In the upper respiratory tract, replicating (culturable) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is recoverable for ∼4-8 days after symptom onset, but there is a paucity of data ...about the frequency and duration of replicating virus in the lower respiratory tract (i.e., the human lung).
We undertook lung tissue sampling (needle biopsy) shortly after death in 42 mechanically ventilated decedents during the Beta and Delta waves. An independent group of 18 ambulatory patients served as a control group.
Lung biopsy cores from decedents underwent viral culture, histopathological analysis, electron microscopy, transcriptomic profiling, and immunohistochemistry.
Thirty-eight percent (16 of 42) of mechanically ventilated decedents had culturable virus in the lung for a median of 15 days (persisting for up to 4 wk) after symptom onset. Lung viral culture positivity was not associated with comorbidities or steroid use. Delta but not Beta variant lung culture positivity was associated with accelerated death and secondary bacterial infection (
< 0.05). Nasopharyngeal culture was negative in 23.1% (6 of 26) of decedents despite lung culture positivity. This hitherto undescribed biophenotype of lung-specific persisting viral replication was associated with an enhanced transcriptomic pulmonary proinflammatory response but with concurrent viral culture positivity.
Concurrent rather than sequential active viral replication continues to drive a heightened proinflammatory response in the human lung beyond the second week of illness and was associated with variant-specific increased mortality and morbidity. These findings have potential implications for the design of interventional strategies and clinical management of patients with severe coronavirus disease (COVID-19).
COVID-19 vaccine rollout is lagging in Africa, where there has been a high rate of SARS-CoV-2 infection. We aimed to evaluate the effect of SARS-CoV-2 infection before vaccination with the ...ChAdOx-nCoV19 (AZD1222) vaccine on antibody responses through to 180 days.
We did an unmasked post-hoc immunogenicity analysis after the first and second doses of AZD1222 in a randomised, placebo-controlled, phase 1b–2a study done in seven locations in South Africa. AZD1222 recipients who were HIV-uninfected, were stratified into baseline seropositive or seronegative groups using the serum anti-nucleocapsid (anti-N) immunoglobulin G (IgG) electroluminescence immunoassay to establish SARS-CoV-2 infection before the first dose of AZD1222. Binding IgG to spike (anti-S) and receptor binding domain (anti-RBD) were measured before the first dose (day 0), second dose (day 28), day 42, and day 180. Neutralising antibody (NAb) against SARS-CoV-2 variants D614G, beta, delta, gamma, and A.VOI.V2, and omicron BA1 and BA.4 variants, were measured by pseudovirus assay (day 28, day 42, and day 180). This trial is registered with ClinicalTrials.gov, NCT04444674, and the Pan African Clinicals Trials Registry, PACTR202006922165132.
Of 185 individuals who were randomly assigned to AZD1222, we included 91 individuals who were baseline seropositive and 58 who were baseline seronegative, in the final analysis. In the seropositive group, there was little change of anti-S IgG (and anti-RBD IgG) or neutralising antibody (NAb) titres at day 42 compared with at day 28. Anti-S (and anti-RBD) IgG geometric mean concentrations (GMCs) were higher throughout in the seropositive compared with the seronegative group, including at day 180 (GMCs 517·8 95% CI 411·3–651·9 vs 82·1 55·2–122·3 BAU/mL). Also D614G NAb geometric mean titres (GMTs) were higher in the seropositive group than the seronegative group, as was the percentage with titres of at least 185 (80% putative risk reduction threshold PRRT against wild-type–alpha COVID-19), including at day 180 (92·0% 74·0–99·0 vs 18·2% 2·3–51·8). Similar findings were observed for beta, A.VOI.V2, and gamma. For delta, BA.1, and BA.4, NAb GMTs and the proportion with titres above the PRRT were substantially higher in the seropositive compared with seronegative group at day 28 and day 42, but no longer differed between the groups by day 180.
A single dose of AZD1222 in the general African population, where COVID-19 vaccine coverage is low and SARS-CoV-2 seropositivity is 90%, could enhance the magnitude and quality of antibody responses to SARS-CoV-2.
The Bill & Melinda Gates Foundation, the South African Medical Research Council, the UK Research and Innovation, the UK National Institute for Health Research, and the South African Medical Research Council.
For the Zulu translation of the abstract see Supplementary Materials section.
The World Health Organization (WHO) recently recommended that linezolid be prioritized in treatment regimens for drug-resistant tuberculosis (TB), but there are limited data on its pharmacokinetics ...(PK) in patients with this disease. We conducted an observational study to explore covariate effects on linezolid PK and to estimate the probability of PK/pharmacodynamic target attainment in South African patients with drug-resistant TB. Consecutive adults on linezolid-based regimens were recruited in Cape Town and underwent intensive PK sampling at steady state. Noncompartmental analysis was performed. Thirty participants were included: 15 HIV positive, 26 on the initial dose of 600 mg daily, and 4 participants on 300 mg daily after dose reduction for linezolid-related toxicity. There was a negative correlation between body weight and exposure, with 17.4% (95% confidence interval CI, 0.1 to 31.7) decrease in area under the concentration-time curve from 0 to 24 h (AUC
) per 10-kg weight increment after adjustment for other covariates. Age was an independent predictor of trough concentration, with an estimated 43.4% (95% CI, 5.9 to 94.2) increase per 10-year increment in age. The standard 600-mg dose achieved the efficacy target of free AUC/MIC of >119 at wild-type MIC values (≤0.5 mg/liter), but the probability of target attainment dropped to 61.5% (95% CI, 40.6 to 79.8) at the critical concentration of 1 mg/liter. When dosed at 600 mg daily, trough concentrations were above the toxicity threshold of 2 mg/liter in 57.7% (95% CI, 36.9 to 76.6). This confirms the narrow therapeutic index of linezolid, and alternative dosing strategies should be explored.
With a prevalence almost twice as high as the national average, people living in South African townships are particularly impacted by the HIV epidemic. Yet, it remains unclear how socioeconomic ...factors impact the risk of HIV infection within township populations. Our objective was to estimate the extent to which socioeconomic factors (dwelling situation, education, employment status, and monthly income) explain the risk of HIV in South African township populations, after controlling for behavioural and individual risk factors. Using Bayesian logistic regression, we analysed secondary data from a quasi-randomised trial which recruited participants (N = 3095) from townships located across three subdistricts of Cape Town. We controlled for individual factors (age, sex, marital status, testing history, HIV exposure, comorbidities, and tuberculosis infection) and behavioural factors (unprotected sex, sex with multiple partners, with sex workers, with a partner living with HIV, under the influence of alcohol or drugs), and accounted for the uncertainty due to missing data through multiple imputation. We found that residing in informal dwellings and not having post-secondary education increased the odds of HIV (aOR, 89% CrI: 1.34, 1.07-1.68 and 1.82, 1.29-2.61, respectively), after controlling for subdistrict of residence, individual, and behavioural factors. Additionally, our results suggest different pathways for how socioeconomic status (SES) affect HIV infection in males and female participants: while socioeconomic factors associated with lower SES seem to be associated with a decreased likelihood of having recently sough HIV testing among male participants, they are associated with increased sexual risk taking which, among female participants, increase the risk of HIV. Our analyses demonstrate that social determinants of health are at the root of the HIV epidemic and affect the risk of HIV in multiple ways. These findings stress the need for the deployment of programs that specifically address social determinants of health.
COVID-19 self-testing strategy (COVIDST) can rapidly identify symptomatic and asymptomatic SARS-CoV-2-infected individuals and their contacts, potentially reducing transmission. In this living ...systematic review, we evaluated the evidence for real-world COVIDST performance. Two independent reviewers searched six databases (PubMed, Embase, Web of Science, World Health Organization database, Cochrane COVID-19 registry, Europe PMC) for the period April 1st, 2020, to January 18th, 2023. Data on studies evaluating COVIDST against laboratory-based conventional testing and reported on diagnostic accuracy, feasibility, acceptability, impact, and qualitative outcomes were abstracted. Bivariate random effects meta-analyses of COVIDST accuracy were performed (n = 14). Subgroup analyses (by sampling site, symptomatic/asymptomatic infection, supervised/unsupervised strategy, with/without digital supports) were conducted. Data from 70 included studies, conducted across 25 countries with a median sample size of 817 (range: 28-784,707) were pooled. Specificity and DOR was high overall, irrespective of subgroups (98.37-99.71%). Highest sensitivities were reported for: a) symptomatic individuals (73.91%, 95%CI: 68.41-78.75%; n = 9), b) mid-turbinate nasal samples (77.79%, 95%CI: 56.03-90.59%; n = 14), c) supervised strategy (86.67%, 95%CI: 59.64-96.62%; n = 13), and d) use of digital interventions (70.15%, 95%CI: 50.18-84.63%; n = 14). Lower sensitivity was attributed to absence of symptoms, errors in test conduct and absence of supervision or a digital support. We found no difference in COVIDST sensitivity between delta and omicron pre-dominant period. Digital supports increased confidence in COVIDST reporting and interpretation (n = 16). Overall acceptability was 91.0-98.7% (n = 2) with lower acceptability reported for daily self-testing (39.5-51.1%). Overall feasibility was 69.0-100.0% (n = 5) with lower feasibility (35.9-64.6%) for serial self-testing. COVIDST decreased closures in school, workplace, and social events (n = 4). COVIDST is an effective rapid screening strategy for home-, workplace- or school-based screening, for symptomatic persons, and for preventing transmission during outbreaks. These data will guide COVIDST policy. Our review demonstrates that COVIDST has paved the way for self-testing in pandemics worldwide.
•COVID-19 vaccine efficacy (VE) varies against SARS-CoV-2 variants of concern.•We present a final VE analysis from a phase 1b/2 AZD1222 trial in South Africa.•VE was 90% for WT, 6.7% for Beta and ...77.1% for Delta ≥ 9 months post-vaccination.•Safety was consistent with the interim analysis and no new concerns were reported.•AZD1222 offers durable protection, potentially due to anamnestic immune responses.
COVID-19 vaccine efficacy (VE) has been observed to vary against antigenically distinct SARS-CoV-2 variants of concern (VoC). Here we report the final analysis of VE and safety from COV005: a phase 1b/2, multicenter, double-blind, randomized, placebo-controlled study of primary series AZD1222 (ChAdOx1 nCoV-19) vaccination in South African adults aged 18–65 years. South Africa’s first, second, and third waves of SARS-CoV-2 infections were respectively driven by the ancestral SARS-CoV-2 virus (wild type, WT), and SARS-CoV-2 Beta and Delta VoCs. VE against asymptomatic and symptomatic infection was 90.6% for WT, 6.7% for Beta and 77.1% for Delta. No cases of severe COVID-19 were documented ahead of unblinding. Safety was consistent with the interim analysis, with no new safety concerns identified. Notably, South Africa’s Delta wave occurred ≥ 9 months after primary series vaccination, suggesting that primary series AZD1222 vaccination offers a good durability of protection, potentially due to an anamnestic response.
Clinical trial identifier: CT.gov NCT04444674.
There is a paucity of data on COVID-19 vaccines in people living with HIV-1, who could be at increased risk of severe illness and death from COVID-19. We evaluated the safety and immunogenicity of a ...Matrix-M adjuvanted recombinant spike protein nanoparticle COVID-19 vaccine (NVX-CoV2373; Novavax) in HIV-negative people and people living with HIV-1.
In this randomised, observer-blinded, multicentre, placebo-controlled phase 2A/B trial in South Africa, participants aged 18–84 years, with and without underlying HIV-1, were enrolled from 16 sites and randomly assigned (1:1) to receive two intramuscular injections of NVX-CoV2373 or placebo, 21 days apart. People living with HIV-1 were on stable antiretroviral therapy and had an HIV-1 viral load of less than 1000 copies per mL. Vaccine dosage was 5 μg SARS-CoV-2 recombinant spike protein with 50 μg Matrix-M adjuvant, whereas 0·9% saline was used as placebo injection (volume 0·5 mL each). All study staff and participants remained masked to study group assignment. We previously reported an interim analysis on the efficacy and safety of the NVX-CoV2373 vaccine (coprimary endpoints). In this Article, we present an expanded safety analysis for the full cohort of participants and report on the secondary objective of vaccine immunogenicity in the full cohort of people living with HIV-1 and in HIV-negative individuals overall and stratified by baseline SARS-CoV-2 serostatus. This trial is registered with ClinicalTrials.gov, NCT04533399, and the Pan-African Clinical Trials Registry, PACTR202009726132275.
Participants were enrolled between Aug 17 and Nov 25, 2020. The safety analysis set included 4164 HIV-negative participants (2089 in the intervention group and 2075 in the placebo group) and 244 people living with HIV-1 (122 in the intervention group and 122 in the placebo group). 1422 (34·1%) of 4164 HIV-negative people and 83 (34·0%) of 244 people living with HIV-1 were categorised as baseline SARS-CoV-2-positive (ie, anti-spike IgG reactive at enrolment or had a reactive SARS-CoV-2 nucleic acid amplification test by 14 days after the second study vaccination). In the NVX-CoV2373 group, solicited local and systemic adverse events were more common in HIV-negative participants (427 30·6% local and 401 28·7% systemic) than in people living with HIV-1 (20 25·3% local and 20 25·3% systemic) among those who were baseline SARS-CoV-2-seronegative (naive). Of the serious adverse events that occurred among HIV-negative people (of whom, two 0·1% were baseline SARS-CoV-2-negative and four 0·6% were baseline SARS-CoV-2-positive) and people living with HIV-1 (for whom there were no serious adverse events) in the NVX-CoV2373 group, none were assessed as related to the vaccine. Among participants who were baseline SARS-CoV-2-negative in the NVX-CoV2373 group, the anti-spike IgG geometric mean titres (GMTs) and seroconversion rates (SCRs) were lower in people living with HIV-1 (n=62) than in HIV-negative people (n=1234) following the first vaccination (GMT: 508·6 vs 1195·3 ELISA units EU/mL; SCR: 51·6% vs 81·3%); and similarly so 14 days after the second vaccination for GMTs (14 420·5 vs 31 631·8 EU/mL), whereas the SCR was similar at this point (100·0% vs 99·3%). In the NVX-CoV2373 group, anti-spike IgG GMTs 14 days after the second vaccination were substantially higher in those who were baseline SARS-CoV-2-positive than in those who were baseline SARS-CoV-2-seronegative for HIV-negative participants (100 666·1 vs 31 631·8 EU/mL) and for people living with HIV-1 (98 399·5 vs 14 420·5 EU/mL). This was also the case for angiotensin-converting enzyme 2 receptor-binding antibody and neutralising antibody titres.
The safety of the NVX-CoV2373 vaccine in people living with HIV-1 was similar to that in HIV-negative participants. However, people living with HIV-1 not previously exposed to SARS-CoV-2 had attenuated humoral immune responses to NVX-CoV2373 compared with their HIV-negative vaccine counterparts, but not so if they were baseline SARS-CoV-2-positive.
Novavax and the Bill & Melinda Gates Foundation; investigational vaccine manufacturing support was provided by the Coalition for Epidemic Preparedness Innovations.
BackgroundTuberculosis (TB) disease remains undiagnosed or unreported in approximately 4.2 million people annually. To address these “missing millions”, we assessed the feasibility and impact of a ...scalable model for transmission-interrupting, community-based active case finding (ACF) in major cities of four African countries: Cape Town, South Africa, Lusaka, Zambia, Harare, Zimbabwe, and Maputo, Mozambique. MethodsIn peri-urban informal settlements using a 1:1 randomised controlled trial (stratified by country), we performed ACF using a low-cost mobile clinic fitted with a portable 2-module Xpert system and compared a point-of-care (POC) Xpert to a standard-of-care centralised laboratory Xpert with sputum culture used as a reference standard. At the Cape Town site, those with microbiologically confirmed TB received infectiousness studies, including smear microscopy, chest x-ray (CXR) and cough aerosol sampling (CASS). ResultsOf 4193 rapidly screened individuals, 1977 were identified as at risk for TB and received targeted screening and randomisation to either POC Xpert (n=988) or centralised Xpert (n=988). Across all sites, 97 (4.9%) of 1977 participants had microbiological confirmation of TB; 53/531 at the Cape Town site (10.0% TB positivity rate; 29/53 54.7% culture-positive). Xpert identified 75% (22/29) of all culture-positive samples. 40/53 participants had all infectiousness studies performed, and 26/40 were identified as probably infectious (defined as cavities on CXR n=26 and/or smear-positivity n=9 and/or CASS-positivity n=3). Xpert identified almost all probably infectious cases (25/26 96.1%). ConclusionCommunity-based active case-finding using portable molecular-based diagnostic tools reliably detects probably infectious, minimally symptomatic TB patients. These data inform key elements of ACF strategies needed to bridge the gap to find, treat and end TB.
BackgroundHIV self-testing (HIV-ST) has the potential to positively impact HIV test access, uptake and early diagnosis. Its widespread adoption could change the nature of how and where patients ...access HIV testing. But concerns remain regarding test conduct, provision and nature of counselling, and support offered during/after HIV-ST. This study investigated an oral HIV-ST application (app) based strategy (an oral self-test with a mobile phone/tablet app), that offered HIV pre-test counselling, risk staging, test conduct/interpretation, and linkages to care. We aimed to identify if and how the app provided counseling and support during/after HIV-ST and how this strategy might impact test access in the South African context.MethodsWe conducted a qualitative study nested within an observational cohort study (November 2016 – May 2018) with concurrent comparators, in the township populations of Cape Town, South Africa. Participants could choose between supervised HIV-ST/unsupervised HIV-ST in private spaces around the clinic, and unsupervised HIV-ST at home. Qualitative data were collected from study participants and study staff using 33 semi-structured interviews, one focus group discussion, and observation notes. Audio files and notes were transcribed and themes were developed iteratively. NVIVO 9 (QSR International) was used during analysis.ResultsCompared to conventional testing, participants perceived the app-based HIV-ST strategy as convenient. The convenience to test anywhere gave participants more control in choosing whom they included in the testing process. It addressed stigma, social visibility and privacy concerns by letting testers answer sensitive questions and receive their results privately. Future concerns centered on affordability, smartphone access, and usability in older and rural users.ConclusionThe innovative app-based strategy addressed multiple HIV testing barriers by making testing convenient and private. The flexible access and support offered by the strategy could aid in expanding access and linkages for HIV-ST and related co-infections in South Africa and beyond.DisclosureNo significant relationships.
•Treating MDR-TB is complicated, long and expensive.•Bedaquiline (BQ) is a new active drug to treat MDR-TB.•No study evaluated safety and effectiveness of surgery in BQ-treated patients.•57 ...BQ-exposed cases resistant to 7 drugs (median) underwent surgery in 9 countries.•60% of cases initiated BQ after surgery, 36.4% before and completed it afterwards.•90% culture-converted and 69.1% achieved treatment success at the end of treatment.
No study evaluated the contribution of adjunctive surgery in bedaquiline-treated patients. This study describes treatment outcomes and complications in a cohort of drug-resistant pulmonary tuberculosis (TB) cases treated with bedaquiline-containing regimens undergoing surgery.
This retrospective observational study recruited patients treated for TB in 12 centres in 9 countries between January 2007 and March 2015.
Patients who had surgical indications in a bedaquiline-treated programme-based cohort were selected and surgery-related information was collected. Patient characteristics and surgical indications were described together with type of operation, surgical complications, bacteriological conversion rates, and treatment outcomes. Treatment outcomes were evaluated according to the time of surgery.
57 bedaquiline-exposed cases resistant to a median of 7 drugs had indication for surgery (52 retreatments; 50 extensively drug-resistant (XDR) or pre XDR-TB). Sixty percent of cases initiated bedaquiline treatment following surgery, while 36.4% underwent the bedaquiline regimen before surgery and completed it after the operation. At treatment completion 90% culture-converted with 69.1% achieving treatment success; 21.8% had unfavourable outcomes (20.0% treatment failure, 1.8% lost to follow-up), and 9.1% were still undergoing treatment.
The study results suggest that bedaquiline and surgery can be safely and effectively combined in selected cases with a specific indication.
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