for more information. Round 1 of the study is finished, and full analyses of data collected in Round 1 are currently in progress. Preliminary results indicate that at the time of screening, 1.2% of our study participants reported at least two recent “COVID”-like symptoms. Testing of the biospecimens revealed that the prevalence of both viral infection and seropositivity in our study sample during the first observational period was low (<1%), consistent with blood bank seroprevalence levels during the same timeframe. Round 2 has started and repeat questionnaires and biospecimen kits are being sent to study participants. In total, sampling and data collection will be repeated for a total of three rounds of viral testing and at least four rounds of antibody testing, every 8-10 weeks through mid-2021.
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Nucleic acid extraction to obtain (potential) viral RNA from study participants was performed in collaboration with our partner laboratory within the University of Minnesota Genomics Center. Briefly, nasal/nares swab samples provided by study participants in collection tubes with a stabilizing solution were first heat-inactivated and transferred to a 96-well plate for further processing to obtain RNA. This RNA was used as input for ‘reverse transcription quantitative real-time polymerase chain reaction’ or RT-qPCR. RT-qPCR is a technique that enables measurement of RNA levels (human or viral) in a PCR reaction (a laboratory-based method that amplifies copies of nucleic acids using enzymes and temperature changes) coupled with fluorescent visualization for rapid detection. In this assay, we are specifically interested in detecting SARs-CoV-2 genes, which would confirm that the virus is present in the participant’s nasal swab sample. Three separate RT-qPCR reactions were set up for each study participant sample in a 384-well plate, and PCR was performed with the N1, N2, or RP primers and probes (these are CDC-recommended sequences), which can be found at this web address: https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-primer-probes.pdf. Following PCR thermocycling steps, the amplification curves for each reaction were manually reviewed, and results were interpreted to determine whether there was evidence of coronavirus infection for each participant. This assay was chosen because it is a sensitive and specific method to measure viral RNA; in addition, it is automated and high throughput.
Antibody testing, also known as serology, was performed using dried blood samples (DBS) provided by study participants. We partnered with Ortho Clinical Diagnostics and Creative Testing Solutions, a nonprofit blood donor testing laboratory, to perform the initial round of serology, due to COVID-related restrictions in UC Berkeley laboratories. DBS provided as part of the study were evaluated for quality and then selected for testing. Two of the DBS discs from each participant were rehydrated by soaking them in a reconstitution solution and were processed for testing on the Ortho VITROS® Anti-SARS-CoV-2 Total test, which detects antibodies to SARS-CoV-2 spike protein. Detection of antibodies that recognize SARS-CoV-2 spike proteins indicates that an individual was previously infected by SARS-CoV-2. This VITROS® antibody test was selected because it is sensitive, specific, and measures persistent antibodies; in addition, it is automated and high throughput, thus reducing human error and allowing us to process the large numbers of samples in this study. Samples with a Signal/Cutoff value greater than 1 were considered to reflect previous infection by SARS-CoV-2. However, due to the small volume of blood collected on the DBS and due to declining antibodies against SARS-CoV-2 in blood over time, a negative result does NOT mean that a person was not infected in the past.
The VITROS® Anti-SARS-CoV-2 Total test works by detecting the ability of antibodies in blood to bind to the SARS-CoV-2 spike protein. The spike protein is fixed to a microwell, and the reconstituted DBS solution is added. Antibodies that recognize the SARS-CoV-2 spike protein will be bound, and the presence of bound antibody is detected by a chemical reaction that produces light. The amount of light produced is proportional to the amount of antibody bound to the microwell and is converted into a numerical score. Samples that have a numerical score greater than 1 are considered to have antibodies against SARS-CoV-2 and thus reflect previous infection with the virus. The VITROS® Anti-SARS-CoV-2 Total test has been granted an FDA Emergency Use Authorization (EUA) for serum/plasma. A separate optimization and validation process for DBS using this test was performed as part of the study.
UC Berkeley School of Public Health
Barcellos Laboratory: Lisa Barcellos (Principal Investigator), Mary Horton, Hong Quach, Diana Quach, Xiaorong Shao, Indro Fedrigo, Cameron Adams, Ella Parsons, Jordan Keen, Yusef Seymens, Luis Lopez, Abigail Broughton, Joan Shim, Janine Solomon, Jose Salinas, Kevin Duong, Joseph Egbunikeokye, Anna Barcellos
In addition, a large group of amazing UC Berkeley undergraduate volunteers in the Barcellos Laboratory have contributed significantly to assembling, performing quality control, shipping and receiving the many thousands of in-home biospecimen kits used in the study, to date. They are: Lila Krop, Kelly Lam, Yan Zhang, Sarah Folkmanis, Sophie Zhai, Dingjun Chen, Ruben Vargas Ethan Garcia, Oliver Li, Manisha Sahoo, Raina Walencewicz, Sophia Wang, Antonia, Gibbs Amrita Ramanathan, Catherine Livelo, Taylor Worley, Amanda Tanaka, Savinnie Ho, Jane Liu Ryan Allen, Sofia Soltero, Victoria Van Metter, Madeleine Fraix, Allie Coyne, Subeksh Sharma Lydia Yu, Shreeya, Garg Sanjeet Paluru, Malika Saxena, Talia Panadero
Harris Laboratory: Eva Harris (Principal Investigator), Josefina Coloma, Marcus Wong, Magelda Montoya, Michelle Meas, Samantha Hernandez, Colin Warnes, José Victor Zambrana, Nicholas Lo, Parnal Narvekar, Fausto Bustos, Gregorio Dias, Reinaldo Mercado-Hernandez, Julia Huffaker, Raymond Montes, Alexandra Zermeno, Alejandra Zeiger
University of Minnesota Genomics Center: Kenny Beckman, Dinesha Walek, Evan Forsberg, Darrell Johnson, Benjamin Auch, Jerry Daniel Veronica Tonnell, Ji Hyun (Jay) Kim, Mary Nieuwenhuis
Creative Testing Solutions: Valerie Green, Sherri Cyrus, Phillip Willamson
Ortho Clinical Diagnostics: Brett Hirsch, Paul Contestable
Vitalant, San Francisco: Mars Stone, Michael Busch
Funding: Open Philanthropy; Fast Grants, Mercatus Center; UC Berkeley Innovative Genomics Institute; UC Berkeley School of Public Health; UC San Francisco