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

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.

• Sample collection (Other): * Optional nasal specimen(s) * Blood collection

Primary outcomes

• SARS-CoV-2-specific Antibody Binding Response Rate (BAMA IgG1) by Region and Enrollment Group Among America Cohort [Measured at Months 0, 2, 4]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (BAMA IgG1) by Region and Enrollment Group Among America Cohort [Measured at Months 0, 2, 4]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (BAMA IgG3) by Region and Enrollment Group Among America Cohort [Measured at Months 0, 2]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (BAMA IgG3) by Region and Enrollment Group Among America Cohort [Measured at Months 0, 2]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (BAMA IgA) by Region and Enrollment Group Among America Cohort [Measured at Months 0, 2]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (BAMA IgA) by Region and Enrollment Group Among America Cohort [Measured at Months 0, 2]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and Enrollment Group Among America Cohort [Measured at Months 0, 2, 4, 12]: 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)
• SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and Enrollment Group Among America Cohort [Measured at Months 0, 2, 4, 12]: 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)
• SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and Enrollment Group Among Africa Cohort [Measured at Months 0, 2, 4, 12]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and Enrollment Group Among Africa Cohort [Measured at Months 0, 2, 4, 12]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (ADCC) by Region and Enrollment Group Among America Cohort [Measured at Months 0]: 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)
• SARS-CoV-2-specific Antibody Binding Response Magnitude (ADCC) by Region and Enrollment Group Among America Cohort [Measured at Months 0]: 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
• SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Rate (ICS) by Region and Enrollment Group Among America Cohort [Measured at Months 0]: 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)
• SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Magnitude (ICS) by Region and Enrollment Group Among America Cohort [Measured at Months 0]: 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)
• SARS-CoV-2-specific Memory B Cell Response Magnitude (B Cell) by Region and Enrollment Group Among America Cohort [Measured at Months 0.]: 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)
• SARS-CoV-2-specific Antibody Binding Response Rate (IgG1) by Region and COVID-19 Severity Among America Cohort [Measured at Months 0, 2, 4]: 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)
• SARS-CoV-2-specific Antibody Binding Response Magnitude (IgG1) by Region and COVID-19 Severity Among America Cohort [Measured at Months 0, 2, 4]: 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)
• SARS-CoV-2-specific Antibody Binding Response Rate (IgG3) by Region and COVID-19 Severity Among America Cohort [Measured at Months 0, 2]: 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)
• SARS-CoV-2-specific Antibody Binding Response Magnitude (IgG3) by Region and COVID-19 Severity Among America Cohort [Measured at Months 0, 2]: 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)
• SARS-CoV-2-specific Antibody Binding Response Rate (IgA) by Region and COVID-19 Severity Among America Cohort [Measured at Months 0, 2]: 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)
• SARS-CoV-2-specific Antibody Binding Response Magnitude (IgA) by Region and COVID-19 Severity Among America Cohort [Measured at Months 0, 2]: 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)
• SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and COVID-19 Severity Among America Cohort [Measured at Months 0, 2, 4, 12]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and COVID-19 Severity Among America Cohort [Measured at Months 0, 2, 4, 12]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and COVID-19 Severity Among Africa Cohort [Measured at Months 0, 2, 4, 12]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and COVID-19 Severity Among Africa Cohort [Measured at Months 0, 2, 4, 12]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (ADCC) by Region and COVID-19 Severity Among America Cohort [Measured at Months 0]: 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)
• SARS-CoV-2-specific Antibody Binding Response Magnitude (ADCC) by Region and COVID-19 Severity Among America Cohort [Measured at Months 0]: 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)
• SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Rate (ICS) by Region and COVID-19 Severity Among America Cohort [Measured at Months 0]: 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)
• SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Magnitude (ICS) by Region and COVID-19 Severity Among America Cohort [Measured at Months 0]: 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
• SARS-CoV-2-specific Memory B Cell Response Magnitude (B Cell) by Region and COVID-19 Severity Among America Cohort [Measured at Months 0]: 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)
• SARS-CoV-2-specific Antibody Binding Response Rate (IgG1) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort [Measured at Months 0, 2, 4]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (IgG1) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort [Measured at Months 0, 2, 4]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (IgG3) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort [Measured at Months 0, 2]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (IgG3) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort [Measured at Months 0, 2]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (IgA) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort [Measured at Months 0, 2]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (IgA) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort [Measured at Months 0, 2]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort [Measured at Months 0, 2, 4, 12]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort [Measured at Months 0, 2, 4, 12]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and Days Since SARS-CoV-2 Diagnosis Group Among Africa Cohort [Measured at Months 0, 2, 4, 12]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and Days Since SARS-CoV-2 Diagnosis Group Among Africa Cohort [Measured at Months 0, 2, 4, 12]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (ADCC) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort [Measured at Months 0]: 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)
• SARS-CoV-2-specific Antibody Binding Response Magnitude (ADCC) by Region and Days Since SARS-CoV-2 Diagnosis Group Among America Cohort [Measured at Months 0]: 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
• 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 [Measured at Months 0]: 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
• 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 [Measured at Months 0]: 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
• 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 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
• SARS-CoV-2-specific Antibody Binding Response Rate (IgG1) by Region and Comorbidity Group Among America Cohort [Measured at Months 0, 2, 4]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (IgG1) by Region and Comorbidity Group Among America Cohort [Measured at Months 0, 2, 4]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (IgG3) by Region and Comorbidity Group Among America Cohort [Measured at Months 0, 2]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (IgG3) by Region and Comorbidity Group Among America Cohort [Measured at Months 0, 2]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (IgA) by Region and Comorbidity Group Among America Cohort [Measured at Months 0, 2]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (IgA) by Region and Comorbidity Group Among America Cohort [Measured at Months 0, 2]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and Comorbidity Group Among America Cohort [Measured at Months 0, 2, 4, 12]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and Comorbidity Group Among America Cohort [Measured at Months 0, 2, 4, 12]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (Nab) by Region and Comorbidity Group Among Africa Cohort [Measured at Months 0, 2, 4, 12]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (Nab) by Region and Comorbidity Group Among Africa Cohort [Measured at Months 0, 2, 4, 12]: 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
• SARS-CoV-2-specific Antibody Binding Response Rate (ADCC) by Region and Comorbidity Group Among America Cohort [Measured at Months 0]: 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
• SARS-CoV-2-specific Antibody Binding Response Magnitude (ADCC) by Region and Comorbidity Group Among America Cohort [Measured at Months 0]: 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
• SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Rate (ICS) by Region and Comorbidity Group Among America Cohort [Measured at Months 0]: 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
• SARS-CoV-2-specific CD4+ and CD8+ T Cell Response Magnitude (ICS) by Region and Comorbidity Group Among America Cohort [Measured at Months 0]: 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
• SARS-CoV-2-specific Memory B Cell Response Magnitude (B Cell) by Region and Comorbidity Group Among America Cohort [Measured at Months 0]: 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
• 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 [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
• 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 [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

Secondary outcomes

• SARS-CoV-2-specific Antibody Binding Response Magnitude (IgA Nasal Sample) by Region and Enrollment Group Among America Cohort [Measured at Months 0, 2, 5]: 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
• Detection of Viral RNA in Nasopharyngeal or Nasal Swab Samples Via RT-PCR [Measured at Months 0, Month 2, Month 4, Month 12]: 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.

Sex: All, ages: 18 Years to any, accepts healthy volunteers

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.

• Results publication: 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. PMID 37352144
• Results publication: 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. PMID 34871308

• Study Protocol, Statistical Analysis Plan, and Informed Consent Form (PDF, 2020-06-04)

• Larry Corey, Study chair, HIV Vaccine Trials Network, Fred Hutch
• Shelly Karuna, Study chair, HIV Vaccine Trials Network, Fred Hutch

NIH grants: 5UM1AI068614-14