SARS-CoV-2 antibody response among people living with HIV: insights from a serological study in Kenya

¹School of Public Health, Amref International University, Nairobi, Kenya

^&Corresponding author
Ann Wanjira Maina, School of Public Health, Amref International University, Nairobi, Kenya

Introduction    

While the World Health Organization has declared that SARS-CoV-2 is no longer a public health emergency of international concern [1,2], its long-term immunological consequences, particularly among people living with HIV (PLHIV), remain inadequately understood. There is growing concern that the quality, durability, and magnitude of antibody responses following SARS-CoV-2 infection or vaccination may be impaired in this population due to ongoing immune dysregulation, age-related immune senescence, and ART-related variations in immune recovery [3-5]. This underscores the importance of evaluating immune responses beyond viral suppression to inform personalized care and vaccine strategies.

In sub-Saharan Africa, which accounts for over 75% of global HIV cases, the combined impact of HIV and COVID-19 continues to challenge public health systems. In Kenya alone, where approximately 1.5 million PLHIV, according to a The Joint United Nations Programme on HIV/AIDS (UNAIDS) report, the pandemic significantly disrupted HIV testing, treatment continuity, and prevention services [6]. Yet, despite this high burden, data on SARS-CoV-2 antibody responses among PLHIV in African settings remain limited [7-10]. Most existing studies have emerged from high-income contexts, with little applicability to Kenya´s unique epidemiological and health system landscape [4,11].

The emergence of SARS-CoV-2 and its sweeping global impact brought to light the heightened vulnerability of immunocompromised populations, notably PLHIV. HIV, a chronic viral infection, gradually erodes immune function through persistent CD4+ T-cell depletion and chronic immune activation [12-14]. This immunosuppression presents unique challenges during acute viral outbreaks like COVID-19, potentially compromising vaccine-induced immunity and increasing the risk of severe disease outcomes [15,16].

This study addresses that critical gap by leveraging secondary data from a seroprevalence survey. It uses the multiplex bead assay (MBA), a sensitive and scalable serological method, to assess IgG responses to SARS-CoV-2 antigens among PLHIV across four Kenyan counties with varying levels of HIV prevalence, service access, and COVID-19 exposure. The MBA approach, which measures antibody responses to the spike receptor-binding domain (RBD), nucleocapsid protein (NP), and a hybrid RBD-NP antigen, allows for nuanced differentiation between natural infection, vaccine-induced responses, and hybrid immunity.

By analyzing antibody profiles in relation to age, antiretroviral therapy (ART) duration, viral load (VL) suppression, and vaccination status, this study provides critical insights into immune responsiveness among PLHIV. These findings can inform context-specific vaccine recommendations, strengthen immunological surveillance systems, and guide the integration of pandemic preparedness into routine HIV care. Ultimately, the evidence generated will support more inclusive, data-driven health strategies for Kenya and other high-burden countries facing the intersection of chronic and emerging infectious diseases [7,17-20].

Methods     

Study design: a secondary data analysis leveraging a large-scale cross-sectional SARS-CoV-2 seroprevalence surveillance initiative conducted among PLHIV in four The U.S. President's Emergency Plan for AIDS Relief (PEPFAR) -supported counties in Kenya (Nairobi, Kisumu, Homa Bay, and Kirinyaga).

Study setting and population: drawing on remnant plasma samples originally collected for routine HIV viral load (VL) testing between February 2021 and October 2022, the study utilized data from four rounds of cross-sectional sampling processed in six accredited reference laboratories. A total of 8,007 remnant VL samples were collected in the parent study, of which 6,993 were tested using enzyme-linked immunosorbent assay (ELISA). Following ELISA screening, 3,861 positive and 175 borderline samples were selected for multiplex bead assay (MBA) testing. Of these, 4,031 samples were successfully tested using MBA, and 3,795 with complete antibody response classification data were included in the final analysis.

Variables: the primary exposures were SARS-CoV-2 infection and COVID-19 vaccination status. The outcome variable was SARS-CoV-2 antibody response, measured using antigen-specific IgG responses (anti-RBD, anti-NP, and hybrid responses). Key predictors included ART regimen, duration on ART, and viral load suppression status. Potential confounders included age, sex, and county of residence. Age was categorized into <15, 15-24, 25-44, 45-64, and ≥65 years in line with WHO and PEPFAR reporting standards.

Laboratory testing: laboratory testing was conducted at The Kenya Medical Research Institute (KEMRI) HIV Research Laboratory in Kisumu using enzyme-linked immunosorbent assay (ELISA) and multiplex bead assay (MBA) techniques. The MBA utilized magnetic microspheres coupled with recombinant SARS-CoV-2 antigens to detect IgG antibodies against three targets: RBD of the spike protein, nucleocapsid protein (NP) and a hybrid RBD-NP antigen. Testing was performed using the Luminex MagPix system (Luminex Corporation, Austin, TX, USA), which measures median fluorescence intensity (MFI). Relative fluorescence intensity (RFI) values were calculated by normalizing MFI against internal controls to ensure assay accuracy. Antibody responses were classified based on predefined RFI thresholds as follows: probable infection: NP-positive response, probable vaccination: RBD-positive, NP-negative response, probable vaccination and infection: RBD and NP positive and negative: no detectable antibody response. These classifications enabled differentiation between natural infection, vaccine-induced immunity, and hybrid immunity.

Data collection: demographic, clinical, and vaccination metadata were abstracted from Amref Health Africa´s database using a structured tool, with strict classification criteria applied to vaccination status. Only anonymized datasets were used, and ethical clearance was obtained from Amref Health Africa Ethics and Scientific Review Committee (AMREF ESRC) and National Commission for Science, Technology and Innovation (NACOSTI).

Ethical considerations: this study was conducted in accordance with the principles outlined in Kenya's national ethical research guidelines. Ethical approval for the use of remnant viral load samples and secondary data analysis was obtained from the Amref Health Africa Ethics and Scientific Review Committee (AMREF-ESRC P1843/2025 and the National Commission for Science, Technology and Innovation (NACOSTI) license no: NACOSTI/P/25/4173862). Waiver of informed consent under 45 CFR 46.116(d) was obtained for the parent study as the investigation posed minimal risk, and no additional blood draws were needed. Samples were stored at -80°C for up to three years in accordance with national biorepository guidelines to preserve antibody integrity.

Sample size: the analytical sample consisted of all available ELISA-positive and borderline remnant samples eligible for MBA testing (n = 4,036). This sample size was based on available data from the parent surveillance study and provided sufficient statistical power to assess associations between demographic and clinical factors and antibody responses.

Data analysis: data were cleaned and analyzed using Stata v17 and R v4.3, with descriptive statistics summarizing participant characteristics and antibody responses. Inferential tests, including the chi-square test, analysis of variance (ANOVA), and multivariable regression, were used to explore associations. Mixed-effects and Bayesian models accounted for clustering and spatial variation. Outputs were disaggregated to inform public health planning and accounted for missing data using imputation techniques.

Results     

Participants characteristics: a total of 4,031 people living with HIV (PLHIV) had complete multiplex bead assay (MBA) results and were included in the analysis. Five samples were excluded due to insufficient volume. Most participants were aged 25-44 years (45.1%, n = 1,819), followed by those aged 45-64 years (33.6%, n = 1,356). Participants aged 15-24 years accounted for 11.0% (n = 442), those under 15 years for 6.7% (n = 270), and those aged ≥65 years for 3.6% (n = 144). The mean age was 39.35 years. Females comprised 68.8% (n = 2,774) of participants, while males accounted for 31.2% (n = 1,257). Participants were evenly distributed across four counties, with Nairobi contributing 26.8% (n = 1,079), Homa Bay 26.0% (n = 1,050), Kisumu 24.1% (n = 972), and Kirinyaga 23.1% (n = 930) (Table 1).

Clinical characteristics: among 4,010 participants with available ART data, 81.8% (n = 3,297) were receiving standard first-line ART regimens, while 17.7% (n = 759) were on alternative or second-line regimens. ART regimen data were missing for 0.5% (n = 21) of participants. Among 3,898 participants with viral load data, 95.3% (n = 3,715) had suppressed viral load (<1,000 copies/mL), while 4.7% (n = 183) had unsuppressed viral load (≥1,000 copies/mL). A total of 1,444 participants (35.8%) had received at least one dose of a COVID-19 vaccine. Of these, 29.9% (n = 1,206) were fully vaccinated, and 5.9% (n = 238) were partially vaccinated. Unvaccinated individuals comprised 23.6% (n = 952), while vaccination status was not documented for 40.6% (n = 1,635). Regarding ART duration, 34.1% (n = 1,347) had been on ART for 1-5 years, 32.0% (n = 1,266) for 5-10 years, 7.8% (n = 308) for less than 1 year, and 26.1% (n = 1,033) for more than 10 years (Table 1).

Antibody classification: among 3,795 participants with complete antibody classification data, 41.9% (n = 1,591) were classified as having probable infection, 30.4% (n = 1,155) as probable vaccination and infection, and 24.5% (n = 929) as probable vaccination. A total of 3.2% (n = 120) had no detectable antibodies (Table 1).

Association between participant characteristics and antibody response: there was no significant difference in antibody response by sex (all p > 0.25). Increasing age was associated with lower antibody responses. Participants aged 45-64 years had reduced odds of antibody positivity compared to those aged <15 years (aOR = 0.77, p = 0.03), and those aged ≥65 years had further reduced odds (aOR = 0.68, p = 0.02). Antiretroviral therapy (ART) regimen type was not significantly associated with antibody response (p > 0.13). Longer duration on ART was associated with reduced antibody response. Participants on ART for more than 10 years had significantly lower odds of antibody positivity compared to those on ART for less than 1 year (aOR = 0.72, p = 0.02). Participants with viral load ≥1,000 copies/mL had lower odds of antibody positivity compared to those with suppressed viral load (aOR = 0.67, p = 0.01) (Table 2).

Association between vaccination and antibody response: vaccination status was significantly associated with antibody response (p < 0.001 for all antibody types). Fully vaccinated individuals had higher antibody positivity compared to unvaccinated participants. Partially vaccinated individuals also showed increased antibody positivity relative to unvaccinated participants. Mean antibody levels differed significantly across vaccination categories (p < 0.001) (Table 2).

Multivariable analysis: in multivariable logistic regression analysis, vaccination status was the strongest predictor of antibody positivity. Fully vaccinated individuals had higher odds of antibody positivity (aOR = 3.26; 95% CI: 2.60-4.08; p < 0.001), while partially vaccinated individuals also had increased odds (aOR = 2.01; 95% CI: 1.30-3.11; p = 0.002), compared to unvaccinated participants. Age was marginally associated with antibody positivity (aOR = 1.01 per year increase; p = 0.034). Sex and ART regimen were not significantly associated with antibody response. Longer duration on ART (>10 years) was associated with reduced odds of antibody positivity (aOR = 0.72; p = 0.02). Participants with viral load ≥1,000 copies/mL had lower odds of antibody positivity (aOR = 0.67; p = 0.01). The intra-class correlation coefficient (ICC = 0.07) indicated modest clustering by county (Table 3).

Discussion     

This study provides key insights into how demographic and clinical factors influence SARS-CoV-2 antibody responses among people living with HIV (PLHIV). Gender was not significantly associated with antibody levels, aligning with studies that reported no meaningful gender-based differences in seroprevalence among virally suppressed PLHIV [18,21]. Increasing age was associated with progressively weaker antibody responses, with participants aged 45-64 years showing reduced responses compared to younger individuals, and those aged 65 years and above exhibiting even more pronounced declines. This pattern was consistent across spike, nucleocapsid, and hybrid antibody responses, suggesting a general age-related reduction in immune responsiveness. These findings are consistent with immunosenescence, a well-documented phenomenon in which aging leads to diminished immune function, and which may be further exacerbated in people living with HIV [21].

Duration on ART also influenced antibody responses. Longer duration on antiretroviral therapy was associated with reduced antibody responses, particularly among individuals who had been on treatment for more than ten years, compared to those more recently initiated on ART. This pattern was consistent across different types of antibody responses, suggesting a generalized decline in humoral immunity with prolonged treatment duration. These findings may reflect the cumulative impact of long-standing HIV infection, incomplete immune recovery despite sustained treatment, or age-related immune decline among long-term survivors. This aligns with studies that noted that prolonged ART, especially when initiated during advanced disease, may not reverse earlier immune damage. While viral suppression improves immune responsiveness, longer ART duration does not necessarily correspond to stronger antibody responses. Instead, longer treatment duration may reflect prolonged exposure to HIV-related immune damage or age-related immune decline. Therefore, the earlier statement suggesting that longer ART duration improves antibody response has been corrected to reflect the observed inverse relationship [22,23].

Viral load suppression was strongly associated with better antibody responses. Individuals with unsuppressed viral load showed weaker immune responses, indicating that uncontrolled HIV infection compromises the body´s ability to mount effective antibody responses. This finding highlights the central role of effective viral load suppression in restoring immune function and supports existing evidence that virological control is essential for achieving optimal vaccine-induced immunity [10,24].

The type of ART regimen, mainly Tenofovir Disoproxil Fumarate (TDF)+3TC+Dolutegravir (DTG), was not significantly associated with antibody levels, echoing findings from researchers who observed no negative impact of integrase strand transfer inhibitor (INSTI)-based regimens on vaccine immunogenicity [25,26] unlike studies that noted that tenofovir offered protective effects [27-29]. Although other studies suggest that protease inhibitor-based regimens may impair immune responses, such effects were not evident here, possibly due to a small number of PI users [30].

Vaccination emerged as the most significant determinant of antibody response. In the multivariable model, fully vaccinated individuals had markedly higher odds of antibody, while partially vaccinated individuals also had increased odds, compared to unvaccinated participants. These findings demonstrate a clear gradient in immune response, with full vaccination conferring substantially greater immunological benefit than partial vaccination [31-33].

This pattern was also consistent in antigen-specific analyses. Compared to unvaccinated individuals, fully vaccinated participants had lower adjusted odds of nucleocapsid response, while partially vaccinated individuals had higher odds than fully vaccinated. This apparent inverse relationship reflects the biological distinction between vaccine-induced and infection-induced immunity, as nucleocapsid antibodies are primarily generated following natural infection rather than vaccination. When these differences are accounted for, the overall multivariable model confirms that full vaccination provides the strongest antibody response among PLHIV. These findings are consistent with previous studies demonstrating enhanced immunogenicity following complete COVID-19 vaccination schedules [31-33].

These findings are consistent with global studies. Some studies reported that PLHIV with suppressed viral loads and stable ART exhibited antibody responses similar to HIV-negative individuals [34-36]. Other studies also highlighted that effective ART management enables sufficient immune recovery to support vaccine-induced antibody production. Our results reinforce and expand on these insights, showing that full vaccination offers consistent protection across diverse demographics and ART categories [37]. However, complexities remain in vaccine response among PLHIV, and hence critical to know that individuals with advanced HIV disease, unsuppressed viral loads, or low CD4+ counts may experience diminished antibody responses, reduced neutralizing activity, and faster waning immunity. Although this study lacked CD4 count for stratified analysis, the broader literature emphasizes that immune status significantly affects vaccine efficacy [5,38-40].

This study found no statistically significant association between antiretroviral therapy (ART) regimens and SARS-CoV-2 antibody positivity among people living with HIV (PLHIV). Individuals on the standard first-line regimen (TDF+3TC+DTG) showed comparable antibody responses to those on alternative or second-line regimens, suggesting that ART type does not significantly influence humoral immune response, especially among virally suppressed individuals with good adherence [41-43]. These findings align with prior research. Studies reported that PLHIV on integrase strand transfer inhibitor (INSTI)-based regimens, including dolutegravir (DTG), mounted vaccine-induced antibody responses similar to HIV-negative individuals [10,44]. INSTIs are known to enhance immune recovery by increasing CD4+ T-cell counts and reducing chronic immune activation [41,42,45]. It has been emphasized that effective ART supports vaccine responsiveness by stabilizing immune function and minimizing inflammation [33].

Nonetheless, ART´s impact on immune responses remains complex. It was noted that protease inhibitor (PI)-based regimens could alter cytokine profiles and reduce the durability of antibody responses post-vaccination [30,46]. Such effects may stem from pharmacodynamic differences or immune signaling interactions. Additionally, factors like ART adherence, timing of initiation, immune status at baseline, and comorbidities contribute to varied outcomes across studies. Non-nucleoside reverse transcriptase inhibitors (NNRTIs), for example, may influence immune and metabolic pathways in ways not fully understood [47].

These complexities underscore the need for caution when generalizing vaccine response based on the ART regimen. While this study supports the continued use of TDF+3TC+DTG, it also highlights the importance of future research to evaluate not only antibody titers but also T-cell immunity, neutralizing capacity, and long-term vaccine effectiveness across diverse ART cohorts. Importantly, switching ART regimens solely to enhance SARS-CoV-2 antibody response is not supported by current evidence. For well-managed PLHIV with high adherence and viral suppression, such changes may pose unnecessary risks, like increased pill burden or reduced tolerability, that could undermine immune stability and overall treatment outcomes. Effective ART remains central to sustained viral suppression and immune reconstitution, and any regimen changes must be based on clinical necessity, not speculative benefits related to vaccination [24,38,48].

Overall, these findings emphasize that vaccination and viral load suppression are central to achieving optimal antibody responses among PLHIV, while highlighting the reduced responsiveness observed among older individuals and those with prolonged ART exposure. These subgroups may benefit from targeted immunological monitoring and tailored vaccination strategies.

Limitations: though limited by the lack of data on ART adherence, HIV staging, CD4 count, and comorbidities, this research provides timely and critical evidence on how ART duration, viral suppression, age, and vaccination status shape antibody responses among PLHIV in Kenya.

Conclusion     

This study provides important insights into SARS-CoV-2 antibody responses among people living with HIV (PLHIV) in Kenya, demonstrating that COVID-19 vaccination and viral load suppression are the primary determinants of humoral immunity in this population. Fully vaccinated individuals had substantially higher odds of antibody positivity compared to partially vaccinated and unvaccinated individuals, highlighting a clear dose-response relationship and reinforcing the importance of completing the full vaccination schedule. Viral load suppression was strongly associated with improved antibody responses, underscoring the central role of effective antiretroviral therapy (ART) in supporting immune recovery and responsiveness to both natural infection and vaccination. In contrast, increasing age and longer duration on ART were associated with reduced antibody responses, suggesting the influence of immunosenescence and cumulative immune dysfunction among long-term ART users. These findings clarify that while clinical stability enhances immune function, prolonged ART exposure does not necessarily translate into stronger antibody responses. ART regimen type was not significantly associated with antibody response, indicating that the effectiveness of immune recovery is more closely linked to viral suppression than to the specific regimen used. Overall, these findings highlight the need to integrate COVID-19 vaccination into routine HIV care, ensure sustained viral suppression, and prioritize targeted immunological monitoring for higher-risk subgroups, particularly older individuals and long-term ART recipients. This study contributes to the growing evidence base on immune responses among PLHIV and underscores the importance of adopting risk-stratified, data-driven approaches to protect vulnerable populations in the context of current and future infectious disease threats. Further research is needed to evaluate the durability of antibody responses and to better understand the long-term effects of ART duration, immune recovery, and aging on vaccine responsiveness among PLHIV.

Competing interests     

The authors declare no competing interests.

Authors' contributions     

Ann Wanjira Maina: conceptualized the study, conducted the data analysis, interpreted the findings, and drafted the manuscript; Collins Owek: provided supervisory guidance, contributed to the interpretation of findings, and critically reviewed the manuscript for intellectual content; Fabian Mwakichwa: provided supervisory support, reviewed the methodology and data interpretation, and offered critical revisions to strengthen the final manuscript. All the authors read and approved the final version of this manuscript.

Acknowledgments     

We acknowledge the Centers for Diseases Control (CDC), Amref Health Africa, the Ministry of Health, Kenya, and all participating laboratories and personnel involved in sample collection and processing. We also thank the PLHIV community whose remnant samples made this study possible.

Tables     

Table 1: demographic and clinical characteristics of study participants from the four sentinel counties in Kenya, (Feb 2021 to Oct 2022)

Table 2: demographic and clinical factors influencing antibody response to severe acute respiratory syndrome coronavirus 2 infection and vaccination among people living with HIV in four sentinel counties in Kenya

Table 3: multivariate logistic regression of factors associated with severe acute respiratory syndrome coronavirus 2 antibody positivity among people living with HIV in four sentinel counties in Kenya

References