Fc effector activity and neutralization against SARS-CoV-2 BA.4 is compromised in convalescent sera, regardless of the infecting variant (preprint)

The SARS-CoV-2 Omicron BA.1 variant, which exhibits high level neutralization resistance, has since evolved into several sub-lineages including BA.4 and BA.5, which have dominated the fifth wave of infection in South Africa. Here we assessed the sensitivity of BA.4 to neutralization and antibody dependent cellular cytotoxicity (ADCC) in convalescent donors infected with four previous variants of SARS-CoV-2, as well as in post-vaccination breakthrough infections (BTIs) caused by Delta or BA.1. We confirm that BA.4 shows high level resistance to neutralization, regardless of the infecting variant. However, breakthrough infections, which trigger potent neutralization, retained activity against BA.4, albeit at reduced titers. Fold reduction of neutralization in BTIs was lower than that seen in unvaccinated convalescent donors, suggesting maturation of neutralizing responses to become more resilient against VOCs in hybrid immunity. BA.4 sensitivity to ADCC was reduced but remained detectable in both convalescent donors and in BTIs. Overall, the high neutralization resistance of BA.4, even to antibodies from BA.1 infections, provides an immunological mechanism for the rapid spread of BA.4 immediately after a BA.1-dominated wave. Furthermore, although ADCC activity against BA.4 was reduced, residual activity may nonetheless contribute to the protection from disease.

SARS-CoV-2 BA.4 infection triggers more cross-reactive neutralizing antibodies than BA.1 (preprint)

SARS-CoV-2 variants of concern (VOCs) differentially trigger neutralizing antibodies with variable cross-neutralizing capacity. Here we show that unlike SARS-CoV-2 Omicron BA.1, which triggered neutralizing antibodies with limited cross-reactivity, BA.4/5 infection triggers highly cross-reactive neutralizing antibodies. Cross-reactivity was observed both in the absence of prior vaccination and also in breakthrough infections following vaccination. This suggests that next-generation vaccines incorporating BA.4, which is spreading globally, might result in enhanced neutralization breadth.

Shared N417-dependent epitope on the SARS-CoV-2 Omicron, Beta and Delta-plus variants (preprint)

As SARS-CoV-2 continues to evolve, several variants of concern (VOCs) have arisen which are defined by multiple mutations in their spike proteins. These mutations have resulted in variable escape from antibody responses and the elicitation of qualitatively different antibody responses during infection. By studying plasma from individuals infected with either the original D614G, Beta or Delta variants, we showed that the Beta and Delta variants elicit antibody responses that are overall more cross-reactive than those triggered by D614G. Patterns of cross-reactivity varied, and the Beta and Delta variants did not elicit cross-reactive responses to each other. However, Beta-elicited plasma was highly cross-reactive against Delta plus (Delta+) which differs from Delta by a single K417N mutation in the receptor binding domain, suggesting the plasma response targets the N417 residue. To probe this further, we isolated monoclonal antibodies from a Beta-infected individual with plasma responses against Beta, Delta+ and Omicron, which all possess the N417 residue. We isolated a N417-dependent antibody, 084-7D, which showed similar neutralization breadth to the plasma. The 084-7D mAb utilized the IGHV3*23*01 germline gene and had similar somatic hypermutations compared to previously described public antibodies which target the 417 residue. Thus, we have identified a novel antibody which targets a shared epitope found on three distinct VOCs. Understanding the antibody response towards escape mutations such as K417N, which repeatedly emerge through convergent evolution in SARS-CoV-2 variants, may aid in the development of next-generation antibody therapeutics and vaccines.

SARS-CoV-2 Omicron triggers cross-reactive neutralization and Fc effector functions in previously vaccinated, but not unvaccinated individuals (preprint)

The SARS-CoV-2 Omicron variant largely escapes neutralizing antibodies elicited by vaccines or infection. However, whether Omicron triggers humoral responses that are cross-reactive to other variants of concern (VOCs) remains largely unknown. We use plasma from 20 unvaccinated and seven vaccinated individuals infected during the Omicron wave in South Africa to test binding, antibody-dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP) and neutralization against VOCs. In unvaccinated individuals, Fc effector function and binding antibodies target Omicron and other VOCs at comparable levels. However, Omicron-triggered neutralization is not extensively cross-reactive to VOCs, with 20 to 43-fold reductions in titer. In contrast, vaccination followed by breakthrough Omicron infection improved cross-neutralization of VOCs, with titers exceeding 1:2,900. This has important implications for the vulnerability of unvaccinated Omicron-infected individuals to reinfection by circulating and emerging VOCs. Further, while Omicron-based immunogens may be adequate boosters, they are unlikely to be superior to existing vaccines for priming in SARS-CoV-2 naive individuals.

COVID-19 severity and in-hospital mortality in an area with high HIV prevalence (preprint)

Background: HIV is moderate risk factor for developing severe COVID-19 and is associated with increased risk of COVID-19 mortality. HIV infection causes immune dysregulation characterised by progressive lymphopenia, chronic immune activation, immunological senescence, and T cell exhaustion. These changes are partly reversed by effective antiretroviral therapy (ART), which reduces morbidity and mortality in people living with HIV (PWH). We investigated the associations among clinical phenotypes, laboratory biomarkers, and hospitalisation outcomes in a cohort of people hospitalised with COVID-19 in a high HIV prevalence area. Methods: : We conducted a prospective observational cohort study in the Tshwane District Hospital complex in Pretoria, South Africa. We analysed data for patients admitted from April to November 2020, before the SARS-CoV-2 Beta variant-driven second wave. Respiratory disease severity was quantified using the respiratory oxygenation (ROX) score. Analysed biomarkers included full blood counts, differential white cell counts, C-reactive protein (CRP), ferritin, procalcitonin (PCT), D-dimer (DDIM), creatinine, alanine aminotransferase (ALT), CD4 T cell counts, and HIV-1 viral loads (HIVVL). Results: : The analysis included 558 patients, of whom 112 (21.7%) died during admission. The mean age of the cohort was 54 (SD ±16) years, and numbers of males (50.5%) and females (49.5%) were equivalent. A total of 82 (15%) were HIV-positive. PWH were younger (mean age 46 years) than HIV-negative people; most were on ART with a suppressed HIVVL (72%) and the median CD4 count was 159 (IQR 66-397) cells/µL at the time of admission. After adjusting for age, HIV was not associated with significantly increased risk of mortality during hospitalisation (aHR=1.1, 95% CI: 0.6-2.0). Levels of supportive care were similar in HIV-negative patients and PWH. Inflammatory biomarker levels were equivalent in PWH and HIV-negative patients. A total of 15 PWH had detectable HIVVLs (>1000 copies/mL). Detectable HIVVL was associated with higher ROX scores - indicating less severe respiratory disease. In PWH, mortality was associated with higher levels of CRP, ferritin, PCT and DDIM. When compared to HIV-negative patients who died, PWH who died were younger, had higher DDIM levels, and were more likely to have tuberculosis. Conclusions: : HIV per se was not associated with substantively increased risk of severe disease, or in-hospital mortality from COVID-19. Respiratory disease was less severe in PWH with detectable HIVVL. Inflammatory biomarker levels were equivalent in PWH and HIV-negative people, regardless of HIVVL. Increased levels of inflammatory biomarkers and DDIM were associated with in-hospital mortality irrespective of HIV status.

SARS-CoV-2 spike T cell responses induced upon vaccination or infection remain robust against Omicron (preprint)

The SARS-CoV-2 Omicron variant has multiple Spike (S) protein mutations that contribute to escape from the neutralizing antibody responses, and reducing vaccine protection from infection. The extent to which other components of the adaptive response such as T cells may still target Omicron and contribute to protection from severe outcomes is unknown. We assessed the ability of T cells to react with Omicron spike in participants who were vaccinated with Ad26.CoV2.S or BNT162b2, and in unvaccinated convalescent COVID-19 patients (n = 70). We found that 70-80% of the CD4 and CD8 T cell response to spike was maintained across study groups. Moreover, the magnitude of Omicron cross-reactive T cells was similar to that of the Beta and Delta variants, despite Omicron harbouring considerably more mutations. Additionally, in Omicron-infected hospitalized patients (n = 19), there were comparable T cell responses to ancestral spike, nucleocapsid and membrane proteins to those found in patients hospitalized in previous waves dominated by the ancestral, Beta or Delta variants (n = 49). These results demonstrate that despite Omicron's extensive mutations and reduced susceptibility to neutralizing antibodies, the majority of T cell response, induced by vaccination or natural infection, cross-recognises the variant. Well-preserved T cell immunity to Omicron is likely to contribute to protection from severe COVID-19, supporting early clinical observations from South Africa.

Ad26.COV2.S breakthrough infections induce high titers of antibodies capable of neutralizing variants of concern (preprint)

The Janssen (Johnson & Johnson) Ad26.COV2.S non-replicating viral vector vaccine, which requires only a single dose and conventional cold chain storage, is a valuable tool for COVID-19 vaccination programs in resource-limited settings. Here we show that neutralizing and binding responses to Ad26.COV2.S vaccination are stable for 6 months post-vaccination, with responses highest against the ancestral vaccine-similar D614G variant. Secondly, using longitudinal samples from individuals who experienced clinically mild breakthrough infections 3-4 months after vaccination, we show dramatically boosted binding antibodies, Fc effector function and neutralization. These responses, which are cross-reactive against diverse SARS-CoV-2 variants and SARS-CoV-1, are of similar magnitude to humoral immune responses measured in severely ill, hospitalized donors. These data highlight the significant priming capacity of Ad26.COV2.S, and have implications for population immunity in areas where the single dose Ad26.COV2.S vaccine has been deployed.

A SARS-CoV-2 variant of concern triggers Fc effector function with increased cross-reactivity (preprint)

SARS-CoV-2 variants of concern (VOCs) exhibit escape from neutralizing antibodies, causing concern about vaccine effectiveness. However, while non-neutralizing cytotoxic functions of antibodies are associated with decreased disease severity and vaccine protection, Fc effector function escape from VOCs is poorly defined. Furthermore, whether VOCs trigger Fc functions with altered specificity, as has been reported for neutralization, is unknown. Here, we demonstrate that the Beta VOC partially evades Fc effector activity in individuals infected with the original (D614G) variant. However, not all functions are equivalently affected, suggesting differential targeting by antibodies mediating distinct Fc functions. Furthermore, Beta infection triggered responses with significantly improved Fc cross-reactivity against global VOCs compared to either D614G infected or Ad26.COV2.S vaccinated individuals. This suggests that, as for neutralization, the infecting spike sequence impacts Fc effector function. These data have important implications for vaccine strategies that incorporate VOCs, suggesting these may induce broader Fc effector responses.

SARS-CoV-2 501Y.V2 (B.1.351) elicits cross-reactive neutralizing antibodies (preprint)

Neutralization escape by SARS-CoV-2 variants, as has been observed in the 501Y.V2 (B.1.351) variant, has impacted the efficacy of first generation COVID-19 vaccines. Here, the antibody response to the 501Y.V2 variant was examined in a cohort of patients hospitalized with COVID-19 in early 2021 - when over 90% of infections in South Africa were attributed to 501Y.V2. Robust binding and neutralizing antibody titers to the 501Y.V2 variant were detected and these binding antibodies showed high levels of cross-reactivity for the original variant, from the first wave. In contrast to an earlier study where sera from individuals infected with the original variant showed dramatically reduced potency against 501Y.V2, sera from 501Y.V2-infected patients maintained good cross-reactivity against viruses from the first wave. Furthermore, sera from 501Y.V2-infected patients also neutralized the 501Y.V3 (P.1) variant first described in Brazil, and now circulating globally. Collectively these data suggest that the antibody response in patients infected with 501Y.V2 has a broad specificity and that vaccines designed with the 501Y.V2 sequence may elicit more cross-reactive responses.

SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma (preprint)

SARS-CoV-2 501Y.V2, a novel lineage of the coronavirus causing COVID-19, contains multiple mutations within two immunodominant domains of the spike protein. Here we show that this lineage exhibits complete escape from three classes of therapeutically relevant monoclonal antibodies. Furthermore 501Y.V2 shows substantial or complete escape from neutralizing antibodies in COVID-19 convalescent plasma. These data highlight the prospect of reinfection with antigenically distinct variants and may foreshadow reduced efficacy of current spike-based vaccines.