Understanding HIV-1 subtype distribution and epidemiology can assist preventive measures and clinical decisions. Sequence variation may affect antiviral drug resistance development, disease progression, evolutionary rates and transmission routes.

Molecular tests for detection of human papillomaviruses (HPVs) play a crucial role in the prevention of cervical cancer, including recently announced elimination efforts. HPV testing is a recommended approach for cervical cancer screening of women over 30 and for management of those with precancerous cervical lesions. In addition, they are widely used in epidemiological studies, HPV surveillance and vaccination impact monitoring. The aim was to provide an updated 2020 inventory of commercial molecular HPV tests available on the market. Data were retrieved from internal files, and a detailed search using Medline/Pubmed, Web of Science, Scopus, Google Scholar, Google and Bing, without language or period restrictions, was performed in September 2019 and again in January 2020. We identified 254 distinct commercial HPV tests and at least 425 test variants available on the global market in 2020, which represents a 31% and 235% increase in the number of distinct tests and variants, respectively, compared with the previous inventory performed in 2015. Although the proportion of commercially available HPV tests with at least one peer-reviewed publication has increased over the past decade, 60% of the HPV tests on the global market are still without a single peer-reviewed publication. Furthermore, 82% of tests lack any published analytical and/or clinical evaluation, and over 90% are not evaluated in line with consensus requirements that ensure safe use in clinical settings. Significant challenges and scope for improvement still exist for both the HPV scientific community and the manufacturers of HPV tests. The latter must put more effort into validating their products, in agreement with standardized procedures, including all steps of HPV testing and various clinical specimens. High throughput capacity and point-of-care HPV tests are needed, both with affordable prices.

Laboratories are currently witnessing extraordinary demand globally for sampling devices, reagents, consumables, and diagnostic instruments needed for timely diagnosis of SARS-CoV-2 infection. To meet diagnostic needs as the pandemic grows, the US Food and Drug Administration (FDA) recently granted several commercial SARS-CoV-2 tests Emergency Use Authorization (EUA), but manufacturer-independent evaluation data are scarce. We performed the first manufacturer-independent evaluation of the fully automated sample-to-result two-target test cobas 6800 SARS-CoV-2 (cobas) (Roche Molecular Systems, Branchburg, NJ), which received US FDA EUA on March 12, 2020. The comparator was a standardized 3-hour SARS-CoV-2 protocol, consisting of RNA extraction using an automated portable instrument, followed by a two-target RT-PCR, which our laboratory has routinely used since January 2020 (Corman VM et al. EuroSurveill 25 (3):2000045). Cobas and the comparator showed overall agreement of 98.1% and a kappa value of 0.95 on an in-house validation panel consisting of 217 well-characterized retrospective samples. Immediate prospective head-to-head comparative evaluation followed on 502 samples, and the diagnostic approaches showed overall percent agreement of 99.6% and a kappa value of 0.98. A good correlation (r² = 0.96) between cycle threshold values for SARS-CoV-2 specific targets obtained by cobas and the comparator was observed. Our results showed that cobas is a reliable assay for qualitative detection of SARS-CoV-2 in nasopharyngeal swab samples collected in the UTM-RT system. Under the extraordinary circumstances that laboratories are facing worldwide, a safe diagnostic platform switch is feasible in only 48 hours and in the midst of the COVID-19 pandemic if carefully planned and executed.

Systematic reviews have concluded that hrHPV DNA testing using target-amplification tests is as accurate on vaginal self-samples as on clinician-taken specimens for the detection of cervical precancer. However, insufficient evidence is available for specific HPV assay/self-sample device combinations. The VALHUDES protocol is designed as a diagnostic test accuracy study that aims to compare the clinical sensitivity and specificity of particular hrHPV assay(s) on vaginal self-samples and first-void-urine, collected in agreement with standardized protocols, with hrHPV testing on matched clinician-taken samples. Five hundred enrolled women referred to a colposcopy clinic are invited to collect a first-void urine sample and one or more vaginal self-samples with particular devices before collection of a cervical sample by a clinician. Sample sets are subsequently analysed in a laboratory accredited for HPV testing. Disease verification for all enrolled patients is provided by colposcopy combined with histological assessment of biopsies. A first VALHUDES study has started in Belgium in December 2017 with enrolment from four colposcopy centres. The following assays are foreseen to be evaluated: RealTime High Risk HPV assay (Abbott), cobas-4800 and -6800 (Roche), Onclarity (BD), Xpert HPV (Cepheid) and Anyplex II HPV HR (Seegene). Given empirical evidence that the relative accuracy of HPV-testing on self- vs clinician-samples is robust across clinical settings, the VALHUDES protocol offers a framework for validation of HPV assay/self-sample device combinations that can be translated to a primary screening setting.