Riaz Y. Seedat

Mite and cockroach sensitisation in patients with allergic rhinitis in the Free State

BACKGROUND Studies in patients with allergic rhinitis living in the Free State have showed grass pollens to be the predominant allergens, with house-dust mite sensitisation being less prevalent than in the coastal areas and a low rate of sensitisation to the storage mite Lepidoglyphus destructor. No studies have been conducted on sensitisation to the other storage mites, spider mites or cockroaches. We aimed to determine the prevalence of sensitisation to various house-dust mites, storage mites, spider mites and cockroaches in patients with allergic rhinitis living in the Free State. METHODS Fifty consecutive patients with allergic rhinitis attending the ear, nose and throat clinic at Universitas Hospital underwent skin-prick testing and/or ImmunoCAP RAST testing for common aero-allergens, house-dust mites, storage mites, spider mites and cockroaches. RESULTS Forty-six per cent of patients were sensitised to one of the house-dust mites, with house mite sensitisation being significantly more common in patients who had previously lived at the coast. Storage mites were not common aero-allergens, while 46% of patients were sensitised to the spider mite Tetranychus urticae. Blatella germanica was the cockroach species to which patients were most commonly found to be sensitised on ImmunoCAP RAST testing, with 38% of patients being sensitised to this aero-allergen. CONCLUSIONS House-dust mites, T. urticae and the cockroach B. germanica appear to be important aero-allergens in the Free State. Storage mite sensitisation is not common.

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

ABSTRACT 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.

Novel HPV-6 variants of human papillomavirus causing recurrent respiratory papillomatosis in southern Africa.

There is currently no information regarding the genetic diversity of HPV-6 variants circulating in South Africa. The aim of this study was to determine the HPV-6 variants affecting patients with recurrent respiratory papillomatosis, to determine whether mutations correlate with disease severity and identify molecular determinants of virulence with prognostic relevance. HPV-6 variants were identified based on genome changes within the 712-991 bp region encompassing the non-coding region (URR) of the genome, with variations in length resulting from insertions and duplications, and the 453-bp gene encoding the E6 protein. Based on manual comparison of sequence data from the URR, the isolates were identified as HPV-6a and HPV-6vc variants. Three novel HPV-6 variants were identified: one based on a mutation in the E6 region; two based on changes in the URR including a unique substitution detected in three isolates and an insertion and 170-bp duplication in the URR genome in one patient, who had clinical features of severe disease.

HPV types causing juvenile recurrent laryngeal papillomatosis in South Africa

OBJECTIVES To identify human papillomavirus (HPV) types associated with juvenile onset recurrent laryngeal papillomatosis (RLP) in southern Africa, to determine if there is a correlation between HPV type and disease aggressiveness and to determine the diagnostic and prognostic value of rapid molecular techniques for detection and typing of HPV using laryngeal biopsies. METHODS Laryngeal biopsies from patients undergoing surgery for RLP were screened for HPV using conventional and real-time PCR techniques. Amplicons were sequenced to determine the HPV type involved. Clinical features were correlated with HPV type. RESULTS HPV was identified in papillomata from 18 out of 19 patients. Only HPV-6 and HPV-11 were identified, with no co-infections. There was 100% concordance between conventional and real-time PCR techniques. Patients with HPV-11 disease required more procedures and tended to have higher Derkay scores than those with HPV-6 disease. The HPV types identified in our patients were genetically similar to HPV types from geographically distinct regions. CONCLUSIONS RLP in our patient population appears to be exclusively due to HPV-6 or HPV-11. HPV-11 disease appears to be more aggressive than HPV-6 disease. Identification of the HPV types provides motivation for inclusion of vaccines against these types in vaccination programs to protect women against infection and subsequently reduce the incidence of RLP.

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.

The incidence and prevalence of juvenile-onset recurrent respiratory papillomatosis in the Free State province of South Africa and Lesotho

BACKGROUND AND OBJECTIVE Although the estimated incidence and prevalence of juvenile-onset recurrent respiratory papillomatosis (JORRP) has been determined in countries in North America and Europe and in Australia, no studies have attempted to determine the incidence or prevalence of JORRP in African countries. The aim of this study is to determine the incidence and prevalence of JORRP in the Free State province of South Africa and Lesotho. METHODS This was a retrospective study in which the records of all patients with JORRP from the Free State province of South Africa or Lesotho treated at Universitas Academic Hospital or by otorhinolaryngologists in private practice between 1 January 2011 and 31 December 2013 were reviewed. RESULTS The estimated incidence and prevalence of JORRP in the Free State were 1.34 and 3.88 per 100,000 population respectively while the estimated incidence and prevalence in Lesotho were 0.49 and 1.04 per 100,000 population respectively. However, these figures are probably an underestimation. CONCLUSION The incidence and prevalence calculated for the Free State were generally higher than those found in other studies, while those calculated for Lesotho was similar to those obtained in other studies.

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.

Laryngeal carcinoma - patient profile and delay in referral

Aim: The aim of this study was to compile a profile of patients with laryngeal carcinoma presenting to the ENT clinic at Universitas Hospital, Bloemfontein. Methods: Fifty consecutive patients with laryngeal carcinoma were prospectively interviewed and information regarding their symptoms, social habits and delay in referral was recorded. Staging was performed in the operating theatre. Results: Hoarseness was the most common symptom (98%). Sixty-four percent of patients presented with airway obstruction and 26% had a visible neck mass. The median patient delay was 1.5 months, while the median professional delay was 5 months. The median total delay was 7 months. Glottic and supraglottic tumours were the most common at 36% and 34% respectively. Eighty percent of patients were either stage 3 or 4, while only 20% were classified as early cancers (stage 1 and 2). Conclusion: In this study the majority of patients presented with advanced tumours. Both patients and medical professionals did not seem to realize the significance of unrelenting hoarseness as a possible symptom of laryngeal cancer. We propose the initiation of an awareness campaign to address this problem.

Determination of the complete genome and functional analysis of HPV6 isolate VBD19/10 from a patient with aggressive recurrent respiratory papillomatosis.

Human papillomavirus (HPV) types 6 and 11 are the aetiological agent of recurrent respiratory papillomatosis (RRP). The complete genome of an HPV6 isolate with a 170 base pair (bp) duplication identified within the long control region (LCR) from a patient with aggressive recurrent respiratory papillomatosis was determined. The promoter sequence from the HPV LCR including the 170 bp duplication was placed upstream of a heterologous reporter gene and the activity of the reporter gene product determined using transfected cells. In total, mutations were observed at 157 nucleotide positions of the complete genome and included nucleotide substitutions, deletions and insertions, resulting in amino acid changes at 43 residue positions. Reporter gene activity using an HPV-derived LCR region with a 170 bp duplication was significantly higher than that using an HPV-derived LCR region with no duplication within this region. The results suggest that novel HPV variants warrant further investigation for potential biomarkers of aggressive disease.

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.