Humoral immune responses associated with control of SARS-CoV-2 breakthrough infections in a vaccinated US military population

Abstract

Background: COVID-19 vaccines have been critical for protection against severe disease following infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) but gaps remain in our understanding of the immune responses that contribute to controlling subclinical and mild infections.

Methods: Vaccinated, active-duty US military service members were enrolled in a non-interventional, minimal-risk, observational study starting in May, 2021. Clinical data, serum, and saliva samples were collected from study participants and were used to characterise the humoral immune responses to vaccination and to assess its impact on clinical and subclinical infections, as well as virologic outcomes of breakthrough infections (BTI) including viral load and infection duration.

Findings: The majority of VIRAMP participants had received the Pfizer COVID-19 vaccine and by January, 2022, N = 149 had a BTI. The median BTI duration (PCR+ days) was 4 days and the interquartile range was 1-8 days. Participants that were nucleocapsid seropositive prior to their BTI had significantly higher levels of binding and functional antibodies to the spike protein, shorter median duration of infections, and lower median peak viral loads compared to seronegative participants. Furthermore, levels of neutralising antibody, ACE2 blocking activity, and spike-specific IgA measured prior to BTI also correlated with the duration of infection.

Interpretation: We extended previous findings and demonstrate that a subset of vaccine-induced humoral immune responses, along with nucleocapsid serostatus are associated with control of SARS-CoV-2 breakthrough infections in the upper airways.

Funding: This work was funded by the DoD Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND) in collaboration with the Defense Health Agency (DHA) COVID-19 funding initiative for the VIRAMP study.

Keywords: Antibody responses; Breakthrough infection duration; COVID-19 vaccine; SARS-CoV-2.

Fig. 1

Viral load and duration of breakthrough infections. Quantitative PCR for N and ORF1AB genes was done on saliva samples collected during breakthrough infections. Panel a) shows all participants (N = 149) duration of breakthrough infection calculated by the number of contiguous days they were qPCR positive (+). Panel b) shows a comparison of the duration of breakthrough infection in participants post primary vaccination series (N = 117) and post a booster vaccination (N = 20). Panel c) shows the viral load (Ct value) for N and ORF1AB gene targets for all participants (N = 149). Panels d and e) show a viral load comparison among participants post primary vaccination series (N = 117) and post a booster vaccination (N = 20) for N and ORF1AB gene targets, respectively. The red bar in all graphs is the median and statistical comparisons between groups were done using a Mann–Whitney test. P values are indicated for each comparison.

Fig. 2

Enrollment nucleocapsid serostatus and antibody levels. Comparisons between nucleocapsid (N) seronegative (Ab−) and seropositive (Ab+) participants are shown for a) ID50 wild-type (Ab− N = 117, Ab+ N = 20), b) ID80 wild-type (Ab− N = 117, Ab+ N = 20), c) ID90 wild-type (Ab− N = 117, Ab+ N = 20), d) ID50 Delta (Ab− N = 117, Ab+ N = 20), e) ID80 Delta (Ab− N = 117, Ab+ N = 20), f) ID90 Delta (Ab− N = 117, Ab+ N = 20), g) wild-type ACE2 blocking (Ab− N = 103, Ab+ N = 18), h) wild-type spike-reactive IgG (Ab− N = 104, Ab+ N = 18), i) wild-type spike-reactive IgA (Ab− N = 104, Ab+ N = 18), j) Delta ACE2 blocking (Ab− N = 103, Ab+ N = 18), k) Delta spike-reactive IgG (Ab− N = 104, Ab+ N = 18), l) Delta spike-reactive IgA (Ab− N = 104, Ab+ N = 18), m) Delta spike-expressing cell opsonizing IgG MFI (Ab− N = 95, Ab+ N = 20), n) Delta spike-expressing cell opsonizing IgA MFI (Ab− N = 95, Ab+ N = 20), o) Delta ADCP (Ab− N = 111, Ab+ N = 20), p) Delta ADCD (Ab− N = 110, Ab+ N = 20), q) Delta ADCC (Ab− N = 95, Ab+ N = 20), r) Delta spike-expressing cell 50% IgG opsonization titer (Ab− N = 95, Ab+ N = 20), and s) Delta spike-expressing cell 50% IgA opsonization titer (Ab− N = 95, Ab+ N = 20). The red bar in all graphs is the median and statistical comparisons between N Ab− and N Ab+ participants were done using a Mann–Whitney test and the P values are indicated for each comparison.

Fig. 3

Enrollment nucleocapsid serostatus, viral load, infection duration. Comparisons between nucleocapsid (N) seronegative (Ab−) (N = 121) and seropositive (Ab+) (N = 23) participants are shown for a) breakthrough infection duration (PCR+ days), b) N ct value, and c) ORF1AB ct value. The red bar in all graphs is the median and statistical comparisons between N Ab− and N Ab+ participants were done using a Mann–Whitney test and the P values are indicated for each comparison.

Fig. 4

Correlations between enrollment antibody responses, viral load, and infection duration. The heat map (N = 88 participants) shows the Spearman r values for correlations between infection duration (PCR+ days) or viral load (N or ORF1AB ct values) and wild-type or Delta ID50, ID80, ID90, ACE2 blocking, spike-reactive IgG and IgA, as well as Delta spike-expressing cell opsonizing IgG and IgA MFI, ADCP, ADCD, ADCC, and spike-expressing cell 50% IgG or IgA opsonization titer. The Spearman r values, 95% CI, and P values are in Supplemental Table S1.

Fig. 5

Correlations between 6-month post vaccination antibody responses, viral load, and infection duration. The heat map (N = 48 participants) shows the Spearman r values for correlations between infection duration (PCR+ days) or viral load (N or ORF1AB ct values) and wild-type or Delta ID50, ID80, ID90, ACE2 blocking, and spike-reactive IgG and IgA. The Spearman r values, 95% CI, and P values are in Supplemental Table S2.