1
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Arts PJ, Kelly JD, Midgley CM, Anglin K, Lu S, Abedi GR, Andino R, Bakker KM, Banman B, Boehm AB, Briggs-Hagen M, Brouwer AF, Davidson MC, Eisenberg MC, Garcia-Knight M, Knight S, Peluso MJ, Pineda-Ramirez J, Diaz Sanchez R, Saydah S, Tassetto M, Martin JN, Wigginton KR. Longitudinal and quantitative fecal shedding dynamics of SARS-CoV-2, pepper mild mottle virus, and crAssphage. mSphere 2023; 8:e0013223. [PMID: 37338211 PMCID: PMC10506459 DOI: 10.1128/msphere.00132-23] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/03/2023] [Indexed: 06/21/2023] Open
Abstract
Wastewater-based epidemiology (WBE) emerged during the coronavirus disease 2019 (COVID-19) pandemic as a scalable and broadly applicable method for community-level monitoring of infectious disease burden. The lack of high-resolution fecal shedding data for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) limits our ability to link WBE measurements to disease burden. In this study, we present longitudinal, quantitative fecal shedding data for SARS-CoV-2 RNA, as well as for the commonly used fecal indicators pepper mild mottle virus (PMMoV) RNA and crAss-like phage (crAssphage) DNA. The shedding trajectories from 48 SARS-CoV-2-infected individuals suggest a highly individualized, dynamic course of SARS-CoV-2 RNA fecal shedding. Of the individuals that provided at least three stool samples spanning more than 14 days, 77% had one or more samples that tested positive for SARS-CoV-2 RNA. We detected PMMoV RNA in at least one sample from all individuals and in 96% (352/367) of samples overall. CrAssphage DNA was detected in at least one sample from 80% (38/48) of individuals and was detected in 48% (179/371) of all samples. The geometric mean concentrations of PMMoV and crAssphage in stool across all individuals were 8.7 × 104 and 1.4 × 104 gene copies/milligram-dry weight, respectively, and crAssphage shedding was more consistent for individuals than PMMoV shedding. These results provide us with a missing link needed to connect laboratory WBE results with mechanistic models, and this will aid in more accurate estimates of COVID-19 burden in sewersheds. Additionally, the PMMoV and crAssphage data are critical for evaluating their utility as fecal strength normalizing measures and for source-tracking applications. IMPORTANCE This research represents a critical step in the advancement of wastewater monitoring for public health. To date, mechanistic materials balance modeling of wastewater-based epidemiology has relied on SARS-CoV-2 fecal shedding estimates from small-scale clinical reports or meta-analyses of research using a wide range of analytical methodologies. Additionally, previous SARS-CoV-2 fecal shedding data have not contained sufficient methodological information for building accurate materials balance models. Like SARS-CoV-2, fecal shedding of PMMoV and crAssphage has been understudied to date. The data presented here provide externally valid and longitudinal fecal shedding data for SARS-CoV-2, PMMoV, and crAssphage which can be directly applied to WBE models and ultimately increase the utility of WBE.
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Affiliation(s)
- Peter J. Arts
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - J. Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- Division of Hospital Medicine, UCSF, San Francisco, California, USA
- F.I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Claire M. Midgley
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Khamal Anglin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Glen R. Abedi
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Raul Andino
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
| | - Kevin M. Bakker
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Bryon Banman
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexandria B. Boehm
- Department of Civil & Environmental Engineering, Stanford University, Stanford, California, USA
| | - Melissa Briggs-Hagen
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andrew F. Brouwer
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Marisa C. Eisenberg
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Sterling Knight
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael J. Peluso
- Division of HIV, Infectious Disease, and Global Medicine, UCSF, San Francisco, California, USA
| | - Jesus Pineda-Ramirez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Ruth Diaz Sanchez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Sharon Saydah
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michel Tassetto
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Krista R. Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
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2
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Deyoe JE, Kelly JD, Grijalva CG, Bonenfant G, Lu S, Anglin K, Garcia-Knight M, Pineda-Ramirez J, Hagen MB, Saydah S, Abedi GR, Goldberg SA, Tassetto M, Zhang A, Donohue KC, Davidson MC, Sanchez RD, Djomaleu M, Mathur S, Shak JR, Deeks SG, Peluso MJ, Chiu CY, Zhu Y, Halasa NB, Chappell JD, Mellis A, Reed C, Andino R, Martin JN, Zhou B, Talbot HK, Midgley CM, Rolfes MA. Association of Culturable-Virus Detection and Household Transmission of SARS-CoV-2, California and Tennessee, 2020-2022. J Infect Dis 2023; 227:1343-1347. [PMID: 36705269 PMCID: PMC10266938 DOI: 10.1093/infdis/jiad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/27/2022] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
From 2 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) household transmission studies (enrolling April 2020 to January 2022) with rapid enrollment and specimen collection for 14 days, 61% (43/70) of primary cases had culturable virus detected ≥6 days post-onset. Risk of secondary infection among household contacts tended to be greater when primary cases had culturable virus detected after onset. Regardless of duration of culturable virus, most secondary infections (70%, 28/40) had serial intervals <6 days, suggesting early transmission. These data examine viral culture as a proxy for infectiousness, reaffirm the need for rapid control measures after infection, and highlight the potential for prolonged infectiousness (≥6 days) in many individuals.
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Affiliation(s)
- Jessica E Deyoe
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- San Francisco VA Medical Center, San Francisco, California, USA
- F.I. Proctor Foundation, University of California, San Francisco, California, USA
| | | | - Gaston Bonenfant
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Khamal Anglin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Miguel Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Jesus Pineda-Ramirez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | | | - Sharon Saydah
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Glen R Abedi
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Michel Tassetto
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Amethyst Zhang
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Kevin C Donohue
- School of Medicine, University of California, San Francisco, California, USA
| | - Michelle C Davidson
- School of Medicine, University of California, San Francisco, California, USA
| | - Ruth Diaz Sanchez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Manuella Djomaleu
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Sujata Mathur
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Joshua R Shak
- San Francisco VA Medical Center, San Francisco, California, USA
- School of Medicine, University of California, San Francisco, California, USA
| | - Steven G Deeks
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, California, USA
| | - Michael J Peluso
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, California, USA
| | - Charles Y Chiu
- Division of Infectious Diseases, University of California, San Francisco, California, USA
| | - Yuwei Zhu
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | | | - Alexandra Mellis
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Carrie Reed
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Bin Zhou
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - H Keipp Talbot
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Claire M Midgley
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Melissa A Rolfes
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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3
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Tassetto M, Garcia-Knight M, Anglin K, Kelly D, Lu S, Pineda-Ramirez J, Saydah S, Briggs-Hagen M, Zhang A, Sanchez RD, Donohue K, Romero M, Peluso MJ, Martin J, Andino R, Midgley C. 1880. Detection of Infectious SARS-CoV-2 in Specimens with High CT Values Is More Common for Omicron than for Delta Variants. Open Forum Infect Dis 2022. [PMCID: PMC9752745 DOI: 10.1093/ofid/ofac492.1507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background Although not validated, cycle threshold (Ct) values from real-time (r)RT-PCR are sometimes used as a proxy for infectiousness to inform public health decision-making. A better understanding of variant-specific viral dynamics, including RNA and infectious virus relationships, is needed to clarify implications for diagnostics and transmission. Methods Non-hospitalized SARS-CoV-2-infected individuals were recruited ≤ 5 days post-onset and self-collected nasal swabs daily for two weeks. Sequencing was used to determine variant, an in-house quantitative rRT-PCR targeting N gene was used to produce Ct values and determine RNA load, and cytopathic effect was used to assess the presence or absence of infectious virus (binary outcome). We used a Ct threshold of 30 to define high-Ct (Ct > 30) or low-Ct (Ct ≤ 30) specimens and assessed the percentage of RNA-positive specimens that had infectious virus; variant-specific percentages were compared by Χ2 test. Results We included 113 and 200 RNA-positive specimens from 18 and 28 Omicron- and Delta-infected participants, respectively; timing of RNA-positive specimen collection was similar in both groups (median = 8d post-onset). Maximum observed RNA levels occurred at median of 5 days post-onset for both variants but were lower for participants with Omicron vs Delta [mean RNA copies/mL = 105.2 vs 107.9]. Despite lower RNA levels, infectious virus was frequently detected for both variants [Omicron: median duration = 4.5d; Delta: median = 6d; p = 0.13]. Omicron specimens with infectious virus had higher Cts vs Delta specimens [mean Ct = 29.9 vs 23.2, p < 0.001]. In high-Ct specimens (Ct > 30; Table), the percentage of specimens with infectious virus was typically higher for Omicron vs Delta, and was significantly higher in adults [27.3% vs 9.5%]. In low-Ct specimens (Ct ≤ 30), the percentage with infectious virus was similar or higher for Omicron vs Delta, and was significantly higher in children [87.5% vs 53.8%] and in those unvaccinated [94.1% vs 47.4%].
![]() Conclusion CDC does not recommend the use of Ct values as a proxy for infectiousness. These data further highlight that Ct values may not provide a reliable or consistent proxy for infectiousness across variants. Disclosures All Authors: No reported disclosures.
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Affiliation(s)
| | | | | | | | | | | | - Sharon Saydah
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | | | | | | | - Michael J Peluso
- University of California San Francisco, San Francisco, California
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4
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Lu S, Anglin K, Tassetto M, Garcia-Knight M, Pineda-Ramirez J, Sanchez RD, Zhang A, Romero M, Goldberg SA, Chen JY, Donohue K, Davidson M, Lugtu K, Yee B, Chenna A, Winslow J, Petropoulos CJ, Briggs-Hagen M, Peluso MJ, Andino R, Midgley C, Martin J, Saydah S, Kelly D, Deeks S. 1048. Biological Determinants of Post-Acute Sequelae of SARS-CoV-2. Open Forum Infect Dis 2022. [DOI: 10.1093/ofid/ofac492.889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Abstract
Background
The biological determinants of post-acute sequelae of SARS-CoV-2 infection (PASC), defined as the persistence or recurrence of symptoms not explained by an alternative medical diagnosis, are poorly understood. We assessed viral and immunological determinants during acute SARS-CoV-2 infection for an association with PASC at 4 to 8 months.
Methods
From September 2020 to February 2022, symptomatic non-hospitalized individuals with laboratory-confirmed SARS-CoV-2 infection were identified within 5 days of symptom onset. We used anterior nasal biospecimens to measure the magnitude and duration of RNA and infectious viral shedding as well as blood samples to measure soluble markers of inflammation during the acute phase (first 28 days post-enrollment). PASC was defined as self-report of 1 or more COVID-19 attributed symptoms between 4 and 8 months after initial illness. We compared virologic and inflammatory markers, GFAP (a marker of neuronal damage) and neutralizing antibody levels from the acute phase between those with and without PASC using Mann-Whitney U tests or repeated measures mixed effects linear models.
Results
Among 71 SARS-CoV-2-positive participants with a completed follow-up visit between 4 to 8 months, we included 69 with virologic data and 61 with inflammatory marker data. Median age was 37 (IQR: 29 to 48) Overall, 16/72 (23%) reported at least one qualifying PASC symptom. Report of PASC was associated with >9 days of RNA shedding (p=0.04); all participants stopped RNA shedding by day 20. During acute illness, those with subsequent PASC had increased levelsof INF-alpha, INF-gamma, IP-10, IL-10, and MCP-1; these differences were greatest in the early period and normalized over 2 to 3 weeks post-illness onset. Compared to those without PASC, during the acute illness those with PASC had increased levels of GFAP and decreased levels of neutralizing antibodies but these differences were not statistically significant.
Conclusion
We found indications that viral and immunological factors during acute illness may be associated with PASC, suggesting acute immunologic response to SARS-CoV-2 may have longer term effects and play a role in PASC. Further understanding of the clinically significance of these observations is needed.
Disclosures
Ahmed Chenna, PhD, LabCorp: Employee John Winslow, PhD, Labcorp-Monogram Bioscience: Issued patents on VeraTag immunoassay-not applicable to present work|Labcorp-Monogram Bioscience: Employee|Labcorp-Monogram Biosciences: Issued patents on VeraTag immunoassay-not applicable to present work|Labcorp-Monogram Biosciences: Employee of Labcorp-Monogram Biosciences Christos J. Petropoulos, PhD, Labcorp-Monogram Biosciences: employee, corporate officer|Labcorp-Monogram Biosciences: Stocks/Bonds.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Brandon Yee
- Monogram Biosciences , San Francisco, California
| | - Ahmed Chenna
- Monogram Biosciences-LabCorp , South San Francisco, California
| | - John Winslow
- Labcorp-Monogram Biosciences , South San Francisco, California
| | | | | | - Michael J Peluso
- University of California San Francisco , San Francisco, California
| | | | - Claire Midgley
- Centers for Disease Control and Prevention , Atlanta , Georgia
| | | | - Sharon Saydah
- Centers for Disease Control and Prevention , Atlanta , Georgia
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5
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Brazer N, Morris MK, Servellita V, Anglin K, Saldhi P, Garcia-Knight M, Bethancourt S, Sotomayor-Gonzalez A, Wang B, Foresythe A, Nguyen J, Gliwa AS, Pineda-Ramirez J, Sanchez RD, Zhang Y, Ott M, Wadford DA, Andino R, Kelly JD, Hanson C, Chiu C. Neutralizing Immunity Induced Against the Omicron BA.1 and BA.2 Variants in Vaccine Breakthrough Infections. J Infect Dis 2022; 226:1688-1698. [PMID: 36134603 PMCID: PMC9619439 DOI: 10.1093/infdis/jiac384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/10/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND As of early 2022, the Omicron variants are the predominant circulating lineages globally. Understanding neutralizing antibody responses against Omicron BA.1 and BA.2 after vaccine breakthrough infections will provide insights into BA.2 infectivity and susceptibility to subsequent reinfection. METHODS Live virus neutralization assays were used to study immunity against Delta and Omicron BA.1 and BA.2 variants in samples from 86 individuals, 24 unvaccinated (27.9%) and 62 vaccinated (72.1%), who were infected with Delta (n = 42, 48.8%) or BA.1 (n = 44, 51.2%). Among the 62 vaccinated individuals, 39 were unboosted (62.9%), whereas 23 were boosted (37.1%). RESULTS In unvaccinated infections, neutralizing antibodies (nAbs) against the three variants were weak or undetectable, except against Delta for Delta-infected individuals. Both Delta and BA.1 breakthrough infections resulted in strong nAb responses against ancestral wild-type and Delta lineages, but moderate nAb responses against BA.1 and BA.2, with similar titers between unboosted and boosted individuals. Antibody titers against BA.2 were generally higher than those against BA.1 in breakthrough infections. CONCLUSIONS These results underscore the decreased immunogenicity of BA.1 compared to BA.2, insufficient neutralizing immunity against BA.2 in unvaccinated individuals, and moderate to strong neutralizing immunity induced against BA.2 in Delta and BA.1 breakthrough infections.
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Affiliation(s)
- Noah Brazer
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Mary Kate Morris
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Khamal Anglin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Prachi Saldhi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Miguel Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Sutana Bethancourt
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | | | - Baolin Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Abiodun Foresythe
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jesus Pineda-Ramirez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Ruth Diaz Sanchez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Yueyuan Zhang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Melanie Ott
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California Berkeley, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Carl Hanson
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California Berkeley, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
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6
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Daniel Kelly J, Lu S, Anglin K, Garcia-Knight M, Pineda-Ramirez J, Goldberg SA, Tassetto M, Zhang A, Donohue K, Davidson MC, Romero M, Sanchez RD, Djomaleu M, Mathur S, Chen JY, Forman CA, Servellita V, Montejano RD, Shak JR, Rutherford GW, Deeks SG, Abedi GR, Rolfes MA, Saydah S, Briggs-Hagen M, Peluso MJ, Chiu C, Midgley CM, Andino R, Martin JN. Magnitude and Determinants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Household Transmission: A Longitudinal Cohort Study. Clin Infect Dis 2022; 75:S193-S204. [PMID: 35788827 PMCID: PMC9278251 DOI: 10.1093/cid/ciac545] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Households have emerged as important venues for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Little is known, however, regarding the magnitude and determinants of household transmission in increasingly vaccinated populations. METHODS From September 2020 to January 2022, symptomatic nonhospitalized individuals with SARS-CoV-2 infection by RNA detection were identified within 5 days of symptom onset; all individuals resided with at least 1 other SARS-CoV-2-uninfected household member. These infected persons (cases) and their household members (contacts) were subsequently followed with questionnaire-based measurement and serial nasal specimen collection. The primary outcome was SARS-CoV-2 infection among contacts. RESULTS We evaluated 42 cases and their 74 household contacts. Among the contacts, 32 (43%) became infected, of whom 5 (16%) were asymptomatic; 81% of transmissions occurred by 5 days after the case's symptom onset. From 21 unvaccinated cases, 14-day cumulative incidence of SARS-CoV-2 infection among contacts was 18/40 (45% [95% confidence interval {CI}, 29%-62%]), most of whom were unvaccinated. From 21 vaccinated cases, 14-day cumulative incidence of SARS-CoV-2 infection was 14/34 (41% [95% CI, 25%-59%]) among all contacts and 12/29 (41% [95% CI, 24%-61%]) among vaccinated contacts. At least 1 comorbid condition among cases and 10 or more days of RNA detection in cases were associated with increased risk of infection among contacts. CONCLUSIONS Among households including individuals with symptomatic SARS-CoV-2 infection, both vaccinated-to-vaccinated and unvaccinated-to-unvaccinated transmission of SARS-CoV-2 to household contacts was common. Because vaccination alone did not notably reduce risk of infection, household contacts will need to employ additional interventions to avoid infection.
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Affiliation(s)
- J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Institute for Global Health Sciences, University of California, San Francisco, CA, USA
- F.I. Proctor Foundation, University of California, San Francisco, CA, USA
- San Francisco VA Medical Center, San Francisco, CA, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Institute for Global Health Sciences, University of California, San Francisco, CA, USA
| | - Khamal Anglin
- Institute for Global Health Sciences, University of California, San Francisco, CA, USA
| | | | - Jesus Pineda-Ramirez
- Institute for Global Health Sciences, University of California, San Francisco, CA, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | | | | | - Kevin Donohue
- School of Medicine, University of California, San Francisco, CA, USA
| | | | - Mariela Romero
- Institute for Global Health Sciences, University of California, San Francisco, CA, USA
| | - Ruth Diaz Sanchez
- Institute for Global Health Sciences, University of California, San Francisco, CA, USA
| | - Manuella Djomaleu
- School of Medicine, University of California, San Francisco, CA, USA
| | - Sujata Mathur
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Jessica Y Chen
- Institute for Global Health Sciences, University of California, San Francisco, CA, USA
| | - Carrie A Forman
- School of Medicine, Drexel University, Philadelphia, PA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Rubi D Montejano
- School of Medicine, University of California, San Francisco, CA, USA
| | - Joshua R Shak
- San Francisco VA Medical Center, San Francisco, CA, USA
| | - George W Rutherford
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Institute for Global Health Sciences, University of California, San Francisco, CA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital, San Francisco, CA, USA
| | - Glen R Abedi
- Respiratory Viruses Branch, Division of Viral Diseases, CDC, Atlanta, GA, USA
| | - Melissa A Rolfes
- Respiratory Viruses Branch, Division of Viral Diseases, CDC, Atlanta, GA, USA
| | - Sharon Saydah
- Respiratory Viruses Branch, Division of Viral Diseases, CDC, Atlanta, GA, USA
| | | | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital, San Francisco, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Claire M Midgley
- Respiratory Viruses Branch, Division of Viral Diseases, CDC, Atlanta, GA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, UCSF
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
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Tassetto M, Garcia-Knight M, Anglin K, Lu S, Zhang A, Romero M, Pineda-Ramirez J, Sanchez RD, Donohue KC, Pfister K, Chan C, Saydah S, Briggs-Hagen M, Peluso MJ, Martin JN, Andino R, Midgley CM, Kelly JD. Detection of Higher Cycle Threshold Values in Culturable SARS-CoV-2 Omicron BA.1 Sublineage Compared with Pre-Omicron Variant Specimens - San Francisco Bay Area, California, July 2021-March 2022. MMWR Morb Mortal Wkly Rep 2022; 71:1151-1154. [PMID: 36074732 PMCID: PMC9470222 DOI: 10.15585/mmwr.mm7136a3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Before emergence in late 2021 of the highly transmissible B.1.1.529 (Omicron) variant of SARS-CoV-2, the virus that causes COVID-19 (1,2), several studies demonstrated that SARS-CoV-2 was unlikely to be cultured from specimens with high cycle threshold (Ct) values§ from real-time reverse transcription-polymerase chain reaction (RT-PCR) tests (suggesting low viral RNA levels) (3). Although CDC and others do not recommend attempting to correlate Ct values with the amount of infectious virus in the original specimen (4,5), low Ct values are sometimes used as surrogate markers for infectiousness in clinical, public health, or research settings without access to virus culture (5). However, the consistency in reliability of this practice across SARS-CoV-2 variants remains uncertain because Omicron-specific data on infectious virus shedding, including its relationship with RNA levels, are limited. In the current analysis, nasal specimens collected from an ongoing longitudinal cohort¶ (6,7) of nonhospitalized participants with positive SARS-CoV-2 test results living in the San Francisco Bay Area** were used to generate Ct values and assess for the presence of culturable SARS-CoV-2 virus; findings were compared between specimens from participants infected with pre-Omicron variants and those infected with the Omicron BA.1 sublineage. Among specimens with culturable virus detected, Ct values were higher (suggesting lower RNA levels) during Omicron BA.1 infections than during pre-Omicron infections, suggesting variant-specific differences in viral dynamics. Supporting CDC guidance, these data show that Ct values likely do not provide a consistent proxy for infectiousness across SARS-CoV-2 variants.
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