Characterizing SARS-CoV-2-specific Immunity in Individuals Who Have Recovered From COVID-19

Characterizing SARS-CoV-2-specific Immunity in Convalescent Individuals

The purpose of this study is to learn more about infection with and recovery from the virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Some people know this virus by the name "coronavirus." It can cause the disease called COVID-19.

The information gained from the study will be used to help develop better tests for SARS-CoV-2 infection and COVID-19 disease and may help in developing future vaccines and treatments by allowing researchers to determine the difference between the body's immune response to natural SARS-CoV-2 infection and immunization with a SARS-CoV-2 vaccine.

Study Overview

• Status: Completed
• Conditions: COVID-19; SARS-CoV-2
• Intervention / Treatment: Other: Sample collection

Detailed Description

This study aims to characterize the SARS-CoV-2-specific immunity in convalescent individuals.

The observational cohort study will include 3 groups, as described in the table below.

Participants will complete a minimum of one visit (1-8 weeks post resolution of COVID-19 OR 2-10 weeks post most recent positive SARS-CoV-2 test, if asymptomatic) and optional visits approximately 2 months, 4 months, and 1 year later. Participants diagnosed with SARS-CoV-2 infection at an optional follow-up visit may be contacted more frequently. Additional follow up visit(s) may be added over time in response to evolving information regarding SARS-CoV-2 infection and COVID-19.

Study visits may include physical examinations, medical history, questionnaires, pregnancy tests (for participants assigned female at birth), blood draws, optional nasal samples, and optional HIV testing.

• Study Type: Observational
• Enrollment (Actual): 760

Contacts and Locations

Study Locations

• Malawi
  • Lilongwe, Malawi
    • Malawi CRS
• Peru
  • Lima, Peru, 15001
    • Via Libra CRS
  • Lima, Peru, 15063
    • Barranco CRS
  • Lima region
    • San Miguel, Lima region, Peru, 32-15088
      • San Miguel CRS
  • Maynas
    • Iquitos, Maynas, Peru, 1
      • Asociacion Civil Selva Amazonica (ACSA) CRS
  • Provincia Constitucional del Callao
    • Bellavista, Provincia Constitucional del Callao, Peru, 15081
      • CITBM - UNIDEC, Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales CRS
• South Africa
  • Bloemfontein, South Africa
    • Josha Research CRS
  • Cape Town, South Africa
    • Emavundleni CRS
  • Cape Town, South Africa
    • Groote Schuur HIV CRS
  • Cape Town, South Africa
    • Khayelitsha CRS / (CIDRI UCT)
  • Cape Town, South Africa
    • Masiphumelele Clinical Research Site (MASI) CRS
  • Chatsworth, South Africa
    • Chatsworth CRS
  • Durban, South Africa
    • Botha's Hill CRS
  • Durban, South Africa
    • CAPRISA eThekwini CRS
  • Durban, South Africa
    • Vulindlela CRS
  • Isipingo, South Africa
    • Isipingo CRS
  • Johannesburg, South Africa
    • Kliptown Soweto CRS
  • Johannesburg, South Africa
    • Soweto HVTN CRS
  • Klerksdorp, South Africa
    • Aurum Institute Klerksdorp CRS
  • Ladysmith, South Africa
    • Qhakaza Mbokodo Research Clinic CRS
  • Mthatha, South Africa
    • Nelson Mandela Academic Research Unit CRS
  • Pretoria, South Africa
    • Synexus Stanza Clinical Research Centre CRS
  • Rustenburg, South Africa
    • Rustenburg CRS
  • Soshanguve, South Africa
    • Setshaba Research Centre CRS
  • Tembisa, South Africa
    • Tembisa Clinic 4 CRS
  • Tembisa, South Africa
    • The Aurum Institute Tembisa Clinical Research Centre CRS
  • Tongaat, South Africa
    • Tongaat CRS
  • Verulam, South Africa
    • Verulam CRS
• United States
  • Alabama
    • Birmingham, Alabama, United States, 35294
      • Alabama Vaccine CRS
  • California
    • Los Angeles, California, United States, 90035
      • UCLA CARE Center CRS
    • San Francisco, California, United States, 94143
      • Bridge HIV CRS
  • District of Columbia
    • Washington D.C., District of Columbia, United States, 20037-1894
      • George Washington University CRS
  • Georgia
    • Atlanta, Georgia, United States, 30308-2012
      • The Ponce de Leon Center CRS
    • Decatur, Georgia, United States, 30030
      • The Hope Clinic of the Emory Vaccine Center CRS
  • Illinois
    • Chicago, Illinois, United States, 60612
      • Adolescent & Young Adult Research at The CORE Center (AYAR at CORE)
  • Louisiana
    • New Orleans, Louisiana, United States, 70112
      • New Orleans Adolescent Trials Unit CRS
  • Maryland
    • Baltimore, Maryland, United States, 21205
      • Johns Hopkins University CRS
  • Massachusetts
    • Boston, Massachusetts, United States, 02115-6110
      • Brigham and Women's Hospital Vaccine CRS (BWH VCRS)
    • Boston, Massachusetts, United States, 02215-4302
      • Fenway Health Clinical Research Site CRS
  • New Jersey
    • Newark, New Jersey, United States, 07103
      • New Jersey Medical School Clinical Research Center CRS
  • New York
    • New York, New York, United States, 10027
      • Harlem Prevention Center CRS
    • New York, New York, United States, 10065
      • New York Blood Center CRS
    • New York, New York, United States, 10032-3732
      • Columbia P&S CRS
    • Rochester, New York, United States, 14642
      • University of Rochester Vaccines to Prevent HIV Infection CRS
    • The Bronx, New York, United States, 10451
      • Bronx Prevention Research Center CRS
  • North Carolina
    • Chapel Hill, North Carolina, United States, 27599
      • Chapel Hill CRS
  • Pennsylvania
    • Philadelphia, Pennsylvania, United States, 19104
      • Penn Prevention CRS
  • Tennessee
    • Nashville, Tennessee, United States, 37232-2582
      • Vanderbilt Vaccine CRS
  • Washington
    • Seattle, Washington, United States, 98109-1024
      • Seattle Vaccine and Prevention CRS
• Zambia
  • Lusaka, Zambia
    • Matero Reference Clinic CRS
• Zimbabwe
  • Chitungwiza, Zimbabwe
    • Zengeza CRS
  • Chitungwiza, Zimbabwe
    • St Mary's CRS
  • Harare, Zimbabwe
    • Seke South CRS

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 18 years and older (Adult, Older Adult)
• Accepts Healthy Volunteers: Yes

• Sampling Method: Probability Sample

Study Population

Persons reporting a positive test for SARS-CoV-2 and resolution of COVID-19 within 1-8 weeks of enrollment OR, if asymptomatic infection, reporting positive SARS-CoV-2 test within 2-10 weeks of enrollment.

Description

Inclusion Criteria:

• Age 18 or older.
• Reports having had a positive test for SARS-CoV-2.
• Reports resolution of COVID-19 within 1-8 weeks of enrollment OR, if asymptomatic infection, reports positive SARS-CoV-2 test within 2-10 weeks of enrollment. Not excluded: individuals with symptoms consistent with residual sequelae of resolved COVID-19, in the clinical judgement of the investigator.
• Access to a participating HVTN or HPTN CRS and willingness to be followed for the planned duration of the study.
• Ability and willingness to provide informed consent.
• Assessment of understanding: volunteer demonstrates understanding of this study.
• Volunteers who were assigned female sex at birth: negative urine or serum beta human chorionic gonadotropin (β-HCG) pregnancy test within 4 days of enrollment visit (ie, prior to enrollment blood draw or nasal collections). Persons who are NOT of reproductive potential due to having undergone hysterectomy or bilateral oophorectomy (verified by medical records) or having reached menopause (no menses for ≥ 1 year ), are not required to undergo pregnancy testing.

Exclusion Criteria:

• Reports current COVID-19.
• Pregnant.
• Receipt of SARS-CoV-2 specific antibodies (eg, convalescent plasma or sera, monoclonal antibodies, hyperimmune globulin). Not excluded: antibody therapy without SARS-CoV-2 specificity (eg, IL-6 pathway inhibitors for COVID-19).
• SARS-CoV-2 vaccine(s) received in a prior vaccine trial.
• Any medical, psychiatric, occupational, or other condition that, in the judgment of the investigator, would interfere with, or serve as a contraindication to, protocol adherence or a volunteer's ability to give informed consent.

Study Plan

How is the study designed?

Design Details

• Observational Models: Cohort
• Time Perspectives: Other

Number of groups / cohorts

3

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
Group 1; Persons not hospitalized for COVID-19, without clinical spectrum or outcomes specified in group 3; 1A: Persons with asymptomatic infection, ages 18 through 55, inclusive; 1B: Persons with asymptomatic infection, age > 55; 1C: Persons with symptomatic infection (ie, COVID-19) ages 18 through 55; 1D: Persons with symptomatic infection (ie, COVID-19), age > 55	Other: Sample collection; Optional nasal specimen(s); Blood collection
Group 2; Persons previously hospitalized for COVID-19, without clinical spectrum or outcomes specified in group 3; 2A: Persons 18 through 55 years of age; 2B: Persons > 55 years of age	Other: Sample collection; Optional nasal specimen(s); Blood collection
Group 3; Persons with specific clinical spectrums or outcomes, regardless of hospitalization history (eg, persons recovered after intubation, with prolonged viral shedding, with myocarditis/pericarditis, with rapid recovery from COVID-19, with a second positive SARS-CoV-2 RT-PCR test result after a negative result)	Other: Sample collection; Optional nasal specimen(s); Blood collection

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
SARS-CoV-2-specific Antibody Binding Response Rate (BAMA IgG1) by Region and Enrollment Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by binding antibody multiplex assay (BAMA IgG1) at Visit 1, 2, 3, overall and by region and enrollment group	Measured at Months 0, 2, 4
SARS-CoV-2-specific Antibody Binding Response Magnitude (BAMA IgG1) by Region and Enrollment Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by binding antibody multiplex assay (BAMA IgG1) at Visit 1, 2, 3, overall and by region and enrollment group	Measured at Months 0, 2, 4
SARS-CoV-2-specific Antibody Binding Response Rate (BAMA IgG3) by Region and Enrollment Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarizedSARS-CoV-2-specific Antibody Binding Response Rate by binding antibody multiplex assay (BAMA IgG3) at Visit 1, 2, overall and by region and enrollment group among America Cohort	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Magnitude (BAMA IgG3) by Region and Enrollment Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarizedSARS-CoV-2-specific Antibody Binding Response Magnitude by binding antibody multiplex assay (BAMA IgG3) at Visit 1, 2, overall and by region and enrollment group among America Cohort	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Rate (BAMA IgA) by Region and Enrollment Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by binding antibody multiplex assay (BAMA IgA) at Visit 1, 2, overall and by region and enrollment group among America Cohort	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Magnitude (BAMA IgA) by Region and Enrollment Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by binding antibody multiplex assay (BAMA IgA) at Visit 1, 2, overall and by region and enrollment group among America Cohort	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and Enrollment Group Among America Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by neutralizing antibody assay (NAb) at Visit 1, 2, 3, 4, overall and by region and enrollment group among America Cohort (USA and Peru only)	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and Enrollment Group Among America Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by neutralizing antibody assay (NAb) at Visit 1, 2,3,4, overall and by region and enrollment group among America Cohort (USA and Peru only)	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and Enrollment Group Among Africa Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by neutralizing antibody assay (NAb) at Visit 1, 2, 3, 4, overall and by region and enrollment group among Africa Cohort	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and Enrollment Group Among Africa Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by neutralizing antibody assay (NAb) at Visit 1, 2, 3, 4, overall and by region and enrollment group among Africa Cohort	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Rate (ADCC) by Region and Enrollment Group Among America Cohort	Antibody-dependent NK cell degranulation will be measured using ADCC assay at a dilution 1:500. Two readouts will be the background-subtracted % CD107A+ NK cells for the infected cells and the background-subtracted % CD107A+ NK cells for the transfected cells. The positive responses will be called if the values of background-subtracted % CD107A+ ≥ 4.07 and ≥5.27 for the infected and transfected cells, respectively. The cutoffs are determined by mean+2SD, respectively, from the SARS-CoV-2 negative controls. Percent CD107a+ NK Cells was the response magnitudes. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by antibody-dependent cellular cytotoxicity assay (ADCC) at Visit 1, overall and by region and enrollment group among America Cohort (USA and Peru only)	Measured at Months 0
SARS-CoV-2-specific Antibody Binding Response Magnitude (ADCC) by Region and Enrollment Group Among America Cohort	Antibody-dependent NK cell degranulation will be measured using ADCC assay at a dilution 1:500. Two readouts will be the background-subtracted % CD107A+ NK cells for the infected cells and the background-subtracted % CD107A+ NK cells for the transfected cells. The positive responses will be called if the values of background-subtracted % CD107A+ ≥ 4.07 and ≥5.27 for the infected and transfected cells, respectively. The cutoffs are determined by mean+2SD, respectively, from the SARS-CoV-2 negative controls. Percent CD107a+ NK Cells was the response magnitudes. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by antibody-dependent cellular cytotoxicity assay (ADCC) Visit 1, overall and by region and enrollment group among America Cohort	Measured at Months 0
SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Rate (ICS) by Region and Enrollment Group Among America Cohort	Flow cytometry was used to examine SARS-CoV-2 specific CD4+ and CD8+ T-cell responses using an intracellular cytokine staining (ICS). Positive calls will be made using Fisher's exact positivity test for all the markers. The magnitudes are % T cells expressing IFN-g/IL-2. The table summarized SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Rate by flow cytometry at Visit 1 , overall and by region and enrollment group among America Cohort (USA and Peru only)	Measured at Months 0
SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Magnitude (ICS) by Region and Enrollment Group Among America Cohort	Flow cytometry was used to examine SARS-CoV-2 specific CD4+ and CD8+ T-cell responses using an intracellular cytokine staining (ICS). Positive calls will be made using Fisher's exact positivity test for all the markers. The magnitudes are % T cells expressing IFN-g/IL-2. The table summarized SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Magnitude by flow cytometry at Visit 1, overall and by region and enrollment group among America Cohort positive responders (USA and Peru)	Measured at Months 0
SARS-CoV-2-specific Memory B Cell Response Magnitude (B Cell) by Region and Enrollment Group Among America Cohort	SARS-CoV-2-specific B cell responses and B cell phenotypic data was identified and characterized using fluorescently-labelled recombinant Env proteins (S6P and RBD) in combination with a flow cytometry antibody panel on all available samples from the enrollment visit (V1). There is no positivity call for B cell phenotypic data. The magnitude is B cell subset frequency. The table summarized SARS-CoV-2-specific Memory B Cell Response Magnitude by flow cytometry at Visit 1, overall and by region and enrollment group among America Cohort (USA and Peru only)	Measured at Months 0.
SARS-CoV-2-specific Antibody Binding Response Rate (IgG1) by Region and COVID-19 Severity Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by binding antibody multiplex assay (BAMA IgG1) at Visit 1, 2, 3 , overall and by region and COVID-19 severity among America Cohort (USA and Peru)	Measured at Months 0, 2, 4
SARS-CoV-2-specific Antibody Binding Response Magnitude (IgG1) by Region and COVID-19 Severity Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by binding antibody multiplex assay (BAMA IgG1) at Visit 1, 2, 3, overall and by region and COVID-19 severity among America Cohort (USA and Peru)	Measured at Months 0, 2, 4
SARS-CoV-2-specific Antibody Binding Response Rate (IgG3) by Region and COVID-19 Severity Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by binding antibody multiplex assay (BAMA IgG3) at Visit 1, 2, overall and by region and COVID-19 severity among America Cohort (USA and Peru)	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Magnitude (IgG3) by Region and COVID-19 Severity Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point.SARS-CoV-2-specific Antibody Binding Response Magnitude by binding antibody multiplex assay (BAMA IgG3) at Visit 1, 2, overall and by region and COVID-19 severity among America Cohort (USA and Peru)	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Rate (IgA) by Region and COVID-19 Severity Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by binding antibody multiplex assay (BAMA IgA) at Visit 1, 2, overall and by region and COVID-19 severity among America Cohort (USA and Peru)	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Magnitude (IgA) by Region and COVID-19 Severity Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by binding antibody multiplex assay (BAMA IgA) at Visit 1, 2, overall and by region and COVID-19 severity among America Cohort (USA and Peru)	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and COVID-19 Severity Among America Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by neutralizing antibody assay (NAb) at Visit 1, 2, 3, 4, overall and by region and COVID-19 severity	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and COVID-19 Severity Among America Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by neutralizing antibody assay (NAb) at Visit 1, 2,3,4, overall and by region and COVID-19 severity among America Cohort	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and COVID-19 Severity Among Africa Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by neutralizing antibody assay (NAb) at Visit 1, 2, 3, 4, overall and by region and COVID-19 severity	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and COVID-19 Severity Among Africa Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by neutralizing antibody assay (NAb) at Visit 1, 2, 3, 4, overall and by region and COVID-19 severity among Africa Cohort	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Rate (ADCC) by Region and COVID-19 Severity Among America Cohort	Antibody-dependent NK cell degranulation will be measured using ADCC assay at a dilution 1:500. Two readouts will be the background-subtracted % CD107A+ NK cells for the infected cells and the background-subtracted % CD107A+ NK cells for the transfected cells. The positive responses will be called if the values of background-subtracted % CD107A+ ≥ 4.07 and ≥5.27 for the infected and transfected cells, respectively. The cutoffs are determined by mean+2SD, respectively, from the SARS-CoV-2 negative controls. Percent CD107a+ NK Cells was the response magnitudes. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by antibody-dependent cellular cytotoxicity assay (ADCC) at Visit 1, overall and by region and COVID-19 severity among America Cohort (USA and Peru)	Measured at Months 0
SARS-CoV-2-specific Antibody Binding Response Magnitude (ADCC) by Region and COVID-19 Severity Among America Cohort	Antibody-dependent NK cell degranulation will be measured using ADCC assay at a dilution 1:500. Two readouts will be the background-subtracted % CD107A+ NK cells for the infected cells and the background-subtracted % CD107A+ NK cells for the transfected cells. The positive responses will be called if the values of background-subtracted % CD107A+ ≥ 4.07 and ≥5.27 for the infected and transfected cells, respectively. The cutoffs are determined by mean+2SD, respectively, from the SARS-CoV-2 negative controls. Percent CD107a+ NK Cells was the response magnitudes. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by antibody-dependent cellular cytotoxicity assay (ADCC) Visit 1, overall and by region and COVID-19 severity among America Cohort (USA and Peru)	Measured at Months 0
SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Rate (ICS) by Region and COVID-19 Severity Among America Cohort	Flow cytometry was used to examine SARS-CoV-2 specific CD4+ and CD8+ T-cell responses using an intracellular cytokine staining (ICS). Positive calls will be made using Fisher's exact positivity test for all the markers. The magnitudes are % T cells expressing IFN-g/IL-2. The table summarized SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Rate by flow cytometry at Visit 1, overall and by region and COVID-19 severity among America Cohort (USA and Peru)	Measured at Months 0
SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Magnitude (ICS) by Region and COVID-19 Severity Among America Cohort	Flow cytometry was used to examine SARS-CoV-2 specific CD4+ and CD8+ T-cell responses using an intracellular cytokine staining (ICS). Positive calls will be made using Fisher's exact positivity test for all the markers. The magnitudes are % T cells expressing IFN-g/IL-2. The table summarized SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Magnitude by flow cytometry at Visit 1, overall and by region and COVID-19 severity among America Cohort	Measured at Months 0
SARS-CoV-2-specific Memory B Cell Response Magnitude (B Cell) by Region and COVID-19 Severity Among America Cohort	SARS-CoV-2-specific B cell responses and B cell phenotypic data was identified and characterized using fluorescently-labelled recombinant Env proteins (S6P and RBD) in combination with a flow cytometry antibody panel on all available samples from the enrollment visit (V1). The sample will be included in the analysis only if the number of IgD- B cells is equal or greater than 1000 for that sample. The table summarized SARS-CoV-2-specific Memory B Cell Response Magnitude by flow cytometry at Visit 1, overall and by region and COVID-19 severity among America Cohort (USA and Peru)	Measured at Months 0
SARS-CoV-2-specific Antibody Binding Response Rate (IgG1) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by binding antibody multiplex assay (BAMA IgG1) at Visit 1, 2, 3, overall and by region and days since SARS-CoV-2 diagnosis group among America Cohort	Measured at Months 0, 2, 4
SARS-CoV-2-specific Antibody Binding Response Magnitude (IgG1) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by BAMA IgG1 at Visit 1, 2, 3, overall and by region and days since SARS-CoV-2 diagnosis group among America Cohort	Measured at Months 0, 2, 4
SARS-CoV-2-specific Antibody Binding Response Rate (IgG3) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by binding antibody multiplex assay (BAMA IgG3) at Visit 1, 2, overall and by region and days since SARS-CoV-2 diagnosis group among America Cohort	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Magnitude (IgG3) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by binding antibody multiplex assay (BAMA IgG3) at Visit 1, 2, overall and by region and days since SARS-CoV-2 diagnosis group among America Cohort	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Rate (IgA) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by binding antibody multiplex assay (BAMA IgA) at Visit 1, 2, overall and by region and days since SARS-CoV-2 diagnosis group among America Cohort	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Magnitude (IgA) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by binding antibody multiplex assay (BAMA IgA) at Visit 1, 2, overall and by region and days since SARS-CoV-2 diagnosis group among America Cohort	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by neutralizing antibody assay (NAb) at Visit 1, 2, 3, 4, overall and by region and days since SARS-CoV-2 diagnosis group among America Cohort	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by neutralizing antibody assay (NAb) at Visit 1, 2,3, 4, overall and by region and days since SARS-CoV-2 diagnosis group among America Cohort	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and Days Since SARS-CoV-2 Diagnosis Group Among Africa Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by neutralizing antibody assay (NAb) at Visit 1, 2, 3, 4, overall and by region and days since SARS-CoV-2 diagnosis group among Africa Cohort	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and Days Since SARS-CoV-2 Diagnosis Group Among Africa Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by neutralizing antibody assay (NAb) at Visit 1, 2, 3, 4, overall and by region and days since SARS-CoV-2 diagnosis group among Africa Cohort	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Rate (ADCC) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort	Antibody-dependent NK cell degranulation will be measured using ADCC assay at a dilution 1:500. Two readouts will be the background-subtracted % CD107A+ NK cells for the infected cells and the background-subtracted % CD107A+ NK cells for the transfected cells. The positive responses will be called if the values of background-subtracted % CD107A+ ≥ 4.07 and ≥5.27 for the infected and transfected cells, respectively. The cutoffs are determined by mean+2SD, respectively, from the SARS-CoV-2 negative controls. Percent CD107a+ NK Cells was the response magnitudes. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by antibody-dependent cellular cytotoxicity assay (ADCC) at Visit 1, overall and by region and days since SARS-CoV-2 diagnosis group among America Cohort (USA and Peru)	Measured at Months 0
SARS-CoV-2-specific Antibody Binding Response Magnitude (ADCC) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort	Antibody-dependent NK cell degranulation will be measured using ADCC assay at a dilution 1:500. Two readouts will be the background-subtracted % CD107A+ NK cells for the infected cells and the background-subtracted % CD107A+ NK cells for the transfected cells. The positive responses will be called if the values of background-subtracted % CD107A+ ≥ 4.07 and ≥5.27 for the infected and transfected cells, respectively. The cutoffs are determined by mean+2SD, respectively, from the SARS-CoV-2 negative controls. Percent CD107a+ NK Cells was the response magnitudes. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by antibody-dependent cellular cytotoxicity assay (ADCC) Visit 1, overall and by region and days since SARS-CoV-2 diagnosis group among America Cohort	Measured at Months 0
SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Rate (ICS) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort	Flow cytometry was used to examine SARS-CoV-2 specific CD4+ and CD8+ T-cell responses using an intracellular cytokine staining (ICS). Positive calls will be made using Fisher's exact positivity test for all the markers. The magnitudes are % T cells expressing IFN-g/IL-2. The table summarized SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Rate by flow cytometry at Visit 1, overall and by region and days since SARS-CoV-2 diagnosis group among America Cohort	Measured at Months 0
SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Magnitude (ICS) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort	Flow cytometry was used to examine SARS-CoV-2 specific CD4+ and CD8+ T-cell responses using an intracellular cytokine staining (ICS). Positive calls will be made using Fisher's exact positivity test for all the markers. The magnitudes are % T cells expressing IFN-g/IL-2. The table summarized SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Magnitude by flow cytometry at Visit 1, overall and by region and days since SARS-CoV-2 diagnosis group among America Cohort	Measured at Months 0
SARS-CoV-2-specific Memory B Cell Response Magnitude (B Cell) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort	SARS-CoV-2-specific B cell responses and B cell phenotypic data was identified and characterized using fluorescently-labelled recombinant Env proteins (S6P and RBD) in combination with a flow cytometry antibody panel on all available samples from the enrollment visit (V1). The sample will be included in the analysis only if the number of IgD- B cells is equal or greater than 1000 for that sample. The table summarized SARS-CoV-2-specific Memory B Cell Response Magnitude (B Cell) by Region and Days Since SARS-CoV-2 Diagnosis Group among America Cohort	Measured at Months 0
SARS-CoV-2-specific Antibody Binding Response Rate (IgG1) by Region and Comorbidity Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by binding antibody multiplex assay (BAMA IgG1) at Visit 1, 2, 3 , overall and by region and comorbidity group among America Cohort	Measured at Months 0, 2, 4
SARS-CoV-2-specific Antibody Binding Response Magnitude (IgG1) by Region and Comorbidity Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by binding antibody multiplex assay (BAMA IgG1) at Visit 1, 2, 3, overall and by region and comorbidity group among America Cohort	Measured at Months 0, 2, 4
SARS-CoV-2-specific Antibody Binding Response Rate (IgG3) by Region and Comorbidity Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by binding antibody multiplex assay (BAMA IgG3) at Visit 1, 2, overall and by region and comorbidity group among America Cohort	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Magnitude (IgG3) by Region and Comorbidity Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by binding antibody multiplex assay (BAMA IgG3) at Visit 1, 2, overall and by region and comorbidity group among America Cohort	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Rate (IgA) by Region and Comorbidity Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by binding antibody multiplex assay (BAMA IgA) at Visit 1, 2, overall and by region and comorbidity group among America Cohort	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Magnitude (IgA) by Region and Comorbidity Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by binding antibody multiplex assay (BAMA IgA) at Visit 1, 2, overall and by region and comorbidity group among America Cohort	Measured at Months 0, 2
SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and Comorbidity Group Among America Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by neutralizing antibody assay (NAb) at Visit 1, 2, 3, 4, overall and by region and comorbidity group among America Cohort	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and Comorbidity Group Among America Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by neutralizing antibody assay (NAb) at Visit 1, 2,3,4, overall and by region and comorbidity group among America Cohort	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and Comorbidity Group Among Africa Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by neutralizing antibody assay (NAb) at Visit 1, 2, 3, 4, overall and by region and comorbidity group among Africa Cohort	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and Comorbidity Group Among Africa Cohort	Neutralizing antibodies against SARS coronaviruses are measured in 293T/ACE2 cells for all HIV negative samples. MPI (maximum percent inhibition) is also measured. Positivity calls are an ID50/ID80 (50% and 80% inhibitory dose) value either >20 (the lower limit of detection (LLOD) of the assay) or MPI is between 10%-50%. The neutralizing antibody ID50/ID80 of all HIV positive samples are measured by a different assay, VSV pseudovirus neutralization assay. Positivity calls are based on whether or not any neutralization is observed through entire titration (starting dilution 1:20) with MPI between 10%-50%. For the positive calls but the neutralization does not reach 50% or 80%, ID50/ID80 titer is first estimated by Prism. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by neutralizing antibody assay (NAb) at Visit 1, 2, 3, 4, overall and by region and comorbidity group among Africa Cohort	Measured at Months 0, 2, 4, 12
SARS-CoV-2-specific Antibody Binding Response Rate (ADCC) by Region and Comorbidity Group Among America Cohort	Antibody-dependent NK cell degranulation will be measured using ADCC assay at a dilution 1:500. Two readouts will be the background-subtracted % CD107A+ NK cells for the infected cells and the background-subtracted % CD107A+ NK cells for the transfected cells. The positive responses will be called if the values of background-subtracted % CD107A+ ≥ 4.07 and ≥5.27 for the infected and transfected cells, respectively. The cutoffs are determined by mean+2SD, respectively, from the SARS-CoV-2 negative controls. Percent CD107a+ NK Cells was the response magnitudes. The table summarized SARS-CoV-2-specific Antibody Binding Response Rate by antibody-dependent cellular cytotoxicity assay (ADCC) at Visit 1, overall and by region and comorbidity group among America Cohort	Measured at Months 0
SARS-CoV-2-specific Antibody Binding Response Magnitude (ADCC) by Region and Comorbidity Group Among America Cohort	Antibody-dependent NK cell degranulation will be measured using ADCC assay at a dilution 1:500. Two readouts will be the background-subtracted % CD107A+ NK cells for the infected cells and the background-subtracted % CD107A+ NK cells for the transfected cells. The positive responses will be called if the values of background-subtracted % CD107A+ ≥ 4.07 and ≥5.27 for the infected and transfected cells, respectively. The cutoffs are determined by mean+2SD, respectively, from the SARS-CoV-2 negative controls. Percent CD107a+ NK Cells was the response magnitudes. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by antibody-dependent cellular cytotoxicity assay (ADCC) Visit 1, overall and by region and comorbidity group among America Cohort	Measured at Months 0
SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Rate (ICS) by Region and Comorbidity Group Among America Cohort	Flow cytometry was used to examine SARS-CoV-2 specific CD4+ and CD8+ T-cell responses using an intracellular cytokine staining (ICS). Positive calls will be made using Fisher's exact positivity test for all the markers. The magnitudes are % T cells expressing IFN-g/IL-2. The table summarized SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Rate by flow cytometry at Visit 1, overall and by region and comorbidity group among America Cohort	Measured at Months 0
SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Magnitude (ICS) by Region and Comorbidity Group Among America Cohort	Flow cytometry was used to examine SARS-CoV-2 specific CD4+ and CD8+ T-cell responses using an intracellular cytokine staining (ICS). Positive calls will be made using Fisher's exact positivity test for all the markers. The magnitudes are % T cells expressing IFN-g/IL-2. The table summarized SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Magnitude by flow cytometry at Visit 1, overall and by region and Comorbidity Group among America Cohort	Measured at Months 0
SARS-CoV-2-specific Memory B Cell Response Magnitude (B Cell) by Region and Comorbidity Group Among America Cohort	SARS-CoV-2-specific B cell responses and B cell phenotypic data was identified and characterized using fluorescently-labelled recombinant Env proteins (S6P and RBD) in combination with a flow cytometry antibody panel on all available samples from the enrollment visit (V1). The sample will be included in the analysis only if the number of IgD- B cells is equal or greater than 1000 for that sample. The table summarized SARS-CoV-2-specific Memory B Cell Response Magnitude by flow cytometry at Visit 1, overall and by region and comorbidity group among America Cohort	Measured at Months 0
SARS-CoV-2-specific Infection Presentation, Including Clinical Course, Along With Demographics and Corresponding Medical History of Participants , Overall and by Region Among America Cohort	SARS-CoV-2-specific Infection Presentation, Including Clinical Course, Along With Demographics and Corresponding Medical History of Participants , overall and by region	Measured at Months 0
SARS-CoV-2-specific Infection Presentation, Including Clinical Course, Along With Demographics and Corresponding Medical History of Participants , Overall and by Region Among Africa Cohort	SARS-CoV-2-specific Infection Presentation, Including Clinical Course, Along With Demographics and Corresponding Medical History of Participants , overall and by region	Measured at Months 0

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
SARS-CoV-2-specific Antibody Binding Response Magnitude (IgA Nasal Sample) by Region and Enrollment Group Among America Cohort	BAMA assays was performed for samples from participants at Visit 1 (Month 0, baseline) and available samples at follow-up visits (Month 2, 4). Serum SARS-CoV-2-specific IgA, IgG1, IgG3 responses (dilution 1:50) to SARS-CoV-2 antigens were measured on a Bio-Plex instrument (Bio-Rad). The Bioplex software provides 2 readouts: a background-subtracted mean fluorescence intensity (MFI), where background refers to a plate level control (i.e., a blank well run on each plate), and a concentration based on a standard curve. Positive responses at each visit will be called if the MFI minus blank values are ≥ isotype, antigen, and dilution-specific cutoff (will be provided by the lab). MFIs minus blank (or net MFI) are used to summarize the magnitude at a given time-point. The table summarized SARS-CoV-2-specific Antibody Binding Response Magnitude by binding antibody multiplex assay (BAMA IgA nasal sample) at Visit 1, 2, 3, overall and by region and enrollment group among America Cohort	Measured at Months 0, 2, 5
Detection of Viral RNA in Nasopharyngeal or Nasal Swab Samples Via RT-PCR	This outcome measures the detection rate of viral RNA in nasopharyngeal or nasal swab samples collected at Visits 1, 2, 3, 4 using RT-PCR. Participation was optional, and not all participants provided samples. Results presented in this table include only participants from the Africa cohort (South Africa and other African countries), whose samples were tested using the RT-RNA Fisher TaqPath assay and Americas cohort (Peru and the United States), samples were tested using the RT-RNA Panther assay.	Measured at Months 0, Month 2, Month 4, Month 12

Collaborators and Investigators

• Sponsor: HIV Vaccine Trials Network
• Collaborators: National Institute of Allergy and Infectious Diseases (NIAID); HIV Prevention Trials Network
• Investigators: Study Chair: Larry Corey, HIV Vaccine Trials Network, Fred Hutch; Study Chair: Shelly Karuna, HIV Vaccine Trials Network, Fred Hutch

Publications and helpful links

General Publications

• Karuna S, Li SS, Grant S, Walsh SR, Frank I, Casapia M, Trahey M, Hyrien O, Fisher L, Miner MD, Randhawa AK, Polakowski L, Kublin JG, Corey L, Montefiori D; HVTN 405/HPTN 1901 Study Team. Neutralizing antibody responses over time in demographically and clinically diverse individuals recovered from SARS-CoV-2 infection in the United States and Peru: A cohort study. PLoS Med. 2021 Dec 6;18(12):e1003868. doi: 10.1371/journal.pmed.1003868. eCollection 2021 Dec.
• Karuna S, Gallardo-Cartagena JA, Theodore D, Hunidzarira P, Montenegro-Idrogo J, Hu J, Jones M, Kim V, De La Grecca R, Trahey M, Karg C, Takalani A, Polakowski L, Hutter J, Miner MD, Erdmann N, Goepfert P, Maboa R, Corey L, Gill K, Li SS; HVTN 405/HPTN 1901 Study Team. Post-COVID symptom profiles and duration in a global convalescent COVID-19 observational cohort: Correlations with demographics, medical history, acute COVID-19 severity and global region. J Glob Health. 2023 Jun 23;13:06020. doi: 10.7189/jogh.13.06020.

Study record dates

Study Major Dates

• Study Start (Actual): May 13, 2020
• Primary Completion (Actual): April 21, 2022
• Study Completion (Actual): April 21, 2022

Study Registration Dates

• First Submitted: May 22, 2020
• First Submitted That Met QC Criteria: May 22, 2020
• First Posted (Actual): May 27, 2020

Study Record Updates

• Last Update Posted (Estimated): January 12, 2026
• Last Update Submitted That Met QC Criteria: December 18, 2025
• Last Verified: December 1, 2025

More Information

Terms related to this study

• Additional Relevant MeSH Terms: Respiratory Tract Infections; Infections; RNA Virus Infections; Virus Diseases; Respiratory Tract Diseases; Lung Diseases; Pneumonia, Viral; Pneumonia; Coronavirus Infections; Coronaviridae Infections; Nidovirales Infections; COVID-19; Investigative Techniques; Clinical Laboratory Techniques; Diagnostic Techniques and Procedures; Diagnosis; Specimen Handling
• Other Study ID Numbers: HVTN 405/HPTN 1901; 5UM1AI068614-14 (U.S. NIH Grant/Contract)

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No