The South African Pollen Monitoring Network: Insights from 2 years of national aerospora sampling (2019-2021).

BACKGROUND: Pollen monitoring has been discontinuously undertaken in South Africa, a country with high biodiversity, a seasonal rainfall gradient, and nine biomes from arid to subtropical. The South African Pollen Monitoring Network was set up in 2019 to conduct the first long-term national aerospora monitoring across multiple biomes, providing weekly reports to allergy sufferers and healthcare providers. METHODS: Daily airborne pollen concentrations were measured from August 2019 to August 2021 in seven cities across South Africa. Updated pollen calendars were created for the major pollen types (>3%), the average Annual Pollen Index over 12 months was calculated, and the results were compared to available historical data. RESULTS: The main pollen types were from exotic vegetation. The most abundant taxa were Poaceae, Cupressaceae, Moraceae and Buddleja. The pollen season start, peak and end varied widely according to the biome and suite of pollen taxa. The main tree season started in the last week of August, peaked in September and ended in early December. Grass seasons followed rainfall patterns: September-January and January-April for summer and winter rainfall areas, respectively. Major urban centres, for example, Johannesburg and Pretoria in the same biome with similar rainfall, showed substantive differences in pollen taxa and abundance. Some major differences in pollen spectra were detected compared with historical data. However, we are cognisant that we are describing only 2 years of data that may be skewed by short-term weather patterns. CONCLUSIONS: Differences in pollen spectra and concentrations were noted across biomes and between geographically close urban centres. Comparison with historical data suggests pollen spectra and seasons may be changing due to anthropogenic climate change and landscaping. These data stress the importance of regional and continuous pollen monitoring for informed care of pollinosis.

Adult-onset Recurrent Respiratory Papillomatosis at a South African Referral Hospital.

Objective: The aim of this study was to describe the clinical presentation and outcome of patients with adult-onset recurrent respiratory papillomatosis (AoRRP) in a developing country with the challenges of poor health care access and high prevalence of HIV infection. Materials and methods: This was a retrospective study of patients diagnosed with AoRRP who were managed in the Department of Otorhinolaryngology at Universitas Academic Hospital in Bloemfontein, South Africa over a 10 year period. Results: There were a total of 41 patients, of which 26 (63.4%) were male. The age at diagnosis ranged between 16.4 and 67.4 years (mean 39.4 ± 14.9 years). All patients presented with a hoarse voice, with three patients also having upper airway obstruction. Eight (19.5%) patients were HIV positive. HPV typing was performed in 29 patients; 14 had HPV11 disease, 12 had HPV6 disease and in 3 patients HPV DNA was not detected. There was no significant difference in initial presentation or outcome between HIV negative and HIV positive patients, or between patients with HPV6 and HPV11 disease. Two patients had malignant transformation of the papillomas. In both these patients, HPV was not detected in the papillomas. Conclusions: HPV type and HIV infection did not appear to influence the clinical presentation and outcome in patients with AoRRP. There is a risk of malignant transformation in patients in which HPV is not detected in the papillomas.

Whole-Genome Sequence and Comparative Analysis of Human Papillomavirus Type 18 Isolated from a Nasopharyngeal Carcinoma from South Africa.

We report the complete genome sequence of human papillomavirus type 18 isolated from a nasopharyngeal carcinoma in South Africa.

Complete genome sequence of a HPV31 isolate from laryngeal squamous cell carcinoma and biological consequences for p97 promoter activity.

Human papillomavirus type 31, although detected less frequently than HPV types 16 and 18, is associated with head and neck squamous cell carcinomas. Previous studies suggest that polymorphisms in the long control region (LCR) may alter the oncogenic potential of the virus. This study reports the first complete genome of a South African HPV31 isolate from a laryngeal squamous cell carcinoma. Sequence variations relative to the HPV31 prototype sequence were identified. The pBlue-Topo® vector, a reporter gene system was used to investigate the possible influence of these variations on the LCR promoter activity in vitro. Using mutagenesis to create two different fragments, ß-galactosidase assays were used to monitor the effect of nucleotide variations on the p97 promoter. Increased ß-galactosidase expression was observed in mutants when compared to the South African HPV31 LCR isolate. Enhanced transcriptional activity was observed with the mutant that possessed a single nucleotide change within the YY1 transcription factor binding site. In conclusion, sequence variation within the LCR of HPV31 isolates may have a functional effect on viral p97 promoter activity.

Pioneering virtual otolaryngology specialist examinations in South Africa in the COVID-19 and post-COVID-19 era.

PURPOSE OF REVIEW: South Africa, and the African continent, have a shortage of ear, nose and throat (ENT) specialists. The coronavirus disease 2019 (COVID-19) pandemic not only had an adverse impact on specialist training, but also impacted the ability of trainees to undertake the final examinations in order to qualify as ENT specialists. RECENT FINDINGS: The response to the COVID-19 pandemic resulted in the postponement of the final examination of the Fellowship of the College of Otorhinolaryngologists of South Africa (FCORL (SA)). A virtual clinical examination was held via videoconferencing to assess clinical judgement, insight, reasoning and decision making. SUMMARY: The virtual clinical assessment allowed trainees to undertake the final examination despite the COVID-19 pandemic, ensuring that they could be added to the limited number of specialists in South Africa and the African continent.

The clinical and genetic features of hereditary haemorrhagic telangiectasia (HHT) in central South Africa-three novel pathogenic variants.

Hereditary haemorrhagic telangiectasia (HHT) is supposedly rare in Africa, with only three pathogenic variants documented to date. We describe the clinical and genetic features of HHT patients in central South Africa, who fulfilled the Curaçao criteria. Sixteen patients (median age 38.5 years, range 12-65 years), from six families were included. Fifteen patients were of African descent and one was of Afrikaner descent. The mean epistaxis severity score was 3.18, and the median haemoglobin was 9.5 g/dL (range 3.5-13.5 g/dL). On transthoracic contrast echocardiography 69% had a shunt grade ≥ 1, but only 20% had pulmonary arteriovenous malformations (AVMs) on computed tomography of the chest. Hepatic AVMs were found in 13% of patients, while 13% had brain vascular malformations. Four patients were HIV positive, of whom two had worsening epistaxis while they had opportunistic infections and poor HIV control. We identified six pathogenic variants (four in ENG and two in ACVRL1) in the six probands, three of which had been described previously. Three variants have apparently not been reported previously: ENG c.[1336_1337dup];[ =] p.[(Asp446fs)];[( =)], ENG c.[ 690?_816+?del] p.[(?)], and ACVRL1 c.[268_274delins57];[ =] p.[(Cys90fs)];[( =)]. We confirmed the diagnosis of HHT in sixteen patients and identified pathogenic variants in ENG or ACVRL1 in all six probands in central South Africa, where HHT has been underreported. We describe three pathogenic variants: two of ENG and one of ACVRL1. We will be able to implement pre-symptomatic screening of patients in our area, and improve their management.

Diagnosis of laryngeal tuberculosis in a high TB burden area.

PURPOSE: The larynx is the second most commonly affected site in the head and neck region in patients with extrapulmonary tuberculosis (TB). Despite this, the prevalence of laryngeal TB is largely unknown, particularly in areas with a high TB burden. The laboratory diagnosis of TB includes microscopy, culture and molecular testing. The aims of this study were to determine the prevalence of laryngeal TB in patients presenting with laryngeal pathology in a region with a high TB burden and to determine the optimal diagnostic methods for the diagnosis of laryngeal TB. METHODS: This was a prospective descriptive study of 80 adult patients undergoing direct laryngoscopy and biopsy for laryngeal pathology in the Department of Otorhinolaryngology, Universitas Academic Hospital, Bloemfontein, South Africa over a 1 year period. Histopathological and microbiological investigations (microscopy, Xpert MTB/RIF, and TB culture) were performed on all laryngeal biopsies. RESULTS: Five (6.25%) out of 80 patients were diagnosed with laryngeal TB. In one patient, the Xpert MTB/RIF assay was positive on the laryngeal tissue and histology showed granulomas. Two patients had granulomas on histology although the microbiological tests on the tissue were negative. Two patients had only positive tissue cultures for Mycobacterium tuberculosis. None of the biopsies had positive Ziehl-Neelsen stains. CONCLUSION: The results suggest that the diagnosis of laryngeal TB required a combination of histopathology, culture and PCR and that the Xpert MTB/RIF assay is not a sensitive test for the diagnosis of laryngeal TB.

Human papillomavirus DNA in head and neck squamous cell carcinomas in the Free State, South Africa.

Human papillomaviruses (HPVs) have been associated with a subset of head and neck squamous cell carcinomas (HNSCCs). The aim of this study was to determine the prevalence of HPV DNA in archived formalin-fixed paraffin-embedded tissue from patients with histologically confirmed HNSCCs in a South African cohort. A nested PCR was used for the detection of HPV DNA targeting the L1 gene. Positive samples were confirmed using an in-house hemi-nested PCR targeting the E6 gene and genotyped by sequence determination of amplicons. HPV DNA was detected in 57/780 (7.3%) samples, with the highest prevalence being in the sinonasal tract (16.0%) and oropharynx (10.8%). HPV16 was the most frequently detected type, being found in 26/57 (45.6%) positive samples. The prevalence of HPV DNA in HNSCCs found in this study was lower than that found in developed countries.

Age at diagnosis, but not HPV type, is strongly associated with clinical course in recurrent respiratory papillomatosis.

BACKGROUND: Recurrent Respiratory Papillomatosis (RRP) is a rare disease characterized by the growth of papillomas in the airway and especially the larynx. The clinical course is highly variable among individuals and there is poor understanding of the factors that drive an aggressive vs an indolent course. METHODS: A convenience cohort of 339 affected subjects with papillomas positive for only HPV6 or HPV11 and clinical course data available for 1 year or more, from a large multicenter international study were included. Exploratory data analysis was conducted followed by inferential analyses with frequentist and Bayesian statistics. RESULTS: We examined 339 subjects: 82% were diagnosed prior to the age of 18 years, 65% were infected with HPV6, and 69% had an aggressive clinical course. When comparing age at diagnosis with clinical course, the probability of aggressiveness is high for children under five years of age then drops rapidly. For patients diagnosed after the age of 10 years, an indolent course is more common. After accounting for confounding between HPV11 and young age, HPV type was minimally associated with aggressiveness. Fast and Frugal Trees (FFTs) were utilized to determine which algorithms yield the highest accuracy to classify patients as having an indolent or aggressive clinical course and consistently created a branch for diagnostic age at ~5 years old. There was no reliable strong association between clinical course and socioeconomic or parental factors. CONCLUSION: In the largest cohort of its type, we have identified a critical age at diagnosis which demarcates a more aggressive from less aggressive clinical course.

Human papillomavirus in head and neck squamous cell carcinomas in a South African cohort.

BACKGROUND: Most tumours of the head and neck are attributable to smoking and alcohol use, but an increasing proportion of head and neck tumours are caused by human papillomaviruses (HPVs). The aim of this study was to use in house molecular assays to detect and genotype HPV in biopsies from patients with histologically confirmed head and neck squamous cell carcinomas. In addition, the results were compared with p16 immunohistochemistry staining, which has been described as a potential marker for HPV infection. METHODS: Biopsies of squamous cell carcinomas of the oropharynx, nasopharynx, larynx and hypopharynx from 112 South African patients were screened using three PCR assays targeting the L1 and E6 regions of HPV and p16 immunohistochemical staining. RESULTS AND CONCLUSION: HPV was identified in 7 (6.3%) tumours, while 22 (19.6%) had positive p16 immunohistochemical staining. There was concordance between the results obtained using the three PCR assays. There was substantial agreement between the results of molecular tests and p16 immunohistochemistry for hypopharyngeal carcinomas, but only fair agreement for laryngeal and oropharyngeal carcinomas.

Lower Lateral Cartilages: An Anatomic and Morphological Study in Noses of Black Southern Africans.

Background: The anatomy of the nose of different ethnic groups has been widely researched in order to facilitate a better understanding of the individual nose as a foundation for improving surgical outcomes. The only anatomical research of the lower lateral cartilages (LLCs) available to the surgeon working with an African patient is to extrapolate data from studies already published on African Americans. Objectives: The aim of this descriptive cadaveric study was to assess the normal anatomy of the LLCs in noses of Black South Africans and compare this to data from studies on noses from Caucasian, Asian, Korean, and African-American populations. Methods: Ninety lower lateral cartilages of 45 cadavers of Black South Africans who did not have previous surgery or trauma to the nose were dissected. The morphological shapes and 12 standard anatomical measurements were recorded. The results were analyzed and compared to data in the literature from studies on lower lateral cartilages of Caucasian, Asian, Korean, and African-American populations. Results: A statistically significant difference was found in terms of overall cartilage dimensions, distance from nasal rim, and morphological shapes, compared to all previously studied groups, including the African-American population. There were significant differences in cartilage dimensions between males and females. This translates to clinically significant data that is useful during reconstructive and aesthetic nasal surgery on patients with a Southern African background. Conclusions: This study sets norms for alar cartilages in Black Southern Africans.

Global Genomic Diversity of Human Papillomavirus 11 Based on 433 Isolates and 78 Complete Genome Sequences.

UNLABELLED: Human papillomavirus 11 (HPV11) is an etiological agent of anogenital warts and laryngeal papillomas and is included in the 4-valent and 9-valent prophylactic HPV vaccines. We established the largest collection of globally circulating HPV11 isolates to date and examined the genomic diversity of 433 isolates and 78 complete genomes (CGs) from six continents. The genomic variation within the 2,800-bp E5a-E5b-L1-upstream regulatory region was initially studied in 181/207 (87.4%) HPV11 isolates collected for this study. Of these, the CGs of 30 HPV11 variants containing unique single nucleotide polymorphisms (SNPs), indels (insertions or deletions), or amino acid changes were fully sequenced. A maximum likelihood tree based on the global alignment of 78 HPV11 CGs (30 CGs from our study and 48 CGs from GenBank) revealed two HPV11 lineages (lineages A and B) and four sublineages (sublineages A1, A2, A3, and A4). HPV11 (sub)lineage-specific SNPs within the CG were identified, as well as the 208-bp representative region for CG-based phylogenetic clustering within the partial E2 open reading frame and noncoding region 2. Globally, sublineage A2 was the most prevalent, followed by sublineages A1, A3, and A4 and lineage B. IMPORTANCE: This collaborative international study defined the global heterogeneity of HPV11 and established the largest collection of globally circulating HPV11 genomic variants to date. Thirty novel complete HPV11 genomes were determined and submitted to the available sequence repositories. Global phylogenetic analysis revealed two HPV11 variant lineages and four sublineages. The HPV11 (sub)lineage-specific SNPs and the representative region identified within the partial genomic region E2/noncoding region 2 (NCR2) will enable the simpler identification and comparison of HPV11 variants worldwide. This study provides an important knowledge base for HPV11 for future studies in HPV epidemiology, evolution, pathogenicity, prevention, and molecular assay development.

Global genomic diversity of human papillomavirus 6 based on 724 isolates and 190 complete genome sequences.

UNLABELLED: Human papillomavirus type 6 (HPV6) is the major etiological agent of anogenital warts and laryngeal papillomas and has been included in both the quadrivalent and nonavalent prophylactic HPV vaccines. This study investigated the global genomic diversity of HPV6, using 724 isolates and 190 complete genomes from six continents, and the association of HPV6 genomic variants with geographical location, anatomical site of infection/disease, and gender. Initially, a 2,800-bp E5a-E5b-L1-LCR fragment was sequenced from 492/530 (92.8%) HPV6-positive samples collected for this study. Among them, 130 exhibited at least one single nucleotide polymorphism (SNP), indel, or amino acid change in the E5a-E5b-L1-LCR fragment and were sequenced in full. A global alignment and maximum likelihood tree of 190 complete HPV6 genomes (130 fully sequenced in this study and 60 obtained from sequence repositories) revealed two variant lineages, A and B, and five B sublineages: B1, B2, B3, B4, and B5. HPV6 (sub)lineage-specific SNPs and a 960-bp representative region for whole-genome-based phylogenetic clustering within the L2 open reading frame were identified. Multivariate logistic regression analysis revealed that lineage B predominated globally. Sublineage B3 was more common in Africa and North and South America, and lineage A was more common in Asia. Sublineages B1 and B3 were associated with anogenital infections, indicating a potential lesion-specific predilection of some HPV6 sublineages. Females had higher odds for infection with sublineage B3 than males. In conclusion, a global HPV6 phylogenetic analysis revealed the existence of two variant lineages and five sublineages, showing some degree of ethnogeographic, gender, and/or disease predilection in their distribution. IMPORTANCE: This study established the largest database of globally circulating HPV6 genomic variants and contributed a total of 130 new, complete HPV6 genome sequences to available sequence repositories. Two HPV6 variant lineages and five sublineages were identified and showed some degree of association with geographical location, anatomical site of infection/disease, and/or gender. We additionally identified several HPV6 lineage- and sublineage-specific SNPs to facilitate the identification of HPV6 variants and determined a representative region within the L2 gene that is suitable for HPV6 whole-genome-based phylogenetic analysis. This study complements and significantly expands the current knowledge of HPV6 genetic diversity and forms a comprehensive basis for future epidemiological, evolutionary, functional, pathogenicity, vaccination, and molecular assay development studies.

Co-morbidities in children presenting with chronic suppurative otitis media--a South African study.

BACKGROUND: Chronic suppurative otitis media (CSOM) is common among children in southern Africa. Managing associated co-morbidities may result in earlier disease resolution. METHODS: Children <13 years of age with otorrhoea lasting >4 weeks were recruited to the study. Each child underwent a full clinical examination, a blood count, an HIV test and CD4 cell count, if found to be infected. RESULTS: The study included 86 children, and the median age was 4.6 years. HIV infection was present in 45 of 83 children (54.2%), of which 23 (51.1%) were receiving antiretroviral treatment at the time of presentation. Underweight was present in 22 of 85 (25.9%) children and in 17 of the 45 (37.8%) HIV-infected children. One or more clinical signs (not aural-related) were found in 46 of 86 (53.4%) children. Cholesteatoma was found in 23 of 113 (20.4%) ears, and 9 of 86 (10.5%) children had serious associated aural or intracranial complications. CONCLUSIONS: A high percentage of children with CSOM have associated pathology that needs to be diagnosed to optimally manage CSOM.

FRET-based detection and genotyping of HPV-6 and HPV-11 causing recurrent respiratory papillomatosis.

Recurrent respiratory papillomatosis (RRP) is a potentially life-threatening disease caused by human papillomavirus (HPV), usually HPV types 6 and 11. The conventional method used for detection and typing the RRP isolates in our laboratory is the polymerase chain reaction (PCR) and DNA sequencing method. A real-time PCR assay based on fluorescence resonance energy transfer (FRET) probe technology was developed for the detection and rapid genotyping of HPV-6 and-11 isolates from biopsy material. The primers and probes were designed using multiple alignments of HPV-6 and HPV-11 partial E6 and E7 sequences that included prototypic and non-prototypic variants. Real-time PCR followed by probe-specific melting-curve analysis allowed differentiation of HPV-6 and HPV-11. HPV-6 and HPV-11 amplicons were used to determine detection limits and inter- and intra-assay variability. The detection limit of the assay was 12.8 DNA copies for HPV-6 and 22.5 DNA copies for HPV-11. A total of 60 isolates were genotyped using the FRET real-time PCR assay and a 100% concordance was obtained when results were compared with genotyping based on conventional DNA sequencing. The real-time PCR assay based on FRET technology was able to detect and rapidly genotype HPV from tissue biopsy obtained from patients with RRP. The assay reduces the time required for genotyping from three working days to less than a day.

Low dose radiotherapy for adenotonsillar lymphoid hyperplasia in HIV-positive patients.

Lymphoid hyperplasia is common in HIV positive patients. The aim of this study was to determine the response to radiotherapy. Thirty-three adult patients with recurrent tonsillitis or upper airway obstruction due to tonsillar hyperplasia and conformed histology of follicular hyperplasia were included. Thirteen underwent a 24 Gy course of radiotherapy and were followed up for a minimum of 16 weeks post-radiotherapy. There was a statistically significant decrease in the median tonsillar size (95% confidence interval [-3;-2]) and in the median CD4 count (95% CI [3;152]) after 16 weeks. None of the patients had acute tonsillitis or airway obstruction after radiotherapy. Low dose radiotherapy is effective in the management of adenotonsillar hyperplasia in HIV positive patients.