Distribution of human papillomavirus genotypes in women with high-grade cervical intraepithelial lesions and cervical carcinoma and analysis of human papillomavirus-16 genomic variants.

AIM: To analyze the distribution of high-risk human papillomavirus (HR-HPV) genotypes and the diversity of HPV-16 genomic variants in Croatian women with high-grade squamous intraepithelial lesions (HSIL) and cervical carcinoma. METHODS: Tissue biopsy specimens were obtained from 324 women with histopathologically confirmed HSIL or cervical carcinoma, 5 women with low-grade SIL, and 49 women with negative histopathology. HR-HPV DNA was detected with Ampliquality HPV-type nucleic-acid hybridization assay, which identifies 29 different HPV genotypes. HPV-16 genomic variants were analyzed by an in-house sequencing. RESULTS: The most common HPV type in women with HSIL was HPV-16, detected in 127/219 (57.9%) specimens. HPV-16 was also the dominant type in squamous cell cervical carcinoma (46/69 or 66.7%) and in adenocarcinoma (18/36 or 50.0%). Out of 378 patients, 360 had HR-HPV (282 single infections and 79 multiple infections), 3 (0.8%) patients had low-risk HPV, and 15 (4%) tested negative. HPV-16 variants were determined in 130 HPV-16 positive specimens, including 74 HSIL and 46 carcinoma specimens. In HSIL specimens, 41 distinct variants were found, 98.6% belonging to the European branch and 1.4% belonging to the African branch. In cervical carcinoma specimens, 95% isolates grouped in 41 variants belonging to the European branch, one isolate (2.5%) belonged to the North American, and one (2.5%) to the Asian-American branch. CONCLUSION: HPV-16, mainly belonging to the European branch, was the most frequent HPV genotype in women from Croatia with histologically confirmed HSIL and cervical cancer.

Clinical Evaluation of the cobas SARS-CoV-2 Test and a Diagnostic Platform Switch during 48 Hours in the Midst of the COVID-19 Pandemic.

Laboratories are currently witnessing extraordinary demand globally for sampling devices, reagents, consumables, and diagnostic instruments needed for timely diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. To meet diagnostic needs as the pandemic grows, the U.S. 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 U.S. FDA EUA on 12 March 2020. The comparator was a standardized 3-h SARS-CoV-2 protocol, consisting of RNA extraction using an automated portable instrument, followed by a two-target reverse transcription real-time PCR (RT-PCR), which our laboratory has routinely used since January 2020 [V. M. Corman, O. Landt, M. Kaiser, R. Molenkamp, et al., Euro Surveill 25(3):pii=2000045, 2020, https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045]. 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 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 Universal Transport Medium System (UTM-RT) (Copan, Brescia, Italy). Under the extraordinary circumstances that laboratories are facing worldwide, a safe diagnostic platform switch is feasible in only 48 h and in the midst of the COVID-19 pandemic if carefully planned and executed.

Identical human papillomavirus (HPV) genomic variants persist in recurrent respiratory papillomatosis for up to 22 years.

Seventy initial and 125 follow-up tissue specimens of laryngeal papillomas, obtained from 70 patients who had had recurrent respiratory papillomatosis for from 1-22 years, were investigated for the presence of human papillomavirus (HPV) DNA and HPV E5a, LCR and/or full-length genomic variants. HPV-6 was found in 130/195, HPV-11 in 63/195, and HPV-6/HPV-11 in 2/195 samples. Within 67/70 (95.7%) patients, all follow-up HPV isolates genetically matched completely initial HPV isolate over the highly variable parts of the genome or over the entire genome. Frequent recurrence of laryngeal papillomas is a consequence of long-term persistence of the identical initial HPV genomic variant.

Sporadic Hepatitis A Virus PCR False-Positive Results Observed during Reflex Testing of Serum Samples Previously Tested for Anti-HAV Antibodies and Caused by Contamination with HAV RNA Present in the Reagents of the Commercial Anti-HAV Immunoassay.

Hepatitis A diagnosis relies on serology and occasionally on hepatitis A virus (HAV) RNA detection. For timely diagnosis and the avoidance of drawing additional blood, molecular testing is often performed as reflex testing by using blood specimens that were initially sent for anti-HAV serology. Reflex molecular testing is preferably performed from different sample aliquots, but, for limited sample quantities, it uses samples that have been preprocessed in an immunoassay analyzer. In 2012, we first observed sporadic HAV RNA-positive cases that were inconsistent with patients' serological profiles and/or medical histories, suggesting that occasional laboratory contamination was causing false-positive PCR results. Multiple external quality assurance (EQA) and laboratory surface contamination checks were performed, questionable specimens were tested with various HAV RNA tests, and follow-up serum/stool samples were collected. All contamination-check samples and samples from healthy individuals tested HAV RNA-negative, and the laboratory successfully passed all EQAs. The HAV RNA-positive results were reproducible with various HAV RNA assays. No patients seroconverted, and their follow-up samples were consistently HAV RNA-negative. Finally, a detailed review of testing protocols revealed a correlation between HAV RNA false positivity and preceding anti-HAV testing with the Cobas-e411 automated immunoassay analyzer. HAV RNA was detected in the Cobas-e411 anti-HAV reagents, with the HAV sequences matching those from the false-positive samples. Preceding anti-HAV testing using two other immunoassay analyzers did not result in subsequent HAV RNA false positivity during reflex testing. The Cobas-e411 pipetting procedure with a single pipette tip collecting samples and anti-HAV reagents contaminated the original sample with the HAV RNA that was present in the immunoassay's reagents, thereby resulting in HAV RNA false positivity during the reflex testing. IMPORTANCE We present the first report of sporadic HAV PCR false-positive results that have been observed during the reflex testing of serum samples that have previously been tested for anti-HAV antibodies and have been caused by contamination with HAV RNA that is present in the reagents of the commercial anti-HAV immunoassay, with potentially serious clinical consequences. Although HAV RNA was consistently detected in the anti-HAV reagents of all three automated immunoassay analyzers that were in use in our laboratory, only the use of one analyzer and the corresponding commercial anti-HAV immunoassay reagents resulted in contamination that led to false positive HAV RNA results, and this was due to a peculiar pipetting mode of action in which the analyzer uses a single pipette tip to collect both anti-HAV reagents and a sample, which consequently causes the permanent contamination of the original sample with HAV RNA. Manufacturers should strongly consider the occasional need for reflex molecular testing from preprocessed samples and design their analyzers in a way that prevents contamination.

An Improved Protocol for Comprehensive Etiological Characterization of Skin Warts and Determining Causative Human Papillomavirus Types in 128 Histologically Confirmed Common Warts.

Human papillomaviruses (HPVs) are etiologically associated with various benign and malignant neoplasms of cutaneous and mucosal epithelia. We describe an improved diagnostic protocol for comprehensive characterization of causative HPV types in common warts, in which broad-spectrum PCRs followed by Sanger sequencing, two previously described and seven newly developed type-specific quantitative real-time PCRs (qPCRs) coupled with the human beta-globin qPCR were used for: (i) diagnosis of HPV infection in warts; (ii) estimation of cellular viral loads of all HPV types detected; and (iii) determination of their etiological role in 128 histologically confirmed fresh-frozen common wart tissue samples. A total of 12 different causative HPV types were determined in 122/126 (96.8%) HPV-positive warts, with HPV27 being most prevalent (27.0%), followed by HPV57 (26.2%), HPV4 (15.1%), HPV2 (13.5%), and HPV65 (7.9%). The cellular viral loads of HPV4 and HPV65 were estimated for the first time in common warts and were significantly higher than the viral loads of HPV2, HPV27, and HPV57. In addition, we showed for the first time that HPV65 is etiologically associated with the development of common warts in significantly older patients than HPV27 and HPV57, whereas HPV4-induced warts were significantly smaller than warts caused by HPV2, HPV27, HPV57, and HPV65.

Real-Life Head-to-Head Comparison of Performance of Two High-Throughput Automated Assays for the Detection of SARS-CoV-2 RNA in Nasopharyngeal Swabs: The Alinity m and cobas 6800 SARS-CoV-2 Assays.

The Alinity m (Abbott Molecular, Des Plaines, IL) automated molecular analyzer allows continuous loading of samples and sample-to-result molecular detection of several microorganisms. The detection of SARS-CoV-2 by the Alinity m was compared with that of the cobas 6800 (Roche Molecular Systems, Branchburg, NJ; standard comparator) in a manufacturer-independent clinical evaluation on 2157 consecutive nasopharyngeal swab samples. Valid initial results on Alinity m and cobas 6800 were obtained from 2129 (98.7%) and 2157 (100%) samples, respectively. The overall percent agreement (95% CI) was 98.3% (2092/2129 [97.6%-98.7%]); positive percent agreement, 100% (961/961 [99.6%-100%]); negative percent agreement, 96.8% (1131/1168 [95.7%-97.7%]); and high κ value, 0.965 (0.954-0.976). There were 37 discordant results on Alinity m and, based on discordant analyses, including previous and/or follow-up PCR results, 22 could be considered analytically true positive with high probability. Due to a lack of additional information and an inability to perform repeated/further testing, the status of the remaining 15 discordant results remained unresolved. The throughput of the two analyzers was compared using testing on 564 samples in parallel across two 8-hour shifts in clinical practice. The turnaround times were compared using processing of 94 routine samples in parallel on each working day for 5 consecutive days. The two analyzers showed similar performance, with certain differences that have potential importance in some laboratory settings.

Digital squamous cell carcinoma associated with possibly carcinogenic human papillomavirus type 73 (HPV73): a case report.

We present a case report of a 64-year-old female patient with a 5-year history of a digital papule that clinically mimicked a common wart but was histologically diagnosed as digital squamous cell carcinoma (DSCC), a rare malignant cutaneous entity etiologically associated with high-risk human papillomaviruses (HR HPVs). This DSCC was positive for HPV73, which is currently classified under possible human carcinogens and has already been identified in DSCCs. Treatment with electrocoagulation and subsequent total excision with safety margins was successful, and no recurrence was detected during 6 years of follow-up. Analogously to cervical and other anogenital carcinomas, we assume that the incidence of DSCC will significantly decrease in the near future due to the widespread use of effective prophylactic HPV vaccines, which cover the majority of HR HPV types also associated with DSCC. However, HPV73 and other possibly carcinogenic and HR HPV types (as classified per the International Agency for Research on Cancer), which are not included in current prophylactic measures, will cause some portion of HPV-associated neoplasms, but this portion will be very minor.

Determination of Causative Human Papillomavirus Type in Tissue Specimens of Common Warts Based on Estimated Viral Loads.

Background: Assessment of human papillomavirus (HPV) type-specific viral load (VL) is a valid tool for determining the etiology of HPV-related skin tumors, especially when more than one HPV type is detected within one lesion. Methods: The causative HPV type was determined in 185 fresh-frozen tissue specimens of histologically confirmed common warts (CWs) collected from 121 immunocompetent patients. All tissues were tested using the type-specific quantitative real-time polymerase chain reactions (PCR) for the most common wart-associated Alpha-PV (HPV2/27/57) and Mu-PV types (HPV1/63/204). The presence of 23 additional low-risk HPVs was evaluated using a conventional wide-spectrum PCR. Results: HPV DNA was detected in 176/185 (95.1%) CWs and multiple HPV types in 71/185 (38.4%) lesions. Using the VL approach and a robust cutoff of one viral copy/cell established in this study, HPV2/27/57 were determined as causative agents in 41/53 (77.3%) and 53/71 (74.7%) CWs with single and multiple HPVs, respectively. Conclusions: CWs are mostly etiologically associated with HPV2/27/57 and only rarely with HPV1. In the majority of CWs containing multiple HPVs, a single HPV type was present in high concentration, indicating etiological association. No significant differences in VLs of lesion-causing HPV types in CWs containing single or multiple HPVs were found.

Transcription factors Snail, Slug, Twist, and SIP1 in spindle cell carcinoma of the head and neck.

Spindle cell carcinoma (SpCC) is a biphasic tumor composed of squamous cell carcinoma (SCC) and malignant spindle cells. There is mounting evidence that epithelial-mesenchymal transition (EMT) plays an important role in the pathogenesis of SpCC. Transcription repression has recently emerged as a fundamental mechanism triggering EMT in experimental models. Our aim is to analyze the expression of transcription repressors Snail, Slug, Twist, and SIP1 in SpCC of the head and neck in comparison to SCC, matched for location and stage. Thirty cases of SpCC and 30 cases of SCC of the head and neck were included. Snail, Slug, Twist, and SIP1 expression was analyzed on mRNA and protein levels, using real-time reverse transcription-polymerase chain reaction (RT-PCR) and immunohistochemistry. By RT-PCR, we found upregulation of mRNA for transcription factors Snail, Slug, Twist, and SIP1 in SpCC when compared to SCC. This upregulation was statistically significant for Slug, Twist, and SIP1 but nonsignificant for Snail. Immunohistochemistry was performed for Snail, Slug, and SIP1 and demonstrated a positive reaction for Slug and SIP1 in all cases and for Snail in two thirds of SpCC cases. Our finding of upregulation of all four tested transcription factors supports the hypothesis that EMT plays an important role in the pathogenesis of SpCC of the head and neck.

Development of a novel multiplex type-specific quantitative real-time PCR for detection and differentiation of infections with human papillomavirus types HPV2, HPV27, and HPV57.

INTRODUCTION: The present study describes the development and evaluation of the first multiplex type-specific quantitative real-time PCR (RT-PCR), enabling simple, rapid, sensitive, and specific concurrent detection and differentiation of human papillomavirus (HPV) types HPV2, 27, and 57 in a single PCR reaction. RESULTS: The HPV2/27/57 multiplex RT-PCR with a dynamic range of seven orders of magnitude (discriminating 10 to 108 viral genome equivalents/reaction) has an analytical sensitivity of at least 10 viral copies of each targeted HPV type/reaction, and no cross-reactivities were observed among the included targets. All three primer/probe combinations were efficient in amplifying 500 copies of targeted DNA in a background of 108, 107, 500, 100, and 10 copies of non-targeted viral DNA/reaction, and the performance of the HPV2/27/57 multiplex RT-PCR was additionally not affected by the presence of background human genomic DNA. When testing DNA isolates obtained from fresh-frozen tissue specimens of various children's warts, the results of the HPV2/27/57 multiplex RT-PCR were completely in line with the results of the conventional Low-risk Alpha-PV PCR. CONCLUSION: The newly developed HPV2/27/57 multiplex RT-PCR is an appropriate test for use in routine clinical laboratory settings and for studies focusing on the molecular epidemiology, pathogenesis, and natural history of HPV2/27/57-related lesions.

Hepatitis D virus infection in Slovenian patients with chronic hepatitis B virus infection: a national prevalence study and literature review.

INTRODUCTION: Of the 350 million individuals chronically infected with hepatitis B virus (HBV) worldwide, approximately 15 to 20 million have been exposed to hepatitis D virus (HDV). This study determined for the first time the HDV prevalence in Slovenian patients with chronic HBV infection. In addition, a literature search was performed to identify all HDV prevalence studies from European countries. METHODS: A total of 1,305 HBsAg-positive serum samples, obtained from the same number of patients, were randomly selected from 2,337 patients referred to the Slovenian national reference laboratory for viral hepatitis between 1998 and 2015. All samples were retrospectively tested for the presence of total anti-HDV antibodies. Anti-HDV-positive patients were additionally tested for the presence of anti-HDV IgM antibodies, HDV antigen, and HDV RNA. RESULTS: Total anti-HDV antibodies were detected in three of the 1,305 patients tested (0.23%; 95% CI: 0.08-0.67%), of whom one patient had recovered from the past HDV infection and two patients had an ongoing chronic HDV infection. The literature search identified 36 peer-reviewed HDV prevalence studies published between 1983 and 2016 and originating from 21 European countries. CONCLUSIONS: The observed prevalence of HDV infection in Slovenia was among the lowest reported in Europe and worldwide. Due to the observed low prevalence of HDV infection, routine diagnostic testing for HDV should not be considered in differential diagnosis of exacerbation of liver disease in Slovenian patients with chronic HBV infection.

Betapapillomaviruses in the anal canal of HIV positive and HIV negative men who have sex with men.

BACKGROUND: Betapapillomaviruses (ß-PV) are etiologically associated with epidermodysplasia verruciformis and a proportion of skin precancerous lesions and cancer, mainly in immunocompromised individuals. OBJECTIVES: The prevalence and persistence of anal ß-PV infection and ß-PV type distribution were determined in a cohort of men who have sex with men (MSM). A correlation with HIV-1 infection status and selected demographic and behavioral risk factors were additionally established. STUDY DESIGN: A total of 181 anal swabs (135 initial and 46 follow-up swabs) obtained from 135 Slovenian MSMs (17.0% HIV-1 positive) were tested for the presence of 25 different ß-PV types using Diassay RHA Kit Skin (beta) HPV assay and, if negative, with an in-house nested M(a)/H(a) PCR. RESULTS: ß-PVs were detected in 88/135 (65.2%) initial anal swabs. Infection with multiple ß-PV types was found in 26 samples; the number of ß-PVs ranged from 2 to 9. A total of 29 distinct ß-PVs were detected: HPV-36 and HPV-38 were the most prevalent, followed by HPV-23, HPV-24, and HPV-93. HIV-1 positive status, promiscuity and use of alkyl nitrites were significantly associated with a higher prevalence of anal ß-PV infection. Three partial DNA sequences suggesting putative new HPV types were identified. CONCLUSION: To the best of our knowledge, this is the first study to investigate and characterize ß-PV infections in the anal region. We showed that anal ß-PV infection is highly prevalent in the MSM population and that ß-PVs can establish persistent infection in the anal region for up to 4.8 years.

Genetic diversity of HPV-6 in concurrent multiple anogenital warts.

INTRODUCTION: Anogenital warts (AGW) are the most common benign tumors in the anogenital area. They are etiologically associated with alpha human papillomaviruses (HPV), in more than 90% of cases with HPV-6 and HPV-11. AGW frequently displays a multifocal and multicentric appearance. However, it is not clear whether the occurrence of multiple AGW in a particular patient is a consequence of infection with single or multiple HPV genomic variants of a given HPV genotype. METHODS: Forty-five HPV-6 isolates from fresh-frozen AGW tissue specimens, obtained from 18 patients with concurrent multiple AGW, were included. The entire HPV-6 L1, E5a, E5b ORFs, and LCR genomic region was sequenced. RESULTS: Fourteen different HPV-6 L1-LCR-E5a-E5b genomic variants were identified among 18 patients with concurrent multiple AGW. In 17 out of 18 patients, a single identical HPV-6 L1-E5a-E5b-LCR genomic variant was identified in all concurrent multiple AGW collected in an individual patient. Co-infection with two different HPV-6 genomic variants was identified in one patient. DISCUSSION: The presence of an identical HPV genomic variant in all concurrently present multiple AGW within an individual patient supports the hypothesis that the occurrence of multiple concurrent AGW is a consequence of infection with a single HPV-6 genomic variant, rather than infection with multiple genomic variants of HPV-6.