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A correlation between neutralization activity after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination and protection against coronavirus disease 2019 (COVID-19) has been demonstrated by several studies. Here, we detect SARS-CoV-2 neutralizing antibody (NAB) production in COVID-19 patients from the Steve Biko Academic Hospital complex (SBAH), South Africa (SA). Samples from COVID-19 patients (mild to severe) were collected. SARS-CoV-2 rapid assays, genotyping (Delta and Omicron variants) and enzyme-linked immunosorbent assays (ELISA) were performed. IBM® Statistical Package for the Social Sciences (SPSS®) version 28 was used for inferential statistical analysis, and the data were presented using the Prism9 software (version 9.4.1). A total of 137 laboratory-confirmed COVID-19 patients, 12 vaccine recipients and 8 unvaccinated participants were evaluated. The production of SARS-CoV-2 NABs was observed in some of the COVID-19 cases, mainly in severe cases, although this should be noted with caution due to the small sample size of this pilot study. NABs were also observed in asymptomatic participants, with the most being found in recipients (n = 6) of the BNT162b2 (Pfizer-BioNTech) COVID-19 vaccine. We found a strong presence of NABs in COVID-19 patients, specifically in mild and severe cases. Severe infection was associated with higher NAB production (82%).

We performed studies investigating the feasibility of human to animal (H2A) model system to test whether patient generated respiratory bioaerosols hold infective capacity when traversing long distance airborne transport within the built environment. South African patients, clinically confirmed by facemask sampling to be exhaling SARS-CoV-2 genomic sequence, were recruited and housed for multiple days in a clinical ward with a uniquely designed building ventilation system continuously channeling exhaust airflow to individual microisolator animal caging units located proximal but segregated from clinic space (University of Pretoria AIR facility).

Acute coronary syndromes due to coronary artery vasospasm occur rarely and are difficult to diagnose in the acute setting. We present a patient with hypocalcaemia-induced coronary artery vasospasm, which resulted in an acute ST-elevation myocardial infarction. This was reversible upon administering intravenous calcium, with no long-term cardiac consequences for our patient.

The SARS-CoV-2 Omicron variant (B.1.1.529) has multiple spike protein mutations1,2 that contribute to viral escape from antibody neutralization3–6 and reduce vaccine protection from infection7,8. 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. Here we assessed the ability of T cells to react to Omicron spike protein in participants who were vaccinated with Ad26.CoV2.S or BNT162b2, or unvaccinated convalescent COVID-19 patients (n = 70). Between 70% and 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 for Beta (B.1.351) and Delta (B.1.617.2) variants, despite Omicron harbouring considerably more mutations. In patients who were hospitalized with Omicron infections (n = 19), there were comparable T cell responses to ancestral spike, nucleocapsid and membrane proteins to those in patients hospitalized in previous waves dominated by the ancestral, Beta or Delta variants (n = 49). Thus, despite extensive mutations and reduced susceptibility to neutralizing antibodies of Omicron, the majority of T cell responses induced by vaccination or infection cross-recognize the variant. It remains to be determined whether well-preserved T cell immunity to Omicron contributes to protection from severe COVID-19 and is linked to early clinical observations from South Africa and elsewhere9–12.

Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.

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 VOCs have shown variable escape from antibody responses, and have been shown to trigger qualitatively different antibody responses during infection. By studying plasma from individuals infected with either the original D614G, Beta or Delta variants, we show 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, enabling their cross-neutralization. Understanding antibodies targetting 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.ImportanceThe evolution of SARS-CoV-2 has resulted in variants of concern (VOCs) with distinct spike mutations conferring varying immune escape profiles. These variable mutations also influence the cross-reactivity of the antibody response mounted by individuals infected with each of these variants. This study sought to understand the antibody responses elicited by different SARS-CoV-2 variants, and to define shared epitopes. We show that Beta and Delta infection resulted in antibody responses that were more cross-reactive compared to the original D614G variant, but each with differing patterns of cross-reactivity. We further isolated an antibody from Beta infection, which targeted the N417 site, enabling cross-neutralization of Beta, Delta+ and Omicron, all of which possess this residue. The discovery of antibodies which target escape mutations common to multiple variants highlights conserved epitopes to target in future vaccines and therapeutics.

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.

SummaryThe 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.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.4 and BA.5 variants caused major waves of infections. Here, we assess the sensitivity of BA.4 to binding, neutralization, and antibody-dependent cellular cytotoxicity (ADCC) potential, measured by FcγRIIIa signaling, 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 neutralization resistance regardless of the infecting variant. However, BTIs retain activity against BA.4, albeit at reduced titers. BA.4 sensitivity to ADCC is reduced compared with other variants but with smaller fold losses compared with neutralization and similar patterns of cross-reactivity. Overall, the high neutralization resistance of BA.4, even to antibodies from BA.1 infection, provides an immunological mechanism for the rapid spread of BA.4 immediately after a BA.1-dominated wave. Furthermore, although ADCC potential against BA.4 is reduced, residual activity may contribute to observed protection from severe disease.

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.

The Janssen (JohnsonJohnson) Ad26.COV2.S non-replicating viral vector vaccine has been widely deployed for COVID-19 vaccination programs in resource-limited settings. Here we confirm that neutralizing and binding antibody responses to Ad26.COV2.S vaccination are stable for 6 months post-vaccination, when tested against multiple SARS-CoV-2 variants. Secondly, using longitudinal samples from individuals who experienced clinically mild breakthrough infections 4 to 5 months after vaccination, we show dramatically boosted binding antibodies, Fc effector function, and neutralization. These high titer responses are of similar magnitude to humoral immune responses measured in convalescent donors who had been hospitalized with severe illness, and are cross-reactive against diverse SARS-CoV-2 variants, including the neutralization-resistant Omicron (B.1.1.529) variant that currently dominates global infections, as well as SARS-CoV-1. These data have implications for population immunity in areas where the Ad26.COV2.S vaccine has been widely deployed, but where ongoing infections continue to occur at high levels.

Tuberculosis poses one of the greatest infectious disease threats of our time, especially when associated with human immunodeficiency virus (HIV) infection. Very little data is available on the lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients. Three patient cohorts were studied: (i) HIV-positive with no respiratory disease (control cohort), (ii) HIV-positive with pneumonia and (iii) HIV-positive with PTB. Sputum specimens were collected in all patients and where possible a paired BALF was collected. DNA extraction was performed using the QIAamp DNA mini kit (QIAGEN, Germany) and extracted DNA specimens were sent to Inqaba Biotechnical Industries (Pty) Ltd for 16S rRNA gene sequence analysis using the Illumina platform (Illumina Inc, USA). Data analysis was performed using QIMME II and R Studio version 3.6.2 (2020). The lung microbiomes of patients with PTB, in the context of HIV co-infection, were dominated by Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Loss of biodiversity and dysbiosis was found in these patients when compared to the HIV-positive control cohort. Microbial community structure was also distinct from the control cohort, with the dominance of genera such as Achromobacter, Mycobacterium, Acinetobacter, Stenotrophomonas and Pseudomonas in those patients with PTB. This is the first study to describe the lung microbiome in patients with HIV and PTB co-infection and to compare findings with an HIV-positive control cohort. The lung microbiomes of patients with HIV and PTB were distinct from the HIV-positive control cohort without PTB, with an associated loss of microbial diversity.

The Janssen (Johnson & Johnson) Ad26.COV2.S non-replicating viral vector vaccine has been widely deployed for COVID-19 vaccination programs in resource-limited settings. Here we confirm that neutralizing and binding responses to Ad26.COV2.S vaccination are stable for 6 months post-vaccination, when tested against multiple SARS-CoV-2 variants. Secondly, using longitudinal samples from individuals who experienced clinically mild breakthrough infections 4 to 5 months after vaccination, we show dramatically boosted binding antibodies, Fc effector function and neutralization. These high titer responses are of similar magnitude to humoral immune responses measured in severely ill, hospitalized donors, and are cross-reactive against diverse SARS-CoV-2 variants, including the extremely neutralization resistant Omicron (B.1.1.529) variant that currently dominates global infections, as well as SARS-CoV-1. These data have implications for population immunity in areas where the Ad26.COV2.S vaccine has been widely deployed, but where ongoing infections continue to occur at high levels.

SummarySARS-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.

Severe acute respiratory syndrome coronavirus-2 (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 improved disease outcome 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 and Delta infection trigger responses with significantly improved Fc cross-reactivity against global VOCs compared with D614G-infected or Ad26.COV2.S-vaccinated individuals. This suggests that, as for neutralization, the infecting spike sequence affects Fc effector function. These data have important implications for vaccine strategies that incorporate VOCs, suggesting these may induce broader Fc effector responses., Graphical abstract, Beyond neutralization, antibodies trigger cytotoxic functions associated with SARS-CoV-2 vaccine protection. Richardson et al. show that these functions are retained against variants of concern (VOC) and that infection by VOCs triggers cross-reactive cytotoxic antibodies. This suggests that SARS-CoV-2 VOC could be used as the basis of vaccines triggering enhanced immune breadth.

Introduction SARS-CoV-2 has resulted in increased worldwide demand for personal protective equipment (PPE). With pressure from ongoing epidemic and endemic episodes, we assessed an adapted snorkel mask that provides full-face protection for healthcare workers (HCWs), particularly during aerosol-generating procedures. These masks have a custom-made adaptor which allows the fitment of standard medical respiratory filters. The aim of this study was to evaluate the fit, seal and clinical usability of these masks. Methods This multicentre, non-blinded in-situ simulation study recruited fifty-two HCWs to don and doff the adapted snorkel mask. Negative pressure seal checks and a qualitative fit test were performed. The HCWs completed intubation and extubation of a manikin in a university skills training laboratory, followed by a web-based questionnaire on the clinical usability of the masks. Results Whilst fit and usability data were generally satisfactory, two of the 52 participants (3.8%) felt that the mask did not span the correct distance from the nose to the chin, and 3 of 34 participants (8.8%) who underwent qualitative testing with a Bitrex test failed. The majority of users reported no fogging, humidity or irritation. It was reportedly easy to speak while wearing the mask, although some participants perceived that they were not always understood. Twenty-one participants (40%) experienced a subjective physiological effect from wearing the mask; most commonly a sensation of shortness of breath. Discussion A fit-tested modified full-face snorkel mask may offer benefit as a substitute for N95 respirators and face shields. It is, however, important to properly select the correct mask based on size, fit testing, quality of the three-dimensional (3D) printed parts and respiratory filter to be used. Additionally, HCWs should be trained in the use of the mask, and each mask should be used by a single HCW and not shared.

BackgroundTargeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients.MethodsSpontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method.ResultsStatistically significant differences were observed in alpha diversity when targeted metagenomics and IS-Pro methods’ data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as theProteobacteria, and higher relative abundance of phyla, such asFirmicuteswhen compared to the IS-Pro method.Haemophilus,PrevotellaandStreptococcuswere most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the IS-Pro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly.ConclusionsIt is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance ofProteobacteria.However, the IS-Pro kit identified most of the important lung pathogens, such asBurkholderiaandPseudomonasand may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use.

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.

The SARS-CoV-2 Omicron variant escapes neutralizing antibodies elicited by vaccines or infection. However, whether Omicron triggers cross-reactive humoral responses to other variants of concern (VOCs) remains unknown. We use plasma from 20 unvaccinated and seven vaccinated individuals infected by Omicron BA.1 to test binding, Fc effector function and neutralization against VOCs. In unvaccinated individuals, Fc effector function and binding antibodies target Omicron and other VOCs at comparable levels. However, Omicron BA.1-triggered neutralization is not extensively cross-reactive for VOCs (14 to 31-fold titer reduction) and we observe 4-fold decreased titers against Omicron BA.2. In contrast, vaccination followed by breakthrough Omicron infection was associated with improved cross-neutralization of VOCs, with titers exceeding 1:2,100. This has important implications for vulnerability of unvaccinated Omicron-infected individuals to reinfection by circulating and emerging VOCs. 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.

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 (B.1.351), a novel lineage of coronavirus causing COVID-19, contains substitutions in two immunodominant domains of the spike protein. Here, we show that pseudovirus expressing 501Y.V2 spike protein completely escapes three classes of therapeutically relevant antibodies. This pseudovirus also exhibits substantial to complete escape from neutralization, but not binding, by convalescent plasma. These data highlight the prospect of reinfection with antigenically distinct variants and foreshadows reduced efficacy of spike-based vaccines. Substitutions in SARS-CoV-2 spike protein present in the B.1.351 variant first detected in South Africa, when expressed in pseudoviruses, mediate escape from neutralization by monoclonal antibodies under clinical development and by plasma from individuals previously infected with SARS-CoV-2, but do not prevent binding of convalescent plasma to recombinant spike protein containing B.1.351 lineage substitutions.

The interaction between obesity, cardiometabolic disorders and COVID-19 represents a syndemic that requires both social intervention and a multipharmacological approach [...]

Purpose In South Africa, many illicit drugs have only recently been introduced and drug-related complications are often new to treating physicians. Heroin-induced leukoencephalopathy has been reported elsewhere in patients who inhale heated heroin vapors, a method known as “chasing the dragon.” The purpose of this paper is to present two patients, known to have inhaled heroin a few weeks prior to presenting with progressive neurological deficits. Design/methodology/approach Case presentations: two young males presented independently within eight weeks of one another with progressive slurring of speech, incoordination and weakness of the limbs over a period of two to three weeks. Both were known heroin addicts, and were known to one another, and both had inhaled heroin prior to the onset of symptoms. Findings The patients presented with a pancerebellar syndrome with marked bilateral upper motor neuron signs. CT scans showed diffuse symmetrical hypodense lesions involving the cerebral and cerebellar white matter with normal CSF. Both patients deteriorated neurologically, became cardiovascularly unstable and demised. Postmortem in one of the patients showed a prominent spongiform leukoencephalopathy consistent with reports of heroin-inhalation injury to the brain. Research limitations/implications Toxic leukoencephalopathy due to heroin vapor inhalation was first described in the Netherlands in 1982. It has not been reported to occur with other modes of heroin use; an unknown toxin contained in heroin pyrolysate which forms when heroin is heated, may be causative. Brain MRI typically shows diffuse, symmetrical white matter hyperintensities on T2 and fluid-attenuated inversion recovery sequences in the cerebellum, posterior cerebrum and posterior limbs of the internal capsule with a posterior-anterior gradient. Pathologically, spongiform degeneration with relative sparing of subcortical U-fibers is seen. No treatment has been proven effective, but antioxidants and Vitamin E may be beneficial. Mortality is high at 23-48 percent. Practical implications This report emphasizes that spongiform leukoencephalopathy as a rare consequence of inhaling heroin vapors does occur in South Africa and clinicians should consider this disorder in their differential diagnosis of acutely developing leukoencephalopathy. Social implications An awareness program regarding this grave condition is planned. Originality/value The cardiovascular complications of patients inhaling heroin vapor has not been highlighted previously. These are the first patients from Africa described with this condition. A toxic component appears likely.

Staphylococcus epidermidis is one of the most prevalent pathogens implicated in catheter-related bloodstream infections (CRBSI) at an academic hospital in Pretoria, South Africa. Little is known about the clonality and the prevalence of antibiotic resistance and virulence genes in S. epidermidis (e.g., icaAB, IS256, mecA, and qacA/B). A total of 508 intravascular catheters (IVCs) from 331 patients were submitted for culture from May to October 2013. Only 50% (n = 253/508) of the IVCs were accompanied by blood cultures (BCs) taken within 48 h. Forty-four percent (44%; n = 112/253) of IVCs were colonised, of which 26% (n = 65/253) were associated with a CRBSI. We identified S. epidermidis as the causal agent in 31% (n = 20/65) of the CRBSI cases. Fifty-nine S. epidermidis isolates were obtained, 23 isolates were cultured from 22 IVCs and 36 isolates were cultured from 36 BCs. All S. epidermidis isolates were resistant to β-lactams (100%; n = 59/59), followed by high levels of resistance toward erythromycin (86%; n = 51/59) and gentamicin (81%; n = 49/59). The mecA gene was prevalent in all the (100%, n = 59/59) isolates. Isolates contained the IS256 element (83%, n = 49/59), the icaAB gene (81%, n = 48/59) and, the qacA/B gene (81%, n = 48/59). All 48 isolates were qacA positive upon restriction enzyme digestion of the qacA/B amplicons. Phenotypic resistance toward 0.5% (m/v) chlorhexidine was not observed. Staphylococcal Cassette Chromosome (SCC) mec typing showed that SCCmec type IV (31%; n = 18/59) was the most prevalent. The remaining SCCmec elements were highly diverse. Pulsed-field gel electrophoresis (PFGE) showed that S. epidermidis isolates from individual patients were mostly clonal. Multilocus sequencing typing (MLST) of 10 sequenced isolates showed that sequence type (ST) 2 (40%; n = 4/10) was the most frequently detected, followed by ST54 (20%; n = 2/10), ST28 (10%; n = 1/10), ST59 (10%; n = 1/10) and ST490 (10%; 1/10). One isolate was newly assigned to ST596. These S. epidermidis infections can be attributed to patients' skin microflora or to poor infection control practices. Currently, S. epidermidis strains circulating in the studied hospital are multidrug-resistant and highly adaptive to environmental changes.

Objective: The purpose of this study was to determine the prevalence of subclinical hypothyroidism among patients with diabetes mellitus at the Kalafong Diabetes Clinic in Pretoria.Design: Cross-sectional study.Setting and subjects: Five hundred and sixty-five patients with diabetes mellitus (type 1, type 2 or unknown), who were following-up at the Kalafong Hospital Diabetes Clinic.Outcome measures: The thyroid stimulating hormone (TSH) levels of patients were evaluated. Patients with TSH levels > 5.66 IU/ml (upper reference limit of the Kalafong National Health Laboratory Services laboratory) subsequently underwent repeat thyroid function evaluation, including T4 level, to determine the prevalence of subclinical hypothyroidism.Results: A total of 563 patients met the inclusion criteria for this study and underwent TSH evaluation. The prevalence of subclinical hypothyroidism was found to be 0.9% in the study population, and 1.6% in a subgroup of patients with type 2 diabetes mellitus.Conclusion: The prevalence of subclinical hypothyroidism in this South African population of patients with diabetes was significantly lower than that stated in the literature. This holds true for both the general population and populations of patients with diabetes mellitus. To our knowledge, there is no data available for the prevalence of subclinical hypothyroidism in the general population in South Africa for comparison with the study group.Keywords: subclinical hypothyroidism, diabetes mellitus, South Africa

Background The burden of catheter-related infections (CRIs) in developing countries is severe. In South Africa, a standardised surveillance definition does not exist and the collection of catheter days is challenging. The aim of the study was to provide baseline data on the prevalence of CRIs and to describe the epidemiology of CRI events within a tertiary academic hospital. Methods Surveillance was laboratory-based and conducted for a six month period. A microbiologically confirmed CRBSI (MC-CRBSI) event was defined as the isolation of the same microorganism from the catheter and concomitant blood cultures (BCs), within 48 h of catheter removal, which were not related to an infection at another site. Results A total of 508 catheters, removed from 332 patients, were processed by the laboratory, of which only 50% (253/508 removed from 143/332 patients) of the catheters were accompanied by BCs within 48 h. Sixty-five episodes of MC-CRBSI in 57 patients were detected, involving 71 catheters and 195 microbial isolates. The institutional prevalence rate was 3.7 episodes per 1 000 admissions and 5.8 episodes per 10 000 in-patient days. Catheter day data was collected in only six wards of the hospital. The pooled laboratory incidence was 10.1 MC-CRBSI episodes per 1 000 catheter days, whereas the hospital-based central line-associated bloodstream infection (CLABSI) rate was pooled at 5.7 episodes per 1 000 catheter days. The majority of patients had an underlying gastro-intestinal condition (33%; 19/56) with a non-tunnelled, triple-lumen central venous catheter, placed in the subclavian vein (38%; 27/71). The most predominant pathogen was methicillin-resistant Staphylococcus epidermidis (28%; 55/195), followed by extensively-drug resistant Acinetobacter baumannii (18%; 35/195). Conclusions Catheter-related infection prevention and control efforts require urgent attention, not only to keep patients safe from preventable harm, but to prevent the spread of multidrug resistant microorganisms.

The diagnosis of porphyria remains challenging as the condition is characterized by a myriad of clinical and biochemical features. More importantly, an acute attack is associated with increased morbidity and mortality. Misdiagnosis of porphyria poses an ongoing problem. We describe a 42-year-old Black female South African patient who presented to Steve Biko Academic Hospital in Pretoria, on the 16 July 2014 with a clinical problem of acute paraparesis. On admission, she had absent reflexes, bilateral cranial nerve VII fallout, patchy sensory fallout and faecal incontinence. When her magnetic resonance imaging of the brain and cervical spine showed no signs suggestive of acute disseminated encephalomyelitis, a diagnosis of Guillain–Barre syndrome was made. On the 21 July her condition deteriorated to the point where she needed ventilator support. She also developed a pulmonary embolism and was treated. Due to deterioration of her condition, urine was sent for porphobilinogen test. This was clearly positive. The diagnosis of acute intermittent porphyria was eventually made. This case highlights the complexity related to the diagnosis of porphyria. It confirms that the diagnosis is often incidental and in a vast majority of patients, neurological complications preceded the final biochemical diagnosis.

Hypercalcaemia is not uncommon in clinical practice. The majority of cases are accounted for by hyperparathyroidism and malignancy. The patient discussed below presented with an unusual case of hypercalcaemia.

The hepatic porphyrias are a group of rare metabolic disorders, each of which is associated with a specific enzymatic alteration in the haem biosynthesis pathway. In South Africa (SA), a high incidence of variegate porphyria (VP) is seen as a result of a founder effect, but acute intermittent porphyria (AIP) is also encountered. The development of acute neurovisceral attacks is related to environmental factors, including medications, hormones and diet. A possible manifestation of a severe attack is rapidly progressing quadriparesis, which may mimic Guillain-Barré syndrome. We present four such cases, highlighting that acute porphyria should be considered in the differential diagnosis of Guillain-Barré syndrome. Three patients presented to Steve Biko Academic Hospital, Pretoria, SA, with progressive quadriparesis, and one to a private hospital with acute abdominal pain followed by rapidly progressive quadriparesis. Two patients had started antiretroviral therapy before the development of symptoms, and one had started antituberculosis therapy. All patients had marked weakness with depressed reflexes, and showed varying degrees of confusion. An initial diagnosis of Guillain-Barré syndrome led to administration of intravenous immunoglobulins in two patients. On testing for porphyria, it was found that two patients had AIP and two VP. Electrophysiological investigations revealed severe mainly motor axonal neuropathy in all. Two patients deteriorated to the point of requiring mechanical ventilation, and one of them died due to complications of critical illness. Haemin was administered to three patients, but the process of obtaining this medication was slow, which delayed the recommended early administration. The surviving patients showed minimal recovery and remained severely disabled. Porphyric neuropathy should always be considered as a differential diagnosis in a patient with an acute neuropathy, especially in SA. Absence of abdominal pain does not exclude the possibility of porphyria, and attacks may be precipitated by antiretroviral and antituberculosis medication. The outcome of our patients was not favourable; specifically, obtaining haemin was a challenge in the state hospital setting.