Immunological insights into COVID-19 in Southern Nigeria

Abstract

Introduction: One of the unexpected outcomes of the COVID-19 pandemic was the relatively low levels of morbidity and mortality in Africa compared to the rest of the world. Nigeria, Africa's most populous nation, accounted for less than 0.01% of the global COVID-19 fatalities. The factors responsible for Nigeria's relatively low loss of life due to COVID-19 are unknown. Also, the correlates of protective immunity to SARS-CoV-2 and the impact of pre-existing immunity on the outcome of the COVID-19 pandemic in Africa are yet to be elucidated. Here, we evaluated the natural and vaccine-induced immune responses from vaccinated, non-vaccinated and convalescent individuals in Southern Nigeria throughout the three waves of the COVID-19 pandemic in Nigeria. We also examined the pre-existing immune responses to SARS-CoV-2 from samples collected prior to the COVID-19 pandemic.

Methods: We used spike RBD and N- IgG antibody ELISA to measure binding antibody responses, SARS-CoV-2 pseudotype assay protocol expressing the spike protein of different variants (D614G, Delta, Beta, Omicron BA1) to measure neutralizing antibody responses and nucleoprotein (N) and spike (S1, S2) direct ex vivo interferon gamma (IFNγ) T cell ELISpot to measure T cell responses.

Result: Our study demonstrated a similar magnitude of both binding (N-IgG (74% and 62%), S-RBD IgG (70% and 53%) and neutralizing (D614G (49% and 29%), Delta (56% and 47%), Beta (48% and 24%), Omicron BA1 (41% and 21%)) antibody responses from symptomatic and asymptomatic survivors in Nigeria. A similar magnitude was also seen among vaccinated participants. Interestingly, we revealed the presence of preexisting binding antibodies (N-IgG (60%) and S-RBD IgG (44%)) but no neutralizing antibodies from samples collected prior to the pandemic.

Discussion: These findings revealed that both vaccinated, non-vaccinated and convalescent individuals in Southern Nigeria make similar magnitude of both binding and cross-reactive neutralizing antibody responses. It supported the presence of preexisting binding antibody responses among some Nigerians prior to the COVID-19 pandemic. Lastly, hybrid immunity and heterologous vaccine boosting induced the strongest binding and broadly neutralizing antibody responses compared to vaccine or infection-acquired immunity alone.

Keywords: COVID-19; Nigeria; SARS-CoV-2; immunity; pre-pandemic; preexisting; vaccine.

Figure 1

Binding antibody responses (IgG) to SARS-CoV-2 S-RBD and N proteins (A) and neutralizing antibody response to SARS-CoV-2 PVs (B) from COVID-19 survivors and their contacts in Southern Nigeria. Specific SARS-CoV-2 S-RBD and N antigen ELISA were used to measure the binding antibody response (IgG) from hospitalized COVID-19 convalescent survivors (89) and non-hospitalized asymptomatic contacts (34). We used a 1:100 dilution of the serum sample. Among those with binding antibody response, we selected some sera and measured the neutralizing titre (IC50) against SARS-CoV-2 PVs expressing the S-RBD of different variants (D614G, Beta, Delta and Omicron). The OD of the negative cutoff was selected as the mean multiplied by three standard deviations of three known negative samples (0.3) for binding antibody and (40) for neutralizing antibody response (limit of detection). The table shows the geometric mean at 95% CI. Statistical significance was calculated by Mann–Whitney test and p values are indicated. (Capped line with * indicating significance.

Figure 2

Binding antibody responses (IgG) to SARS-CoV-2 S-RBD proteins (A) and neutralizing antibody response to SARS-CoV-2 PVs (B) from COVID-19 vaccinees in Southern Nigeria. Specific SARS-CoV-2 S-RBD antigen ELISA was used to measure the binding antibody response (IgG) from COVID-19 vaccinees (521). We used a 1:100 dilution of the serum sample. Among those with binding antibody response, we selected some sera (50) and measured the neutralizing titre (IC50) against SARS-CoV-2 PVs expressing the S-RBD of different variants (D614G, Beta, Delta and Omicron). The OD of the negative cutoff was selected as the mean multiplied by three standard deviations of three known negative samples (0.3) for binding antibody and (40) for neutralizing antibody response (limit of detection). The table shows the geometric mean at 95% CI. Statistical significance was calculated by Mann–Whitney test and p values are indicated. (Capped line with * indicating significance).

Figure 3

Binding antibody responses (IgG) to SARS-CoV-2 S-RBD and N proteins (B) and neutralizing antibody response to SARS-CoV-2 PVs (C) from COVID-19 survivors based on the waves of pandemic (A) in Southern Nigeria. Specific SARS-CoV-2 S-RBD and N antigen ELISA were used to measure the binding antibody response (IgG) from hospitalized COVID-19 convalescent survivors (89). The serum was grouped based on the time of infection/ diagnosis into the three waves of the COVID-19 pandemic. We used a 1:100 dilution of the serum sample. We also measured the neutralizing titre (IC50) against SARS-CoV-2 PVs expressing the S-RBD of different variants (D614G, Beta, Delta and Omicron). The OD of the negative cutoff was selected as the mean multiplied by three standard deviations of three known negative samples (0.3) for binding antibody and (40) for neutralizing antibody response (limit of detection ). The table shows the geometric mean at 95% CI. Statistical significance was calculated by Mann–Whitney test and p values are indicated. (Capped line with * indicating significance).

Figure 4

Pre-pandemic sera has detectable binding antibody responses (IgG) to SARS-CoV-2 S-RBD and N proteins similar to sera from COVID-19 survivors in Southern Nigeria. Specific SARS-CoV-2 S-RBD and N antigen ELISA were used to measure the binding antibody response (IgG) from sera (N=64) collected prior to the COVID-19 pandemic. We used a 1:100 dilution of the serum sample. The OD of the negative cutoff was selected as the mean multiplied by three standard deviations of three known negative samples (0.3).The table shows the geometric mean at 95% CI. Statistical significance was calculated by Mann–Whitney test and p values are indicated. (Capped line with * indicating significance).

Figure 5

Stronger T cell responses to the SARS-CoV-2 spike proteins compared to the Nucleoprotein in COVID-19 survivors. The result (table showing geometric mean at 95% CI) showed stronger T cell response to both S1 and 2 compared to the N peptides. The average limit of detection (red dotted line=200) was calculated as the mean multiplied by one standard deviation of the three known negative samples.

Figure 6

Cases of vaccine failures among COVID-19 vaccinees in Southern Nigeria. Vaccine failures were most frequent in individuals who only received a single dose of the vaccine compared to those with multiple booster immunizations, and no difference in cases of vaccine failure among those who received different types of vaccines.