Comorbidities in Privately Insured South Africans With Systemic Lupus Erythematosus.

Introduction Comorbidities in systemic lupus erythematosus (SLE) impact negatively on health-related quality of life (HRQoL) and life expectancy. We investigated the frequency and spectrum of comorbidities in privately insured South Africans with SLE. Methods The data of SLE patients based on International Classification of Diseases, Tenth Revision (ICD-10) codes and insured with Discovery Health Medical Scheme (DHMS), South Africa, aged ≥16 years at diagnosis and with ≥6 months of follow-up were reviewed. Demographics, comorbidities listed in the Charlson comorbidity index (CCI), other common comorbidities, intercurrent illnesses, and drug therapy were documented. Results Of the 520 patients coded as SLE, 207 met the inclusion criteria. Most were females (90.8%), with a median (interquartile range {IQR}) age and follow-up duration of 39 (30.3-53.0) and 6.1 (3.7-8.1) years, respectively. All patients had at least one comorbidity; the most frequent CCI comorbidities were pulmonary disease (30.9%), congestive heart failure (CHF, 15%), and renal disease (14.0%). Other common comorbidities were hypertension (53.1%) and mood and anxiety disorders (46.9%). Urinary tract infections (UTIs, 37.7%) and pneumonia (33.8%) were common intercurrent illnesses. The independent predictors of CHF were renal disease (odds ratio {OR}=855), dyslipidemia (OR=15.3), and male gender (OR=43.0); the independent predictors of hypertension were age at diagnosis (OR=1.03), type 2 diabetes (OR=4.45), and renal disease (OR=4.34); and the independent predictors of mood and anxiety disorders were female gender (OR=3.98), stroke (OR=3.18), UTI (OR=2.39), and chloroquine use (OR=1.94). Conclusion In this study of privately insured South Africans with SLE, comorbidities were common, and all patients had at least one comorbidity. Hypertension, infections, and mood and anxiety disorders were the leading comorbidities overall, and pulmonary disease was the most common CCI comorbidity. There is an obvious need to formally study the burden of mental health disorders in South African SLE patients.

The Performance of Pulmonary Function Tests in Predicting Systemic Sclerosis-Interstitial Lung Disease in the European Scleroderma Trial and Research Database.

BACKGROUND AND OBJECTIVES: In SSc, ILD is a major cause of morbidity and mortality. We aimed to investigate the performance of DLCO (diffusing capacity of lung carbon monoxide) and FVC (forced vital capacity) delta change (Δ) and baseline values in predicting the development of SSc-ILD. METHODS: Longitudinal data of DLCO, FVC, and ILD on the HRCT of SSc patients from the EUSTAR database were evaluated at baseline (t0) and after 12 (±4) (t1) and 24 (±4) (t2) months. RESULTS: 474/17805 patients were eligible for the study (403 females); 46 (9.7%) developed ILD at t2. Positivity for anti-topoisomerase antibodies (117 patients) showed an association with ILD development at t2 (p = 0.0031). Neither the mean t0 to t1 change (Δ) of DLCO nor the mean t0 to t1 FVCΔ predicted the appearance of ILD at t2. Investigating the possible role of baseline DLCO and FVC values in predicting ILD appearance after 24 (±4) months, we observed a moderate predictive capability of t0 DLCO < 80%, stronger than that of FVC < 80%. CONCLUSIONS: We suggest that an impaired baseline DLCO may be predictive of the appearance of ILD after 2 years of follow-up. This result advances the hypothesis that a reduction in gas exchange may be considered an early sign of lung involvement. However, further rigorous studies are warranted to understand the predictive role of DLCO evaluation in the course of SSc.

Choosing to End African American Health Disparities in SLE.

Systemic Lupus erythematosus (SLE) is 3 times more common and its' manifestations more severe in African American (AA) women compared to women of other races. It is not clear whether this is due to genetic differences or factors related to the physical or social environments, differences in health care or a combination of these factors. Health disparities in SLE between AAs and persons of other races have been reported since the 1960's and are correlated with measures of lower socioeconomic status. Risk factors for these disparities have been demonstrated but whether their mitigation improves outcomes for AA patients has not been tested except in self-efficacy. In 2002, Sacks conducted the first true U.S. population-based study of SLE with death certificate records and demonstrated a wide disparity between the number of AA women and white women dying from SLE. Five years ago, Yen showed that SLE mortality in the U.S. had improved, but that the AA mortality disparity persisted. Between 2014 and 2021 Lim and others demonstrated racism's deleterious effects in SLE. Racism may have been the unmeasured confounder, the proverbial "elephant in the room" - unnamed and unstudied. The etymology of "risk factor" has evolved from environmental risk factors to social determinants to now include structural injustice/structural racism. Racism in the U.S. has centuries long existence and is deeply ingrained and intertwined making its detection and resolution difficult. However, its being man-made means mankind can choose to change the situation. Health disparities in SLE should be addressed by viewing healthcare as a basic human right. We offer a conceptual framework and goals for both individual and national actions.

Osteoporosis in Black South Africans With Rheumatoid Arthritis.

Background Osteoporosis is a common comorbidity associated with rheumatoid arthritis (RA). The aim of this study was to determine the risk factors and possible predictors of osteoporosis in black patients with RA. Methods A retrospective study of 120 randomly selected RA patients attending an arthritis clinic in Johannesburg, South Africa, was carried out, in which 60 patients were with and 60 without osteoporosis. The demographics, disease activity, American College of Rheumatology (ACR) functional status, treatment, and dual-energy X-ray absorptiometry (DEXA) characteristics were compared. Statistical analysis was performed using SPSS version 25.0 (IBM Corp, Armonk, NY). Bivariate comparisons of demographic factors, disease factors, and T-scores between patients with and without osteoporosis were performed, using two-sided t-tests for continuous variables and chi-squared tests for categorical variables. Possible predictors of osteoporosis were subsequently entered into a multivariate logistic regression model with osteoporosis being the dependent variable. The level of significance for all analyses was set at p < 0.05. Results The median (IQR) age of the overall cohort was 67 (61.0, 72.8) years, the majority (95.5%) were female, of which 97.4% were postmenopausal. The mean disease duration from diagnosis to the DEXA was 8.6 ± 6.2 years. Rheumatoid factor (RF) positivity was 89.2% and anti-cyclic citrullinated peptide (ACCP) positivity was 82.7%. The median (IQR) for disease activity score 28 swollen and tender joint count using the erythrocyte sedimentation rate (DAS-28 ESR) was 3.4 (2.8-4.7) and the median (IQR) for ESR was 41 (22, 64.3) mm/h. There were significantly more patients treated with triple therapy in the no osteoporosis group, 38 (63.3%), than in the osteoporosis group, 21 (35%) (p = 0.00). The ACR functional class was significantly worse in the RA patients with osteoporosis than in the RA patients without osteoporosis [median (IQR), 2 (2, 3) vs 2 (1, 2), (p = 0.03)], respectively. Conclusion This study found that a worse ACR functional class was significantly associated with osteoporosis. In addition, the use of triple therapy had a protective effect. Early recognition of the risk factors for osteoporosis should be sought, with prompt preventative measures, screening, and treatment.

Clinical spectrum and outcomes of idiopathic inflammatory myopathies in South Africans.

Background: Idiopathic inflammatory myopathies (IIM) are rare diseases for which there is a paucity of data in Africa. We undertook a retrospective records review of clinical and laboratory features of patients with IIM attending a tertiary service in Gauteng, South Africa. Materials and methods: Case records of patients seen between January 1990 and December 2019 and fulfilling the Bohan and Peter criteria for IIM were reviewed for demographics, clinical features, special investigations and drug therapy. Results: Of 94 patients included in the study, 65 (69.1%) had dermatomyositis (DM) and 29 (30.9%) had polymyositis (PM). Overall, the mean (SD) age at presentation and disease duration were 41.5 (13.6) and 5.9 (6.2) years, respectively. 88 (93.6%) were Black Africans. The most common cutaneous features in DM patients were Gottron's lesions (72.3%) and abnormal cuticular overgrowth (67.7%). Dysphagia was the most common extra-muscular feature (31.9%), more so in PM than DM (p = 0.02). Creatine kinase, total leucocyte count and CRP were similarly higher in PM than DM patients (p = 0.006, 0.002, and 0.01, respectively). Anti-nuclear and anti-Jo-1 antibodies were positive in 62.2 and 20.4% of patients tested, respectively, the latter significantly more in PM than DM patients (OR = 5.1, p = 0.03) and more likely to be positive with ILD (p = 0.001). Corticosteroids were prescribed in all patients, 89.4% had additional immunosuppressive drugs and 6.4% required intensive/high care. Malignancies occurred in three patients, all of whom had DM. There were seven known deaths. Conclusion: The present study provides further insights into the spectrum of clinical features of IIM, especially cutaneous features of DM, anti-Jo-1 antibodies and associated ILD, in a cohort of predominantly black African patients.

Geo-epidemiology of autoantibodies in rheumatoid arthritis: comparison between four ethnically diverse populations.

BACKGROUND: Rheumatoid arthritis (RA) occurs across the globe in different ethnic populations. Most RA patients harbor anti-modified protein antibodies (AMPA); however, it is unclear whether differences exist in autoantibody responses at different geographic locations and between different ethnic groups, which could provide new clues regarding factors underlying autoantibody development. We therefore investigated AMPA prevalence and association with HLA DRB1 alleles and smoking in four ethnically diverse populations on four different continents. METHODS: Anti-carbamylated (anti-CarP), anti-malondialdehyde acetaldehyde (anti-MAA), and anti-acetylated protein antibodies (anti-AcVim) IgG were determined in anti-citrullinated protein antibody-positive Dutch (NL, n = 103), Japanese (JP, n = 174), First Nations Peoples in Canada (FN, n = 100), and black South African (SA, n = 67) RA patients. Ethnicity-matched local healthy controls were used to calculate cut-offs. Risk factors associated with AMPA seropositivity in each cohort were identified using logistic regression. RESULTS: Median AMPA levels were higher in First Nations Peoples in Canada and especially South African patients, as reflected by percentage seropositivity: NL, JP, FN, and SA: anti-CarP: 47%, 43%, 58%, and 76% (p < 0.001); anti-MAA: 29%, 22%, 29%, and 53% (p < 0.001); and anti-AcVim: 20%, 17%, 38%, and 28% (p < 0.001). Total IgG levels also differed markedly, and when autoantibody levels were normalized to total IgG, differences between cohorts became less pronounced. Although there were some associations with AMPA and HLA risk alleles and smoking, none was consistent across all four cohorts. CONCLUSIONS: AMPA against various post-translational modifications could consistently be detected on different continents across ethnically diverse RA populations. Differences in AMPA levels corresponded to differences in total serum IgG levels. This suggests that, despite differences in risk factors, a common pathway may be involved in AMPA development across geographic locations and ethnicities.

A genome-wide association study for rheumatoid arthritis replicates previous HLA and non-HLA associations in a cohort from South Africa.

The complex pathogenesis of rheumatoid arthritis (RA) is not fully understood, with few studies exploring the genomic contribution to RA in patients from Africa. We report a genome-wide association study (GWAS) of South-Eastern Bantu-Speaking South Africans (SEBSSAs) with seropositive RA (n = 531) and population controls (n = 2653). Association testing was performed using PLINK (logistic regression assuming an additive model) with sex, age, smoking and the first three principal components as covariates. The strong association with the Human Leukocyte Antigen (HLA) region, indexed by rs602457 (near HLA-DRB1), was replicated. An additional independent signal in the HLA region represented by the lead SNP rs2523593 (near the HLA-B gene; Conditional P-value = 6.4 × 10-10) was detected. Although none of the non-HLA signals reached genome-wide significance (P < 5 × 10-8), 17 genomic regions showed suggestive association (P < 5 × 10-6). The GWAS replicated two known non-HLA associations with MMEL1 (rs2843401) and ANKRD55 (rs7731626) at a threshold of P < 5 × 10-3 providing, for the first time, evidence for replication of non-HLA signals for RA in sub-Saharan African populations. Meta-analysis with summary statistics from an African-American cohort (CLEAR study) replicated three additional non-HLA signals (rs11571302, rs2558210 and rs2422345 around KRT18P39-NPM1P33, CTLA4-ICOS and AL645568.1, respectively). Analysis based on genomic regions (200 kb windows) further replicated previously reported non-HLA signals around PADI4, CD28 and LIMK1. Although allele frequencies were overall strongly correlated between the SEBSSA and the CLEAR cohort, we observed some differences in effect size estimates for associated loci. The study highlights the need for conducting larger association studies across diverse African populations to inform precision medicine-based approaches for RA in Africa.

Prevalence and Predictors of Abdominal Aorta Calcification in Patients With Psoriasis-A Case Control Study.

Background: Psoriasis is associated with a high prevalence of cardiovascular disease in Caucasians, but only a few studies from sub-Saharan Africa have investigated the prevalence of cardiovascular disease in patients with psoriasis. Abdominal aortic calcification (AAC) is a strong predictor of future cardiovascular events and all-cause mortality in the general population. We investigated the prevalence and risk factors for AAC in a predominantly non-Caucasian cohort of South African patients with psoriasis. Methods: A cross-sectional case-control study of adult psoriasis patients (n = 69) and controls (n = 80), matched for gender, ethnicity and body mass index, attending tertiary Dermatology and Rheumatology clinics in Johannesburg, South Africa. Demographic, anthropometric, clinical and biochemical data were recorded. All participants underwent non-contrast abdominal CT scans. Images were assessed for AAC at the supra-coeliac aorta, supra-mesenteric aorta and aortic bifurcation using Horos DICOM viewer software. Results: Abdominal aortic calcification at any site was more prevalent in the psoriasis than control group (47.8% vs 22.5%, p < 0.005). The aortic bifurcation was the commonest site for AAC in both groups, but more prevalent in the psoriasis group (42.0% vs 21.3%, p < 0.005). The psoriasis group was also more likely to smoke, have hypertension and type 2 diabetes (56.5% vs 25.0%, p < 0.005; 72.0% vs 55.0%, p < 0.005; 24.6% vs 3.80%, p < 0.0005, respectively). Multivariable logistic regression analysis demonstrated that age, smoking and type 2 (T2DM) diabetes were independently associated with AAC (odds ratio (95% CIs): 1.16 (1.07, 1.20), 4.30 (2.15, 8.61) and 3.45 (1.09, 15.7) respectively), but psoriasis was not. Forward regression analysis demonstrated that smoking attenuated the association of psoriasis with AAC. Conclusion: Our findings show AAC to be more common in psoriasis patients compared to controls. Age, T2DM and smoking were independent predictors of AAC. Smoking cessation is essential in psoriatic patients to reduce the risk of cardiovascular events. The clinical utility of AAC detection by CT imaging to risk stratify for hard cardiovascular outcomes needs to be explored.

Comorbidities in Black South Africans with established rheumatoid arthritis.

OBJECTIVE: Comorbidities contribute both to morbidity and mortality in rheumatoid arthritis (RA). The aim of the current study was to investigate the prevalence and spectrum of comorbidities in South Africans with established RA. METHODS: A retrospective, consecutive case record review of 500 Black South African patients with established disease of ≥5 years attending a tertiary rheumatology service was performed. Common comorbidities including those listed in the Charlson Comorbidity Score (CCS) were documented. RESULTS: Most patients, 463 known alive (AG) and 37 known deceased (DG), were female (87%). Mean (SD) age and disease duration were 60 (11.1) and 10.7 (5.0) years respectively, and 98% had ≥1 comorbidities. Median CCS was 2, significantly higher in DG than AG (4 vs 2, P < .0001). Despite hypertension (70%) and hypercholesterolemia (47%) being the commonest comorbidities overall and type 2 diabetes (T2D) occurring in 15.4%, clinical cardiovascular events were rare (0.6%). Peptic ulcer disease (odds ratio [OR] = 8.67), congestive cardiac failure (OR = 7.09), serious infections (OR = 7.02) and tuberculosis (OR = 2.56) were significantly more common in DG than AG. Multivariate analysis showed that American College of Rheumatology functional class 3/4 was associated with increased risk for serious infections (OR = 3.84) and tuberculosis (OR = 2.10). CONCLUSION: Despite the high burden of cardiometabolic comorbidities in South Africans with established RA, cardiovascular events were rare. Serious infections and tuberculosis, both associated with severe functional disability, are a major cause of morbidity and mortality.

Response to botulinum neurotoxin injections in large-angle infantile esotropia: a post hoc analysis.

PURPOSE: To determine the anticipated reduction of baseline angle of esotropia and identify predictors of change following botulinum neurotoxin (BNT) injections in large-angle infantile esotropia. METHODS: This was a prospective, longitudinal study of children <10 years of age diagnosed with infantile esotropia of >30Δ and given either 1, 2, or 3 BNT injections. Post-injection change from baseline deviation was recorded, and predictors of reduction were analyzed. For this study, children were further divided into subgroups based on initial deviation of ≤60Δ (group 1) and >60Δ (group 2). The outcomes of subsequent surgeries in failed cases were analyzed. RESULTS: A total of 117 children were included, 55 in group 1 and 62 in group 2. Mean age was 30.3 ± 18.8 months. Mean baseline deviation was 62.5Δ ± 13.1Δ: 51.4Δ ± 8.4Δ in group 1 and 73Δ ± 7.5Δ in group 2. The mean number of injections was 2.2 ± 0.7. Success was achieved in 25.6% of patients (33.4% in group 1; 16.2% in group 2). The mean percentage reduction of deviation after BNT injection was 55.2% ± 26%, larger in group 1 than in group 2 (61.3% vs 51.1% [P = 0.001]). Five children reverted to baseline deviation. In multivariate analysis, adjusting for number of injections, younger age and larger baseline deviation were significant independent predictors of a larger absolute amount of reduction (P = 0.02, and 0.002, resp.). Thirty-two children had subsequent surgery; 22 were followed for a minimum of 6 months, and 20 were aligned within 10Δ of orthotropia. CONCLUSIONS: In large-angle esotropia there was a reduction of approximately 50% of baseline deviation, with greater relative reduction for smaller baseline deviations; the absolute change in angle was greater in younger children. Alignment after subsequent surgery appeared to remain stable and surgery required less recession than would have been needed for the original angle of esotropia.

Cost comparison between botulinum neurotoxin and surgery in the treatment of infantile esotropia in a tertiary public hospital.

OBJECTIVE: To compare the cost implications of botulinum neurotoxin (BNT) injection to surgery in infantile esotropia (IE) in a public/government funded hospital. METHODS AND ANALYSIS: A simple costing comparison was undertaken for a randomised clinical trial in IE. Patients were randomised to receive either BNT or standard surgery. The participants in the BNT arm were further subdivided into subgroups based on their age in months and degree of esotropia in prism dioptres (PD) at presentation: G1 ≤60 PD/24 months, G2 ≤24 months/>60 PD, G3 >24 months/≤60 PD, G4 >24 months/>60 PD. The costs were calculated for each arm from primary treatment to eventual satisfactory outcome defined as orthophoria or microtropia (≤10 PD). A bottom-up costing analysis was done for single and multiple procedures for each arm. Comprehensive variable costs as well as fixed costs were calculated at each point of intervention and expressed in local currency ZAR (US$1=ZAR15.00). Costing was analysed for surgery and BNT subgroups (based on clinical success). RESULTS: There were 101 patients enrolled in the trial. 54 in the BNT arm and 47 in the surgery arm. Cost for single surgery and single BNT was ZAR 7743.04 and 1713.14, respectively. A favourable clinical outcome was achieved in 72% of surgery arm and 37% of BNT arm. The mean cost for eventual favourable outcome in BNT arm was ZAR9158.08 and in surgery arm ZAR9124.27 (p=0.26). Mean cost in G1 was ZAR6328.45, in G2 ZAR7197.45, in G3 ZAR11891.93 and G4 ZAR12882.44 (p=0.018). CONCLUSION: BNT has a cost-benefit in IE and is a viable option in the primary treatment of IE in resource constrained regions. Clinical outcomes and economic benefit in smaller angle of esotropia and younger patients are comparable to surgery.

Laser speckle contrast analysis is a reliable measure of digital blood perfusion in Black Africans with systemic sclerosis.

OBJECTIVES: Laser speckle contrast analysis (LASCA) is evolving as a promising non-invasive tool to assess cutaneous microvascular function in systemic sclerosis (SSc). Reliability studies have mainly focused on Caucasian populations. To determine for the first time the inter-rater reliability of fingertip blood perfusion (BP) using LASCA in Black South African patients with SSc. METHODS: Consecutive Black adult patients with SSc were evaluated for peripheral BP using LASCA. Mean BP in defined regions of interest for dorsal fingertips and volar fingertips were measured in two subgroups of 20 SSc patients, each by three independent operators. Two operators were experienced in the use of the LASCA instrument and one was newly trained. Standardised protocols for conditions were followed for all measurements. Inter-rater reliability was tested using the intraclass correlation coefficient (ICC). RESULTS: The majority (87.5%) of the 40 patients included were females and 67.5% had diffuse cutaneous SSc. The mean age (standard deviation) was 48.5 (9.9) years and the median disease duration (interquartile range) was 8.5 (4, 13) years. There was good to excellent agreement, inter-rater ICC (dorsal fingertip range: 0.86-0.97 and volar fingertip range: 0.85-0.96), in both subgroups irrespective of operator skill. CONCLUSIONS: LASCA is a credible instrument in patients of Black ethnicity with SSc, and across operator experience.

Rheumatic diseases in Africa.

Historically, rheumatic diseases have not received much attention in Africa, particularly in sub-Saharan Africa, possibly owing to a focus on the overwhelming incidence of infectious diseases and the decreased life span of the general population in this region. Global attention and support, together with better health policies and planning, have improved outcomes for many infectious diseases; thus, increasing attention is being turned to chronic non-communicable diseases. Rheumatic diseases were previously considered to be rare among Africans but there is now a growing interest in these conditions, particularly as the number of rheumatologists on the continent increases. This interest has resulted in a growing number of publications from Africa on the more commonly encountered rheumatic diseases, as well as case reports of rare diseases. Despite the limited amount of available data, some aspects of the epidemiology, genetics and clinical and laboratory features of rheumatic diseases in African populations are known, as is some detail on the use of therapeutics. Similarities and differences in these conditions can be seen across the multi-ethnic and genetically diverse African continent, and it is hoped that increased awareness of rheumatic diseases in Africa will lead to earlier diagnosis and better outcomes for patients.

African League Against Rheumatism (AFLAR) preliminary recommendations on the management of rheumatic diseases during the COVID-19 pandemic.

OBJECTIVES: To develop recommendations for the management of rheumatic and musculoskeletal diseases (RMDs) during the COVID-19 pandemic. METHOD: A task force comprising of 25 rheumatologists from the 5 regions of the continent was formed and operated through a hub-and-spoke model with a central working committee (CWC) and 4 subgroups. The subgroups championed separate scopes of the clinical questions and formulated preliminary statements of recommendations which were processed centrally in the CWC. The CWC and each subgroup met by several virtual meetings, and two rounds of voting were conducted on the drafted statements of recommendations. Votes were online-delivered and recommendations were pruned down according to predefined criteria. Each statement was rated between 1 and 9 with 1-3, 4-6 and 7-9 representing disagreement, uncertainty and agreement, respectively. The levels of agreement on the statements were stratified as low, moderate or high according to the spread of votes. A statement was retired if it had a mean vote below 7 or a 'low' level of agreement. RESULTS: A total of 126 initial statements of recommendations were drafted, and these were reduced to 22 after the two rounds of voting. CONCLUSIONS: The preliminary statements of recommendations will serve to guide the clinical practice of rheumatology across Africa amidst the changing practices and uncertainties in the current era of COVID-19. It is recognized that further updates to the recommendations will be needed as more evidence emerges. Key Points • AFLAR has developed preliminary recommendations for the management of RMDs in the face of the COVID-19 pandemic. • COVID-19 is an unprecedented experience which has brought new concerns regarding the use of some disease-modifying anti-rheumatic drugs (DMARDs), and these recommendations seek to provide guidelines to the African rheumatologists. • Hydroxychloroquine shortage has become rampart across Africa as the drug is being used as prophylaxis against COVID-19 and this may necessitate a review of treatment plan for some patients with RMDs. • Breastfeeding should continue for as long as possible if a woman is positive for SARS-CoV-2 as there is currently no evidence that the infection can be transmitted through breast milk.

nf-rnaSeqCount: A Nextflow pipeline for obtaining raw read counts from RNA-seq data.

The rate of raw sequence production through Next-Generation Sequencing (NGS) has been growing exponentially due to improved technology and reduced costs. This has enabled researchers to answer many biological questions through "multi-omics" data analyses. Even though such data promises new insights into how biological systems function and understanding disease mechanisms, computational analyses performed on such large datasets comes with its challenges and potential pitfalls. The aim of this study was to develop a robust portable and reproducible bioinformatic pipeline for the automation of RNA sequencing (RNA-seq) data analyses. Using Nextflow as a workflow management system and Singularity for application containerisation, the nf-rnaSeqCount pipeline was developed for mapping raw RNA-seq reads to a reference genome and quantifying abundance of identified genomic features for differential gene expression analyses. The pipeline provides a quick and efficient way to obtain a matrix of read counts that can be used with tools such as DESeq2 and edgeR for differential expression analysis. Robust and flexible bioinformatic and computational pipelines for RNA-seq data analysis, from QC to sequence alignment and comparative analyses, will reduce analysis time, and increase accuracy and reproducibility of findings to promote transcriptome research.

The impact of COVID-19 on rheumatology practice across Africa.

OBJECTIVES: To identify the changes in rheumatology service delivery across the five regions of Africa from the impact of the COVID-19 pandemic. METHODS: The COVID-19 African Rheumatology Study Group created an online survey consisting of 40 questions relating to the current practices and experiences of rheumatologists across Africa. The CHERRIES checklist for reporting results of internet e-surveys was adhered to. RESULTS: A total of 554 completed responses were received from 20 countries, which include six in Northern Africa, six in West Africa, four in Southern Africa, three in East Africa and one in Central Africa. Consultant grade rheumatologists constituted 436 (78.7%) of respondents with a mean of 14.5 ± 10.3 years of experience. A total of 77 (13.9%) rheumatologists avoided starting a new biologic. Face-to-face clinics with the use of some personal protective equipment continued to be held in only 293 (52.9%) rheumatologists' practices. Teleconsultation modalities found usage as follows: telephone in 335 (60.5%), WhatsApp in 241 (43.5%), emails in 90 (16.3%) and video calls in 53 (9.6%). Physical examinations were mostly reduced in 295 (53.3%) or done with personal protective equipment in 128 (23.1%) practices. Only 316 (57.0%) reported that the national rheumatology society in their country had produced any recommendation around COVID-19 while only 73 (13.2%) confirmed the availability of a national rheumatology COVID-19 registry in their country. CONCLUSION: COVID-19 has shifted daily rheumatology practices across Africa to more virtual consultations and regional disparities are more apparent in the availability of local protocols and registries.

Racial differences in systemic sclerosis disease presentation: a European Scleroderma Trials and Research group study.

OBJECTIVES: Racial factors play a significant role in SSc. We evaluated differences in SSc presentations between white patients (WP), Asian patients (AP) and black patients (BP) and analysed the effects of geographical locations. METHODS: SSc characteristics of patients from the EUSTAR cohort were cross-sectionally compared across racial groups using survival and multiple logistic regression analyses. RESULTS: The study included 9162 WP, 341 AP and 181 BP. AP developed the first non-RP feature faster than WP but slower than BP. AP were less frequently anti-centromere (ACA; odds ratio (OR) = 0.4, P < 0.001) and more frequently anti-topoisomerase-I autoantibodies (ATA) positive (OR = 1.2, P = 0.068), while BP were less likely to be ACA and ATA positive than were WP [OR(ACA) = 0.3, P < 0.001; OR(ATA) = 0.5, P = 0.020]. AP had less often (OR = 0.7, P = 0.06) and BP more often (OR = 2.7, P < 0.001) diffuse skin involvement than had WP. AP and BP were more likely to have pulmonary hypertension [OR(AP) = 2.6, P < 0.001; OR(BP) = 2.7, P = 0.03 vs WP] and a reduced forced vital capacity [OR(AP) = 2.5, P < 0.001; OR(BP) = 2.4, P < 0.004] than were WP. AP more often had an impaired diffusing capacity of the lung than had BP and WP [OR(AP vs BP) = 1.9, P = 0.038; OR(AP vs WP) = 2.4, P < 0.001]. After RP onset, AP and BP had a higher hazard to die than had WP [hazard ratio (HR) (AP) = 1.6, P = 0.011; HR(BP) = 2.1, P < 0.001]. CONCLUSION: Compared with WP, and mostly independent of geographical location, AP have a faster and earlier disease onset with high prevalences of ATA, pulmonary hypertension and forced vital capacity impairment and higher mortality. BP had the fastest disease onset, a high prevalence of diffuse skin involvement and nominally the highest mortality.