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SARS-CoV-2 exhibits extreme differences in early viral loads among specimen types suggesting improved detection of pre-infectious and infectious individuals using combination specimen types

Winnett, Alexander Viloria and Akana, Reid and Shelby, Natasha and Davich, Hannah and Caldera, Saharai and Yamada, Taikun and Reyna, John Raymond B. and Romano, Anna E. and Carter, Alyssa M. and Kim, Mi Kyung and Thomson, Matt and Tognazzini, Colten and Feaster, Matthew and Goh, Ying-Ying and Chew, Yap Ching and Ismagilov, Rustem F. (2022) SARS-CoV-2 exhibits extreme differences in early viral loads among specimen types suggesting improved detection of pre-infectious and infectious individuals using combination specimen types. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20220720-917402000

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Abstract

Background. Screening testing, often via self-collected specimens, remains a key strategy to detect infections early and prevent SARS-CoV-2 transmission, and to enable earlier initiation of treatment. However, which specimen type best detects the earliest days of infection remains controversial. Further, the analytical sensitivity of diagnostic tests must also be considered, as viral loads below a test’s limit of detection (LOD) are likely to yield false-negative results. Comparisons of quantitative, longitudinal SARS-CoV-2 viral-load timecourses in multiple specimen types can determine the best specimen type and test analytical sensitivity for earliest detection of infection. Methods. We conducted a COVID-19 household transmission study between November 2021 and February 2022 that enrolled 228 participants and analyzed 6,825 samples using RT-qPCR to quantify viral-load timecourses in three specimen types (saliva [SA], anterior-nares swab [ANS], and oropharyngeal swab [OPS]). From this study population, 14 participants enrolled before or at the incidence of infection with the Omicron variant. We compared the viral loads in specimens collected from each person at the same timepoint, and the longitudinal viral-load timecourses from each participant. Using these viral loads, we inferred the clinical sensitivity of each specimen type to detect infected, pre-infectious, and infectious individuals (based on presumably infectious viral-load levels) using assays with a range of analytical sensitivities. We also inferred the clinical sensitivity of computationally-contrived specimen types representing combinations of single specimen types. Results. We found extreme differences (up to 109 copies/mL) in viral loads between paired specimen types in the same person at the same timepoint, and that longitudinal viral-load timecourses across specimen types did not correlate. Because of this lack of correlation, infectious viral loads were often observed in different specimen types asynchronously throughout the course of the infection. In the first 4 days of infection, no single specimen type was inferred to achieve >95% detection of infected or infectious individuals, even with the highest analytical sensitivity assays. In nearly all participants (11/14), a rise in ANS viral loads was delayed (as many as 7 days) relative to SA and OPS. We also observed that ANS and OPS had the most complementary viral-load timecourses, resulting in optimal inferred performance with a computationally-contrived combined anterior-nares–oropharyngeal (AN–OP) swab specimen type. The combination AN–OP swab had superior inferred clinical sensitivity the first 8 days of infection with both high- and low-analytical-sensitivity assays. This AN–OP swab was also inferred to significantly improve detection of pre-infectious and infectious individuals over any single specimen type. Conclusion. Our work demonstrates that the viral load in one specimen type cannot reliably predict the viral load in another specimen type. Combination specimen types may offer a more robust approach for earliest detection of new variants and respiratory viruses when viral kinetics are still unknown.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2022.07.13.22277113DOIDiscussion Paper
https://www.medrxiv.org/content/10.1101/2022.07.13.22277113v1.supplementary-materialPublisherSupporting Information
http://dx.doi.org/10.22002/D1.20223DOIDataset
ORCID:
AuthorORCID
Winnett, Alexander Viloria0000-0002-7338-5605
Akana, Reid0000-0003-4422-587X
Shelby, Natasha0000-0001-9097-3663
Davich, Hannah0000-0001-6880-3086
Caldera, Saharai0000-0001-5057-9186
Romano, Anna E.0000-0002-7148-0668
Carter, Alyssa M.0000-0002-2776-9421
Thomson, Matt0000-0003-1021-1234
Feaster, Matthew0000-0001-9966-2845
Goh, Ying-Ying0000-0001-5136-7214
Chew, Yap Ching0000-0002-1686-6541
Ismagilov, Rustem F.0000-0002-3680-4399
Additional Information:The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. Paper in collection COVID-19 SARS-CoV-2 preprints from medRxiv and bioRxiv. We sincerely thank the study participants for making this work possible. We thank Lauriane Quenee, Grace Fisher-Adams, Junie Hildebrandt, Megan Hayashi, RuthAnne Bevier, Chantal D’Apuzzo, Ralph Adolphs, Victor Rivera, Steve Chapman, Gary Waters, Leonard Edwards, Gaylene Ursua, Cynthia Ramos, and Shannon Yamashita for their assistance and advice on study implementation and/or administration. We thank Jessica Leong, Ojas Pradhan, Si Hyung Jin, Emily Savela, Bridget Yang, Ekta Patel, Hsiuchen Chen , Paresh Samantaray, Zeynep Turan, Cindy Kim, Trinity Lee, Vanessa Mechan, Katherine Stiefel, Rosie Zedan, Rahulijeet Chadha, Minkyo Lee, and Jenny Ji for volunteering their time to help with this study. We thank Prabhu Gounder, Tony Chang, Jennifer Howes, and Nari Shin for their support with recruitment. Finally, we thank all the case investigators and contact tracers at the Pasadena Public Health Department and Caltech Student Wellness Services for their efforts in study recruitment and their work in the pandemic response. This work was funded by the Ronald and Maxine Linde Center for New Initiatives at the California Institute of Technology and the Jacobs Institute for Molecular Engineering for Medicine at the California Institute of Technology. AVW is supported by a UCLA DGSOM Geffen Fellowship. AUTHOR CONTRIBUTIONS (listed alphabetically by last name): Reid Akana (RA): Collaborated with AVW in creating digital participant symptom surveys; assisted with data quality control/curation with NS, HD, SC; created current laboratory information management system (LIMS) for specimen logging and tracking. Creation of iOS application for sample logging/tracking. Configured an SQL database for data storage. Created an Apache server and websites to view study data. Configured FTPS server to catalog PCR data. Wrote a Python package to access study data. Trained study coordinators on SQL. Troubleshooting and QC of LIMS. Made Fig 3(C-D) and SI Figs S3, S4, S5, Table S2, S3, S4, S5, S6. Wrote and edited the manuscript with AVW and NS. Alyssa M. Carter (AMC): Assisted with the inventory and archiving of >6,000 samples at Caltech; coordinated shipment of samples to Caltech with AER and JRBR; assisted with procurement of antigen tests; assisted with organizing volunteers and making participant kits; assisted AER in developing and implementing QC for participant kits. Provided feedback and edited the manuscript. Yap Ching Chew (YCC): Primary liaison with Caltech team. Prepared and provided Zymo SafeCollect kits and related materials to Caltech team. Supervised the extraction, PCR, and QC teams at Pangea Laboratory. Sent PCR results daily to Caltech team. Arranged for Pangea team to perform viral-variant sequencing on selected samples; reported results and provided sequencing files. Saharai Caldera (SC): Study coordinator; recruited, enrolled and maintained study participants with NS and HD; study-data quality control, curation and archiving with RA, NS, HD and MKK; supplies acquisition with AER, NS, HD and MKK. Hannah Davich (HD): Lead study coordinator; co-wrote participant informational sheets with NS; developed recruitment strategies and did outreach with NS; participant kit creation and co-coordinated kit-making by volunteers with AER; recruited, enrolled and maintained study participants with NS and SC; managed the study-coordinator inventory; study-data quality control, curation and archiving with RA, NS, SC and MKK; supplies acquisition with AER, NS, SC and MKK. Matthew Feaster (MF): Co-investigator; collaborated with AVW, MMC, NS, YG, RFI on study design and recruitment strategies; provided guidance and expertise on SARS-CoV-2 epidemiology and local trends. Ying-Ying Goh (Y-YG): Co-investigator; collaborated with AVW, MMC, NS, MF, RFI on study design and recruitment strategies; provided guidance and expertise on SARS-CoV-2 epidemiology and local trends. Rustem F. Ismagilov (RFI): Principal investigator; collaborated with AVW, MMC, NS, MF, YYG on study design and recruitment strategies; provided leadership, technical guidance, oversight of all analyses, and was responsible for obtaining the primary funding for the study. Mi Kyung Kim (MKK): Study coordinator (part-time); maintaining participants with NS, HD, and SC; study-data quality control, curation and archiving with RA, NS, SC and HD; supplies acquisition with AER, NS, SC and HD; collected contact info for local university/college student health centers for recruitment outreach; assembled Table S1 with NS. John Raymond B. Reyna (JRBR): Organized sample labeling and short-term storage of all samples at Pangea Laboratories. Arranged shipment of all samples to Caltech team. Assisted with processing of the specimens. Anna E. Romano (AER): Co-coordinated kit-making by volunteers with HD; implemented QC process for kit-making; participated in kit-making; managed logistics for the inventory and archiving of >6,000 samples at Caltech; supplies acquisition with HD, NS, SC and MKK; assisted with securing funding; compiled Table S3; organized and performed QC on sequencing data. Provided feedback and edited the manuscript. Natasha Shelby (NS): Study administrator; collaborated with AVW, RFI, YG, MF on initial study design and recruitment strategies; co-wrote IRB protocol and informed consent with AVW; co-wrote enrollment questionnaire and post-study questionnaire with AVW; initiated the collaboration with Zymo and served as primary liaison throughout study; reviewed pilot sampling data and amended instructional sheets/graphics for specimen collections in collaboration with Zymo; co-wrote participant informational sheets with HD; hired, trained, and supervised the study-coordinator team; developed recruitment strategies and did outreach with HD; recruited, enrolled and maintained study participants with HD and SC; co-developed participant keep/drop criteria with AVW; performed the daily upload, review, and QC of PCR data received from Zymo; made the daily keep/drop decisions based on viral-load trajectories in each household; made all phone calls to alert presumptive positives of their status and provide resources; study-data quality control, curation and archiving with RA, HD, SC and MKK; organized archiving of all participant data and antigen-test photographs; supplies acquisition with AER, HD, SC and MKK; assisted with securing funding; managed the overall study budget; assembled Fig 1 with AVW; assembled Table S1 with MKK; made Fig 2 with AVW; managed citations and reference library; verified the underlying data with AVW and RA; co-wrote and edited the manuscript with AVW and RA. Matt Thomson (MT): Assisted with statistical approach and analyses. Colten Tognazzini (CT): Coordinated the recruitment efforts at PPHD with case investigators and contact tracers; provided guidance and expertise on SARS-CoV-2 epidemiology and local trends. Alexander Viloria Winnett (AVW): Collaborated with NS, RFI, YG, MF on initial study design and recruitment strategies; co-wrote IRB protocol and informed consent with NS; co-wrote enrollment questionnaire and post-study questionnaire with NS; co-developed participant keep/drop criteria with NS; funding acquisition; designed and coordinated LOD validation experiments; selected and prepared specimen for viral-variant sequencing with NS, YC, and AER; assisted with the inventory and archiving of >6,000 specimen at Caltech with AER and AMC; minor role supporting outreach by HD and NS; minor role supporting kit-making by AER, HD and AMC; verified the underlying data with NS and RA; assembled Fig 1 with NS; made Fig 2 with NS; performed analysis and prepared Figs 4-7, Table S2, Fig S1, S2, S6, S7, S8, S9. Co-wrote and edited the manuscript with NS and RA. Taikun Yamada (TY): Performed the RT-qPCR COVID-19 testing at Pangea Laboratory. DATA AVAILABILITY. The data underlying the results presented in the study can be accessed at CaltechDATA: https://data.caltech.edu/records/20223. COMPETING INTERESTS STATEMENT. RFI is a co-founder, consultant, and a director and has stock ownership of Talis Biomedical Corp.
Group:COVID-19, Jacobs Institute for Molecular Engineering for Medicine
Funders:
Funding AgencyGrant Number
Ronald and Maxine Linde Center for New InitiativesUNSPECIFIED
Jacobs Institute for Molecular Engineering for MedicineUNSPECIFIED
UCLAUNSPECIFIED
DOI:10.1101/2022.07.13.22277113
Record Number:CaltechAUTHORS:20220720-917402000
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20220720-917402000
Official Citation:SARS-CoV-2 exhibits extreme differences in early viral loads among specimen types suggesting improved detection of pre-infectious and infectious individuals using combination specimen types Alexander Viloria Winnett, Reid Akana, Natasha Shelby, Hannah Davich, Saharai Caldera, Taikun Yamada, John Raymond B. Reyna, Anna E. Romano, Alyssa M. Carter, Mi Kyung Kim, Matt Thomson, Colten Tognazzini, Matthew Feaster, Ying-Ying Goh, Yap Ching Chew, Rustem F. Ismagilov medRxiv 2022.07.13.22277113; doi: https://doi.org/10.1101/2022.07.13.22277113
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:115694
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:22 Jul 2022 14:32
Last Modified:22 Jul 2022 14:37

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