Longitudinal IgA and IgG Response, and ACE2 Binding Blockade, to Full-length SARS-CoV-2 Spike Protein Variants in a Population of Black PLWH Vaccinated with ChAdOx1 nCoV-19 (preprint)

Vaccines against SARS-CoV-2 have been pivotal in overcoming the Covid-19 pandemic yet understanding the subsequent outcomes and immunological effects remain crucial, especially for at-risk groups e.g. people living with human immunodeficiency virus (HIV) (PLWH). In this study we report the longitudinal IgA and IgG antibody titers, as well as antibody-mediated angiotensin converting enzyme 2 (ACE2) binding blockade, against the SARS-CoV-2 spike (S) proteins after 1 and 2 doses of the ChAdOx1 nCoV-19 vaccine in a population of Black PLWH. Here, we report that PLWH (N = 103) did not produce an anti-S IgA response after infection or vaccination, however, anti-S IgG was detected in response to vaccination and infection, with the highest level detected for infected vaccinated participants. The anti-IgG and ACE2 blockade assays revealed that both vaccination and infection resulted in IgG production, however, only vaccination resulted in a moderate increase in ACE2 binding blockade to the ancestral S protein. Vaccination with a previous infection results in the greatest anti-S IgG and ACE2 blockade for the ancestral S protein. In conclusion, PLWH produce an anti-S IgG response to the ChAdOx1 nCoV-19 vaccine and/or infection, and ChAdOx1 nCoV-19 vaccination with a previous infection produced more neutralizing antibodies than vaccination alone.

Efficacy of the AZD1222 (ChAdOx1 nCoV-19) COVID-19 Vaccine Against SARS-CoV-2 Variants of Concern (preprint)

In this South African phase 1/2b study, we demonstrated vaccine efficacy (VE) of two doses of AZD1222 for asymptomatic and symptomatic SARS-CoV-2 infection: 90.6% against wild-type and 77.1% against the Delta variant [≥]9 months after vaccination. VE against infection with the Beta variant, which preceded circulation of Delta, was 6.7%. Clinical trial identifierCT.gov NCT04444674

SARS-CoV-2 infections during Omicron (BA.1) dominant wave and subsequent population immunity in Gauteng, South Africa (preprint)

ABSTRACT Background The B.1.1.529 (Omicron BA.1) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global resurgence of coronavirus disease 2019 (Covid-19). The contribution of BA.1 infection to population immunity and its effect on subsequent resurgence of B.1.1.529 sub-lineages warrant investigation. Methods We conducted an epidemiologic survey to determine the sero-prevalence of SARS-CoV-2 IgG from March 1 to April 11, 2022, after the BA.1-dominant wave had subsided in Gauteng (South Africa), and prior to a resurgence of Covid-19 dominated by the BA.4 and BA.5 (BA.4/BA.5) sub-lineages. Population-based sampling included households in an earlier survey from October 22 to December 9, 2021 preceding the BA.1 dominant wave. Dried-blood-spot samples were quantitatively tested for IgG against SARS-CoV-2 spike protein and nucleocapsid protein. Epidemiologic trends in Gauteng for cases, hospitalizations, recorded deaths, and excess deaths were evaluated from the inception of the pandemic to the onset of the BA.1 dominant wave (pre-BA.1), during the BA.1 dominant wave, and for the BA.4/BA.5 dominant wave through June 6, 2022. Results The 7510 participants included 2420 with paired samples from the earlier survey. Despite only 26.7% (1995/7470) of individuals having received a Covid-19 vaccine, the overall sero-prevalence was 90.9% (95% confidence interval [CI], 90.2 to 91.5), including 89.5% in Covid-19 unvaccinated individuals. Sixty-four percent (95%CI, 61.8-65.9) of individuals with paired samples had serological evidence of SARS-CoV-2 infection during the BA.1 dominant wave. Of all cumulative recorded hospitalisations and deaths, 14.1% and 5.9% were contributed by the BA.1 dominant wave, and 5.1% and 1.6% by the BA.4/BA.5 dominant wave. The SARS-CoV-2 infection fatality risk was lower in the BA.1 compared with pre-BA.1 waves for recorded deaths (0.02% vs. 0.33%) and Covid-19 attributable deaths based on excess mortality estimates (0.03% vs. 0.67%). Conclusions Gauteng province experienced high levels of infections in the BA.1 -dominant wave against a backdrop of high (73%) sero-prevalence. Covid-19 hospitalizations and deaths were further decoupled from infections during BA.4/BA.5 dominant wave than that observed during the BA.1 dominant wave. (Funded by the Bill and Melinda Gates Foundation.)

SARS-CoV-2 Omicron symptomatic infections in previously infected or vaccinated South African healthcare workers (preprint)

We investigated Omicron infections among healthcare workers (HCW) presenting with symptoms of SARS-CoV-2 infection and evaluated the protective effect of vaccination or prior infection. Between 24th November and 31st December 2021, HCW in Johannesburg, South Africa, were tested for SARS-CoV-2 infection by Nucleic Acid Amplification Test (NAAT). Blood samples collected either at the symptomatic visit or within 3-months prior, were tested for spike protein immunoglobulin G (IgG). Overall, 433 symptomatic HCW were included in the analysis, with 190 (43.9%) having an Omicron infection; 69 (16.7%) were unvaccinated and 270 (62.4%) received a single dose of Ad26.COV.2 vaccine. There was no difference in the odds of identifying Omicron between unvaccinated and Ad26.COV.2 vaccinated HCW (adjusted odds ratio [aOR] 0.81, 95% confidence interval [CI]: 0.46, 1.43). One-hundred and fifty-four (35.3%) HCW had at least one SARS-CoV-2 NAAT-confirmed prior infection; these had lower odds of Omicron infection compared with those without past infection (aOR 0.55, 95%CI: 0.36, 0.84). Anti-spike IgG concentration of 1549 binding antibody unit/mL was suggestive of significant reduction in the risk of symptomatic Omicron infection. We found high reinfection and vaccine breakthrough infection rates with the Omicron variant among HCW. Prior infection and high anti-spike IgG concentration were protective against Omicron infection.

South African Population Immunity and Severe Covid-19 with Omicron Variant (preprint)

ABSTRACT Background We conducted a seroepidemiological survey from October 22 to December 9, 2021, in Gauteng Province, South Africa, to determine SARS-CoV-2 immunoglobulin G (IgG) seroprevalence primarily before the fourth wave of coronavirus disease 2019 (Covid-19), in which the B.1.1.529 (Omicron) variant was dominant. We evaluated epidemiological trends in case rates and rates of severe disease through to January 12, 2022, in Gauteng. Methods We contacted households from a previous seroepidemiological survey conducted from November 2020 to January 2021, plus an additional 10% of households using the same sampling framework. Dry blood spot samples were tested for anti-spike and anti-nucleocapsid protein IgG using quantitative assays on the Luminex platform. Daily case, hospital admission, and reported death data, and weekly excess deaths, were plotted over time. Results Samples were obtained from 7010 individuals, of whom 1319 (18.8%) had received a Covid-19 vaccine. Overall seroprevalence ranged from 56.2% (95% confidence interval [CI], 52.6 to 59.7) in children aged <12 years to 79.7% (95% CI, 77.6 to 81.5) in individuals aged >50 years. Seropositivity was more likely in vaccinated (93.1%) vs unvaccinated (68.4%) individuals. Epidemiological data showed SARS-CoV-2 infection rates increased and subsequently declined more rapidly than in previous waves. Infection rates were decoupled from Covid-19 hospitalizations, recorded deaths, and excess deaths relative to the previous three waves. Conclusions Widespread underlying SARS-CoV-2 seropositivity was observed in Gauteng Province before the Omicron-dominant wave. Epidemiological data showed a decoupling of hospitalization and death rates from infection rate during Omicron circulation.

Association of antepartum and intrapartum SARS-CoV-2 infection on pregnancy outcomes in South African women, two observational studies (preprint)

Objective: Evaluate the impact of the timing of SARS-CoV-2 infection on pregnancy outcomes in a low-middle income setting. Design: two parallel, observational studies. Setting and population: pregnant women or women presenting for labour, enrolled between April-September 2020, in South Africa. Methods: i) longitudinal follow-up study of symptomatic or asymptomatic pregnant women investigated for SARS-CoV-2 infection antenatally, ii) cross-sectional study of SARS-CoV-2 infection at time of labour. SARS-CoV-2 infection was investigated by nucleic acid amplification test (NAAT). Main Outcome Measures: association of SARS-CoV-2 infection on nasal swab and birth outcomes. Results: Antenatally, 793 women were tested for SARS-CoV-2. Overall SARS-CoV-2 infection was confirmed in 138 women, including 119/275 with symptomatic illness (COVID-19) and 19/518 asymptomatic women; 493 women were asymptomatic and SARS-CoV-2 non-reactive. Women with COVID-19 were 1.66-times (95%CI: 1.02, 1.71) more likely to have a low-birthweight newborn (30%) compared to asymptomatic women without SARS-CoV-2 (21%). Overall, 3117 women were tested for SARS-CoV-2 infection at delivery, including 1560 healthy women with an uncomplicated term delivery. Adverse birth outcomes or pregnancy-related complications were not associated with infection at delivery. Among women with SARS-CoV-2 infection at delivery, NAAT was reactive on 6/98 of maternal blood samples, 8/93 of cord-blood, 14/54 of placentas and 3/22 of nasopharyngeal swabs from newborns collected within 72-hours of birth. Conclusions: Antenatal, but not intrapartum, SARS-CoV-2 infection was associated with low-birthweight delivery. Maternal infection at the time of labour was associated with in utero foetal and placental infection, and possible vertical and/or horizontal viral transfer to the newborn.

The continuous evolution of SARS-CoV-2 in South Africa: a new lineage with rapid accumulation of mutations of concern and global detection (preprint)

Global genomic surveillance of SARS-CoV-2 has identified variants associated with increased transmissibility, neutralization resistance and disease severity. Here we report the emergence of the PANGO lineage C.1.2, detected at low prevalence in South Africa and eleven other countries. The emergence of C.1.2, associated with a high substitution rate, includes changes within the spike protein that have been associated with increased transmissibility or reduced neutralization sensitivity in SARS-CoV-2 VOC/VOIs. Like Beta and Delta, C.1.2 shows significantly reduced neutralization sensitivity to plasma from vaccinees and individuals infected with the ancestral D614G virus. In contrast, convalescent donors infected with either Beta or Delta showed high plasma neutralization against C.1.2. These functional data suggest that vaccine efficacy against C.1.2 will be equivalent to Beta and Delta, and that prior infection with either Beta or Delta will likely offer protection against C.1.2.

Population Based SARS-CoV-2 Sero-Epidemiological Survey and Estimated Infection Incidence and Fatality Risk in Gauteng Province, South Africa (preprint)

Background: Limitations in laboratory testing capacity undermine the ability to quantify the overall burden of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection. We undertook a cross-sectional population based sero-survey for SARS-CoV-2 infection in 26 sub-districts, Gauteng Province (population 15·9 million), South Africa. Furthermore, we estimated SARS-CoV-2 mortality risk triangulating seroprevalence, recorded COVID-19 deaths and excess mortality data.Methods: We employed multi-stage random household sampling with selection probability proportional to sub-district size, stratifying sub-district census-sampling frame by housing type and selecting clusters within household type strata. Serum SARS-CoV-2 receptor binding domain (RBD) Immunoglobulin G (IgG) was measured using a quantitative assay on Luminex platform.Findings: Overall RBD IgG seroprevalence was 19·1% (95%Confidence interval [CI]: 18·1-20·1%), being similar in children and adults. Seroprevalence varied from 5·5% to 43·2% across sub-districts. Conservatively, there were 2 897 120 (95%CI: 2 743 907-3 056 866) SARS-CoV-2 infections, yielding an incidence of 19 090 per 100 000 until January 9, 2021, when 330 336 COVID-19 cases were recorded. The estimated mortality risk using recorded COVID-19 deaths (n=8198) was 0·28% (95%CI: 0·27-0·30) and 0·67% (95%CI: 0·64-0·71) assuming 90% of modelled natural excess deaths were due to COVID-19 (n=21 582). Notably, 53·8% (65/122) of individuals with previous self-reported confirmed SARS-CoV-2 infection were RBD IgG sero-negative.Interpretation: The imputed number of SARS-CoV-2 infections was 8·8 fold greater than recorded number of COVID-19 cases. The imputed SARS-CoV-2 infection mortality risk varied 2·39 fold when calculated using reported COVID-19 deaths (0·28%) compared with excess mortality derived COVID-19 attributable deaths (0·67%). Waning of RBD IgG may have inadvertently under-estimated number of SARS-CoV-2 infections, and conversely over-estimated mortality risk, by a factor of two. Funding Information: Bill and Melinda Gates Foundation.Declaration of Interests: We declare no competing interests.Ethics Approval Statement: The University of the Witwatersrand Human Research Ethics Committee granted a waiver for formal approval of the survey, which was deemed to be part of public-health good and surveillance to manage the COVID-19 pandemic. Electronic signed informed consent was administered to individuals older than 15 years age, parental consent obtained for children <12 years of age, and assent and parental consent for adolescents 12-15 years old.

T-cell responses to SARS CoV-2 in unexposed South African women (preprint)

A potential explanation for the fact that the high force of infection for SARS-CoV-2 in South Africa did not translate into high rates of severe illness and death, may be the presence of cross-reactive immunity induced by common cold coronaviruses (CCoV). We used SARS-CoV-2 peptide pools and whole virus antigen to stimulate peripheral blood mononuclear cells collected pre-2020 from South African women and measured interferon gamma (IFNγ) and interleukin 2 (IL2) production. IFNγ responses were observed in 29.9% of the women and IL2 among 39.2%. Overall, 51.6% of women demonstrated response to at least one stimulant. The responses to SARS-CoV-2 might have been induced by past exposure to CCoV.

ChAdOx1 nCoV-19 (AZD1222) Vaccine in People Living With and Without HIV (preprint)

Coronavirus disease 2019 (COVID-19) is a public health emergency of international concern1. People living with HIV (PLWH) are at increased risk for adverse COVID-19 outcomes compared with HIV-negative individuals2-5, and are a high-risk group for COVID-19 prevention4. The ChAdOx1 nCoV-19 (AZD1222) vaccine has demonstrated safety and efficacy against COVID-19 in clinical trials6-8. To date, there are no reports on the safety and immunogenicity of this, or any COVID-19 vaccine, in PLWH, and reports on the immunogenicity of COVID-19 vaccines in Africa are limited9. Here, we show comparable safety and immunogenicity of two doses of ChAdOx1 nCoV-19 between PLWH and HIV-negative individuals in South Africa. Furthermore, in PLWH previously exposed to SARS-CoV-2, antibody responses increased substantially from baseline following a priming dose, with modest increases after a booster dose. Full-length spike and receptor-binding domain IgG geometric mean concentrations after a single dose of ChAdOx1 nCoV-19 in PLWH previously exposed to SARS-CoV-2 were 6.49–6.84-fold higher than after two doses in those who were SARS-CoV-2 naïve at enrollment. Neutralizing antibody responses were consistent with the antibody-binding responses. This is the first report of a COVID-19 vaccine specific to PLWH, and specific to Africa, and demonstrates favorable safety and immunogenicity of ChAdOx1 nCoV-19 in PLWH.

SARS-CoV-2 Infection Among Healthcare Workers in South Africa: A Longitudinal Cohort Study (preprint)

Background: Healthcare workers (HCWs) are at high risk for SARS-CoV-2 infection. We investigated the burden of SARS-CoV-2 infection in a longitudinal cohort of frontline HCWs in South Africa from April to September 2020.Methods: HCWs working in five departments at Chris Hani Baragwanath Academic Hospital were followed-up weekly, independent of clinical symptomatology, during the first wave of the COVID-19 pandemic and tested for SARS-CoV-2 infection by polymerase chain reaction (PCR). Furthermore, paired sera collected at enrolment and end of surveillance were tested for IgG to receptor binding domain of the spike protein to evaluate for sero-response.Findings: Overall 137 (34·6%) of 396 enrolled HCWs had PCR-confirmed SARS-CoV-2 infection (132·1 [95%CI: 111·8, 156·2] per 1,000 person-months), and an additional 27 only showed sero-response at the end of follow-up. HCWs in the Internal Medicine department had the highest rate of SARS-CoV-2 infection (61·7%; 103/167), with HCWs from other departments (27·5%; 63/229) experiencing 70% lower odds of infection (adjust odds ratio 0·29 [95%CI: 0·17, 0·49]) in multivariable analysis. Among SARS-CoV-2 PCR-confirmed cases, 14 (10·4%) HCWs remained asymptomatic, 41 (30·4%) were pre-symptomatic and 80 (59·3%) were symptomatic. Symptomatic cases compared to asymptomatic had lower PCR cycle threshold values at diagnosis (24·2 vs. 28·9) and longer duration of PCR-positivity (18·9 vs. 13·0 days).Interpretation: The high rates of SARS-CoV-2 infection among HCWs in a relatively well-resourced middle-income setting attest to the threat that the COVID-19 pandemic poses to health care systems.Funding: This study was supported by the European & Developing Countries Clinical Trials Partnership (grant number RIA2020EF-3020) and The Bill & Melinda Gates Foundation (grant number INV018148_2020). There was also partial support from the Department of Science and Technology and National Research Foundation: South African Research Chair Initiative in Vaccine Preventable Diseases; and the South African Medical Research Council.Conflict of Interest: MCN has received grant support from the Bill & Melinda Gates Foundation, MedImmune and Pfizer outside the submitted work; has received honoraria from Pfizer and Sanofi Pasteur outside the submitted work. CLC has received grant support from the Bill & Melinda Gates Foundation, Pfizer and IMPRINT outside the submitted work; has received honoraria from Pfizer outside the submitted work. SAM has received grant support from the Bill & Melinda Gates Foundation, Pfizer, GlaxoSmithKline, Minervax and Novavx outside the submitted work; personal fees from Bill & Melinda Gates Foundation outside the submitted work. All other authors have nothing to disclose.Ethical Approval: The study was approved by the Human Research Ethics Committee of the University of the Witwatersrand (reference number 200405) and conducted in accordance with Good Clinical Practice guidelines. All study participants provided written informed consent.

Single Dose Administration, And The Influence Of The Timing Of The Booster Dose On Immunogenicity and Efficacy Of ChAdOx1 nCoV-19 (AZD1222) Vaccine (preprint)

Background: The ChAdOx1 nCoV-19 (AZD1222) vaccine has been approved for emergency use by the UK regulatory authority, MHRA, with a regimen of two standard doses given with an interval of between 4 and 12 weeks. The planned rollout in the UK will involve vaccinating people in high risk categories with their first dose immediately, and delivering the second dose 12 weeks later.Here we provide both a further prespecified pooled analysis of trials of ChAdOx1 nCoV-19 and exploratory analyses of the impact on immunogenicity and efficacy of extending the interval between priming and booster doses. In addition, we show the immunogenicity and protection afforded by the first dose, before a booster dose has been offered.Methods: We present data from phase III efficacy trials of ChAdOx1 nCoV-19 in the United Kingdom and Brazil, and phase I/II clinical trials in the UK and South Africa, against symptomatic disease caused by SARS-CoV-2. The data cut-off date for these analyses was 7th December 2020. The accumulated cases of COVID-19 disease at this cut-off date exceeds the number required for a pre-specified final analysis, which is also presented. As previously described, individuals over 18 years of age were randomised 1:1 to receive two standard doses (SD) of ChAdOx1 nCoV-19 (5x1010 viral particles) or a control vaccine/saline placebo. In the UK trial efficacy cohort a subset of participants received a lower dose (LD, 2.2x1010 viral particles) of the ChAdOx1 nCoV-19 for the first dose. All cases with a nucleic acid amplification test (NAAT) were adjudicated for inclusion in the analysis, by a blinded independent endpoint review committee. Studies are registered at ISRCTN89951424 and ClinicalTrials.gov; NCT04324606, NCT04400838, and NCT04444674.Findings: 17,177 baseline seronegative trial participants were eligible for inclusion in the efficacy analysis, 8948 in the UK, 6753 in Brazil and 1476 in South Africa, with 619 documented NAAT +ve infections of which 332 met the primary endpoint of symptomatic infection >14 days post dose 2.The primary analysis of overall vaccine efficacy >14 days after the second dose including LD/SD and SD/SD groups, based on the prespecified criteria was 66.7% (57.4%, 74.0%). There were no hospitalisations in the ChAdOx1 nCoV-19 group after the initial 21 day exclusion period, and 15 in the control group.Vaccine efficacy after a single standard dose of vaccine from day 22 to day 90 post vaccination was 76% (59%, 86%), and modelled analysis indicated that protection did not wane during this initial 3 month period. Similarly, antibody levels were maintained during this period with minimal waning by day 90 day (GMR 0.66, 95% CI 0.59, 0.74).In the SD/SD group, after the second dose, efficacy was higher with a longer prime-boost interval: VE 82.4% 95%CI 62.7%, 91.7% at 12+ weeks, compared with VE 54.9%, 95%CI 32.7%, 69.7% at <6 weeks. These observations are supported by immunogenicity data which showed binding antibody responses more than 2-fold higher after an interval of 12 or more weeks compared with and interval of less than 6 weeks GMR 2.19 (2.12, 2.26) in those who were 18-55 years of age.Interpretation: ChAdOx1 nCoV-19 vaccination programmes aimed at vaccinating a large proportion of the population with a single dose, with a second dose given after a 3 month period is an effective strategy for reducing disease, and may be the optimal for rollout of a pandemic vaccine when supplies are limited in the short term.Trial Registration: Studies are registered at ISRCTN89951424 and ClinicalTrials.gov; NCT04324606, NCT04400838, and NCT04444674.Funding: UKRI, NIHR, CEPI, the Bill & Melinda Gates Foundation, the Lemann Foundation, Rede D’OR, the Brava and Telles Foundation, NIHR Oxford Biomedical Research Centre, Thames Valley and South Midland's NIHR Clinical Research Network, and Astra Zeneca.Conflict of Interest: Oxford University has entered into a partnership with Astra Zeneca for further development of ChAdOx1 nCoV-19. SCG is co-founder of Vaccitech (collaborators in the early development of this vaccine candidate) and named as an inventor on a patent covering use of ChAdOx1-vectored vaccines and a patent application covering this SARS-CoV-2 vaccine. TL is named as aninventor on a patent application covering this SARS-CoV-2 vaccine and was a consultant to Vaccitech for an unrelated project. PMF is a consultant to Vaccitech. AJP is Chair of UK Dept.Health and Social Care’s (DHSC) Joint Committee on Vaccination & Immunisation (JCVI), but does not participate in discussions on COVID-19 vaccines, and is a member of the WHO’sSAGE. AJP and SNF are NIHR Senior Investigator. The views expressed in this article do not necessarily represent the views of DHSC, JCVI, NIHR or WHO. AVSH reports personal feesfrom Vaccitech, outside the submitted work and has a patent on ChAdOx1 licensed to Vaccitech, and may benefit from royalty income to the University of Oxford from sales of this vaccine by AstraZeneca and sublicensees. MS reports grants from NIHR, non-financial support fromAstraZeneca, during the conduct of the study; grants from Janssen, grants fromGlaxoSmithKline, grants from Medimmune, grants from Novavax, grants and non-financialsupport from Pfizer, grants from MCM, outside the submitted work. CG reports personal fees from the Duke Human Vaccine Institute, outside of the submitted work. SNF reports grants from Janssen and Valneva, outside the submitted work. ADD reports grants and personal fees from AstraZeneca, outside of the submitted work. In addition, ADD has a patent manufacturingprocess for ChAdOx vectors with royalties paid to AstraZeneca, and a patent ChAdOx2 vector with royalties paid to AstraZeneca. The other authors declare no competing interests.