Countries globally are affected by the COVID-19 pandemic, with nearly two million cases and 120 000 deaths occurring within 4 months of the discovery of the severe acute respiratory syndrome coronavirus-2 in December 2019 in China. Accurate diagnoses of cases is key in managing the pandemic by identification, isolation and treatment of patients and defining the epidemiology of the virus. By mid-January 2020, a scientist from China published the full genome of the virus, which facilitated the development of accurate molecular diagnostic assays. By the end of January 2020, the WHO, in collaboration with laboratories in Asia, Europe and the USA, published several real-time reverse transcriptase PCR (rtRT-PCR) protocols that allowed identification of cases and development of commercial assays. Clinical investigations facilitated development of accurate case definition and guidance for laboratories on the optimum specimens and procedures for diagnoses. Currently, laboratory-based rtRT-PCR is the recommended test for diagnoses of acute cases to ensure patients can be identified and isolated and to facilitate the public health response. However, due to delays in diagnoses, severe shortage of tests and laboratory capacity, point-of-care molecular or antigen tests are becoming more attractive. Although serological tests are not suitable for diagnoses of acute cases, they are important to define epidemiological questions, including attack rate in the population, and to identify immune individuals. This review aimed to summarise the current available information for diagnoses of cases and to aid laboratories and healthcare workers to select the best assays and procedures.

Background. Women accessing the public health system in Gauteng province, South Africa are largely unscreened for cervical cancer and have a high background prevalence of human immunodeficiency virus (HIV) infection. Objectives. This cross-sectional study describes the age-specific prevalence of human papillomavirus (HPV) infection and cytological abnormalities among this urban and peri-urban population. Method. Over the period March 2009 -September 2011, 1 524 women attending public sector primary healthcare clinics were invited to participate in a cervical cancer screening study. All participants were screened with conventional cytology and HPV testing undertaken using the HPV linear array genotyping kit (Roche Molecular Systems). Results. Of 1 472 women with valid cytology results, abnormalities were detected in 17.3% (n=255), of which 9.1% (n=134) were high-grade squamous intraepithelial lesions, and 0.5% (n=8) suggestive of squamous carcinoma. Of the 1 445 women with complete data, the overall and high-risk HPV DNA prevalences were 74.6% (n=1 078) and 54.3% (n=784), respectively. HPV type 16 and/or 18 were detected in 19.5% (n=282) of women. Age-specific prevalence of HPV showed a plateau-shaped curve. Conclusions. The prevalences of HPV infection and abnormal cytology were much higher than previously reported in general populations in South Africa and elsewhere. Higher age-specific prevalence and similar plateau-like age-specific epidemiological curves have previously only been described in studies among HIV-positive women. These findings have implications for planning and development of cervical screening programmes in developing countries with largely unscreened populations with a high background prevalence of HIV. Specimen collection and testingAll participants were screened with conventional cytology (Pap smear) as per national protocol. Cytopathology reports were based on the Bethesda system. [13] Specimens for HPV genotyping were either healthcare worker-collected dry cervical swabs (N=951) or patientcollected tampon specimens (N=573). Tampons were placed in a phosphate buffered saline and 10% methanol solution directly after collection. DNA extraction was performed in batches on washed cell pellets of the tampon specimens or directly on the dry swab specimens using the DNA Isolation Kit (Roche Molecular Systems, Branchburg, NJ) on the MagNA Pure automated extraction system. HPV genotyping was done using the HPV linear array (LA) genotyping kit (Roche Molecular Systems, Branchburg, NJ). The pool of primers is designed to amplify HPV DNA from 15 high-risk genotypes (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68, 73 and 82), 3 probable high-risk genotypes (26, 53 and 66) and 19 low/undetermined-risk types (6,11, 40, 42, 54, 55, 61, 62, 64, 67, 69, 70, 71, 72, 81, 83, 84, IS39 and CP6108). The β-globin gene was amplified concurrently to assess cellular adequacy, extraction and amplification for each individually processed specimen. Strict procedures were followed to avoid contamination, with ne...

Background. Human papillomavirus (HPV) infection is well known to be associated with head and neck cancers (HNCs). HPV-associated HNCs are related to sexual behaviour, particularly the lifetime number of oral sex partners, but the epidemiology of oral and oropharyngeal HPV in South African men has not yet been studied. Objectives. To determine the oral and oropharyngeal HPV strain prevalence and associated factors in a selected male population in Pretoria, South Africa (SA). Methods. Male factory workers were recruited. Oral rinse and gargle samples were tested for 37 HPV types using the Linear Array HPV Genotyping Test (Roche Molecular Systems). A questionnaire was used to obtain information regarding age, medical conditions, substance and alcohol use and sexual behaviour. HIV testing was optional. Results. The HPV prevalence was 5.6% among men (N=125) aged 17 -64 years. High-risk HPV (hrHPV) types 16 and 68 were found in two men. Oral sex seemed to be an uncommon practice in the majority of respondents, but the two respondents with hrHPV did practise oral sex. There was a statistically significant association between HPV infection and an increased number of sexual partners (p=0.027), but not between HPV and substance use, HIV status or clinical mucosal pathology. Conclusion. The prevalence of oral and oropharyngeal HPV was lower than reported in other countries. An association between oral HPV and having multiple sexual partners was found. A larger nationwide study would give a more representative view of the burden of oral and oropharyngeal HPV infection in SA.