Evaluation of two RT-PCR screening assays for identifying SARS-CoV-2 variants.

BACKGROUND: The recent emergence of new SARS CoV-2 variants (variants of concern, VOC) that spread rapidly and may lead to immune escape has emphasized the urgent need to monitor and control their spread. METHODS: We analyzed 2018 SARS-CoV-2 positive specimens collected between February 9 and March 22, 2021 using the Thermofisher® TaqPath™ COVID-19 CE-IVD RT-PCR kit (TaqPath) and the ID solutions® ID™ SARS-CoV-2/UK/SA Variant Triplex RT-PCR (ID triplex) assay to screen for VOCs. RESULTS: The ID triplex assay identified 62.8% of them as VOCs: 61.8% B.1.1.7 and 0.9% B.1.351/P.1. The agreement between the ID triplex results for B.1.1.7 and the TaqPath S gene target failure (SGTF)/ S gene target late detection (SGTL) profile for this variant agreed very well (k = 0.86). A low virus load was the main cause of discrepancies. Sequencing discordant results with both assays indicated that the TaqPath assay detected the B.1.1.7 lineage slightly better. Both assays suggested that the virus loads of B.1.1.7 variants were significantly higher than those of non-B.1.1.7 strains. Only 10/20 B1.351/P.1 strains detected with the ID triplex assay were confirmed by sequencing. CONCLUSIONS: We conclude that the SGTF/SGTL profiles identified using the TaqPath assay and ID triplex results are suitable for detecting the B.1.1.7 lineage. The ID triplex assay, which rapidly determines all three current VOCs simultaneously, could be a valuable tool for limiting virus spread by supporting contact-tracing and isolation.

JC virus DNA in the peripheral blood of renal transplant patients: a 1-year prospective follow-up in France.

There is little information on JC virus (JCV) infection in renal transplant patients. A long-term prospective follow-up study was conducted to assess the incidence of JCV DNA in the blood of 103 adult renal transplant patients enrolled prospectively between 1 January and 31 December 2006. Patients were monitored until April 2008. JCV DNA was quantified by a real-time polymerase chain reaction in whole blood samples collected regularly for at least 1 year post-transplant. JCV was detected in seven patients (6.8%) (31/1,487 whole blood samples) at a median time of 139 days post-transplant. The median JC virus load of the first positive DNA blood sample was 3.4 log(10) copies/ml (1.9-5.7 log(10) copies/ml). Induction therapy were either anti-CD25 monoclonal antibodies (n = 5) or antithymocyte globulins (n = 2). Post-transplant immunosuppressive treatment included steroids with tacrolimus/mycophenolate mofetil (MMF) (n = 2), or ciclosporin/MMF (n = 1), or belatacept/MMF (n = 4). Two patients were also treated with rituximab. All seven patients infected with JCV had other viral infections(s): BK virus (3), Epstein-Barr virus (2), Cytomegalovirus (1) or both BK virus and Epstein-Barr virus (1). Three patients had BKV-associated nephropathy and decoy cells shedding. JCV infection was not associated with acute rejection episodes or nephropathy, regardless of the virus load. No patient developed progressive multifocal leukoencephalopathy during follow-up. Thus the incidence of JCV infection in renal transplant patients was low and not associated with any specific clinical manifestations. JCV replication must still be diagnosed and differentiated from BK virus infection because of its non-aggressive course.

Acute hepatitis E in south-west France over a 5-year period.

BACKGROUND: Hepatitis E was found in people living in industrialized countries who had not travelled to highly endemic areas. OBJECTIVES: To study the cases of acute hepatitis E confirmed thanks to viral genomic detection over a 5 years period in south-west France. STUDY DESIGN: 62 cases of hepatitis E were identified between 2003 and 2007. Their demographic, clinical, and virological features were analyzed. RESULTS: Cases of acute hepatitis E occurred regularly throughout this period. No seasonal variation was found. Patients, usually male (sex ratio=1.95), were adults living in both urban and rural areas. Sixty (96.8%) patients had not travelled abroad during the 6 months before diagnosis. Clinical manifestations ranged from asymptomatic infection to severe hepatitis. HEV was genotyped in 55 specimens. All the patients who had not travelled abroad were infected with genotype 3. CONCLUSION: The incidence of hepatitis E in south-west France was stable from 2003 to 2007, 96.8% of the cases were autochthonous. There was an age-related increase in the disease and patients tended to be men. The predominant genotype and subtype was 3f. However, contaminations pathways involved in hepatitis E in our area remain to clarify.

[Management of occupational and sexual exposure to HIV in the Toulouse teaching hospital]. / Prise en charge des accidents d'exposition au VIH d'origine professionnelle et sexuelle: etat des lieux au centre hospitalo-universitaire de Toulouse.

OBJECTIVE: This study had aim to describe the management of occupational and sexual HIV exposure in the Toulouse teaching hospital. DESIGN: A prospective descriptive study was made of patients reporting with potential HIV exposure in Toulouse between 01/01/2000 and 12/31/2002. RESULTS: Six hundred and ninety three cases were reported, 236 after occupational and, 457 after sexual exposure. The frequency of sexual exposures increased with time. 61.2% of patients received post-exposure treatment and no seroconversion was diagnosed during their follow-up. Eighty-four percent of treated patients received three anti-retroviral drugs, with a protease inhibitor in 57%. Treatment was more frequently prescribed in sexual exposures than in occupational ones. For occupational exposures, the median time between exposure and consultation was 4 h and was decreased by spontaneous bleeding but not affected by source patient serostatus or injury deepness. Treatment was more frequent when injury was deep, when there was spontaneously bleeding, and when the source patient serostatus was positive or unknown. For sexual exposures, the median time between exposure and consultation was significantly superior to 4 h. That was diminished by positive source person serostatus but not affected by the partner's gender, nature of intercourse, or rape. Treatment was more frequently prescribed in case of positive or unknown source person serostatus, rape and homosexual intercourse. CONCLUSIONS: Given the delay before consultation for sexual exposures and out of delay treatment in occupational exposures, discussion with health professionals on implementing procedures and means seems mandatory.

Use of two real-time polymerase chain reactions (PCRs) to detect herpes simplex type 1 and 2-DNA after automated extraction of nucleic acid.

Herpes simplex virus infections may be diagnosed by several techniques, including conventional cell culture and the polymerase chain reaction (PCR). This prospective study compares the analytical performances and usefulness of an in-house real-time PCR method and the Light Cycler HSV (1/2) detection kit (Roche Diagnostics, Mannheim, Germany). The results of both PCRs were then compared to those obtained by conventional cell culture. A total of 313 samples were tested (70 dermal samples, 81 cerebrospinal fluids (CSF), 47 ocular, 42 anogenital, 34 throat swabs, and 33 oral samples, 3 whole blood, 2 biopsies, and 1 bronchoalveolar lavage). Samples for molecular assays were extracted twice with the MagNa Pure instrument (Roche Molecular Biochemicals, Mannheim, Germany) and tested blind in parallel by the two PCR methods. Most (226) samples were also examined by cell culture. Forty three samples were found positive by both PCRs, whereas 267 were negative. The HSV-1 and -2 typing of positive samples was identical. Three of the samples were positive in the in-house PCR and negative in the Light Cycler HSV (1/2) detection kit. There was no statistically significant difference between the two tests. Only one sample gave an invalid result due to negative PCR and negative internal control result. Seven samples were positive by both real-time PCRs and negative in conventional culture. The PCRs were significantly (P < 0.05) more sensitive. The results show good agreement between the two real-time PCR methods, with the molecular tests being more sensitive than cell culture.

Virological exploration of individuals with discordant HIV screening tests.

Screening for HIV infection can use many algorithms. When two different HIV antibody assays are used, discordant results may occur. To discriminate between HIV seroconversion, HIV variant infection and false positive reactivity, 30 consecutive subjects with two discordant HIV antibody-screening assays were extensively investigated for HIV infection. No subject had HIV seroconversion or reached HIV seropositivity criteria after a follow-up of 3 months. By contrast 36% became HIV negative by the use of both HIV screening assays. p24 Antigen, HIV-1 RNA, HIV-1 DNA, HIV-2 DNA assays and HIV isolation by sensitive culture were unable to identify HIV infection in the 30 subjects with discordant HIV screening assays. The data suggest that the use of two HIV screening assays increase false-positive HIV results without increasing clinical sensitivity. To compliment follow-up of HIV screening, early testing for HIV RNA could be useful to identify or eliminate a recent infection.

Screening for hepatitis B virus DNA in serum of organ donors and renal transplant recipients.

In order to determine the impact of screening potential organ donors for hepatitis B virus DNA using a standardized test, the serum of 145 donor candidates was tested. All of the candidates were negative for hepatitis B virus DNA, but the status of one donor was doubtful for hepatitis B virus surface antigen and seven donors tested positive for hepatitis B virus core antibody without hepatitis B virus surface antigen. Nine transplant recipients tested positive for hepatitis B virus surface antibody; they were given kidneys from the donor with a doubtful hepatitis B virus surface antigen result and from four of the seven donors who tested positive for hepatitis B core antibody. Follow-up revealed no case of hepatitis B transmission. In this study, screening for hepatitis B virus DNA was useful and did not lead to donor organ shortage. Patients with hepatitis B virus surface antibodies can safely be given kidneys from donors who are positive for hepatitis B core antibody but negative for hepatitis B virus DNA.

Carcinoembryonic antigen as an independent prognostic factor of recurrence and survival in patients resected for colorectal liver metastases: a systematic review.

PURPOSE: We attempted to answer the question of whether serum levels of carcinoembryonic antigen provide prognostic information, in terms of survival, in patients resected for colorectal liver metastases, independently of that provided by other commonly used radioclinical and pathologic factors. METHOD: We performed a systematic review, without meta-analysis, of the biomedical literature using the methodology recommended by the Committee on Evidence-Based Laboratory Medicine of the International Federation of Clinical Chemistry and Laboratory Medicine. RESULTS: Despite the absence of sufficient details about the methods used to measure serum carcinoembryonic antigen in the 14 studies reviewed, strong arguments exist to include preoperative carcinoembryonic antigen measurements in future trials on the subject. In particular, preoperative carcinoembryonic antigen was found to be significant in the two studies with the greatest number of patients having a preoperative carcinoembryonic antigen assay, in the four studies with the most recent series of patients, in the study in which preoperative carcinoembryonic antigen was used as a continuous variable, and in the study in which preoperative carcinoembryonic antigen was used in terms of doubling time. Postoperative carcinoembryonic antigen was found to have a prognostic significance in the only two studies that evaluated this variable. CONCLUSION: Taking into account the possible reasons for disagreements regarding carcinoembryonic antigen prognostic value between the 14 studies reviewed, we propose some recommendations to improve the reproducibility and the quality of future studies in this field. In particular, we stress the need for a higher degree of multidisciplinary collaboration in clinical trials.

High levels of cytokeratin 19 fragments but no evidence of cytokeratins 1, 2, 10/11, 14 or filaggrin in the serum of squamous cell lung carcinoma patients.

The CYFRA 21-1 assay detects circulating fragments of cytokeratin 19, which is a sensitive marker for the diagnosis of lung cancers, particularly squamous cell carcinomas and adenocarcinomas. Epidermis-type proteins, such as cytokeratins 1, 2, 10/11 and 14 or filaggrin, are also expressed in squamous cell carcinomas. These could also be pertinent tumor markers, ideally as sensitive as CYFRA 21-1 and more specific for squamous cell lung cancer. To verify this hypothesis, using monoclonal antibodies produced in our laboratory, we developed immunoassays specific for these proteins. After optimization, the immunoassays were evaluated in sera from 91 controls and 138 patients with squamous cell lung cancer and compared to conventional tumor markers (CEA, SCC Ag and CYFRA 21-1). Less than 14% of the sera were above the lower limit of detection of the cytokeratin- and filaggrin-specific immunoassays. Moreover, part of these positive sera were induced by the presence of interfering heterophilic antibodies in sera. Thus, in patients with squamous cell lung cancer, we confirmed the high diagnostic sensitivity of CYFRA 21-1 (55.6%) but were unable to detect significant levels of epidermis-type cytokeratins or filaggrin.

[Unresected colorectal liver metastases: prognostic value of laboratory variables]. / Métastases hépatiques non opérées des cancers colorectaux: valeur pronostique des variables biologiques.

OBJECTIVE: To search for laboratory variables having independent prognostic signification in patients with unresected colorectal liver metastases. METHODS: We have systematically reviewed the biomedical literature using the methodology recommended by the Committee on Evidence-Based Laboratory Medicine of the International Federation of Clinical Chemistry and Laboratory Medicine, and taking into account the Consolidated Standards of Reporting Trials Statement. RESULTS: Of 644 publications retrieved, the application of strict exclusion and inclusion criteria allowed us to include only eight studies in our systematic review. The main laboratory variables evaluated in these eight studies were serum carcino-embryonic antigen, alkaline phosphatase, albumin, bilirubin, and plasma prothrombin time. None of these variables were unanimously found to have an independent prognostic significance. A meta-analysis was not possible, mainly because of heterogeneity within the primary studies and these contradictory results. CONCLUSIONS: Current evidence would not support the routine use of laboratory variables as independent prognostic variables in patients with unresected colorectal liver metastases. Taking into account the inadequate quality of the published studies, this negative conclusion might be provisory only. Until better designed studies are published, a number of arguments would support to recommend pre-treatment measurement of serum carcino-embryonic antigen and alkaline phosphatase in patients participating in clinical trials.

Prostate-specific antigen in acute hepatitis and hepatocellular carcinoma.

BACKGROUND: Prostate-specific antigen (PSA) is the most important tumor marker in prostate cancer diagnosis and follow-up. Its catabolism by the liver has not influenced its use as a prostate marker until the recent report of a significant increase in a man and a woman with acute hepatitis. In addition, PSA was detected in liver tumor extracts, which warranted its evaluation in liver cytolysis and hepatocellular carcinoma. In this study, PSA was evaluated in a cohort of both sexes presenting either acute hepatitis or hepatocellular carcinoima. METHODS: Forty-two patients with acute hepatitis (21 male patients, 21 female patients) and 54 patients with hepatocellular carcinoma (31 male patients, 23 female patients) were tested for PSA by equimolar immunoassay (Abbott AxSYM Total PSA, Abbott Diagnostics, Rungis, France) and for relevant liver biological parameters (alpha-fetoprotein, alanine aminotransferase, aspartate aminotransferase, total bilirubin, and prothrombin rate). RESULTS: PSA was undetectable in all the female patients and was consistent with age in the males (PSA median and range in acute hepatitis, 0.36 microg/l (range, 0.05-1.3); in hepatocellular carcinoma, 0.36 microg/l (range, 0.02-3.9)). It did not correlate with alpha-fetoprotein and aminotransferases. CONCLUSIONS: Our results confirm the well-established reliability of PSA, and show that PSA remains a valid prostate marker in patients with acute hepatitis and hepatocellular carcinoma.

Evaluation of seven tumour markers in pleural fluid for the diagnosis of malignant effusions.

Carcinoembryonic antigen (CEA), carbohydrate antigens 15-3, 19-9 and 72-4 (CA 15-3, CA 19-9 and CA 72-4), cytokeratin 19 fragments (CYFRA 21-1), neuron-specific enolase (NSE) and squamous cell carcinoma antigen (SCC) were evaluated in pleural fluid for the diagnosis of malignant effusions. With a specificity of 99%, determined in a series of 121 benign effusions, the best individual diagnostic sensitivities in the whole series of 215 malignant effusions or in the subgroup of adenocarcinomas were observed with CEA, CA 15-3 and CA 72-4. As expected, a high sensitivity was obtained with SCC in squamous cell carcinomas and with NSE in small-cell lung carcinomas. CYFRA and/or CA 15-3 were frequently increased in mesotheliomas. Discriminant analysis showed that the optimal combination for diagnosis of non-lymphomatous malignant effusions was CEA + CA 15-3 + CYFRA + NSE: sensitivity of 94.4% with an overall specificity of 95%. In malignant effusions with a negative cytology, 83.9% were diagnosed using this association. The association CYFRA + NSE + SCC was able to discriminate adenocarcinomas from small-cell lung cancers. Regarding their sensitivity and their complementarity, CEA, CA 15-3, CYFRA 21-1, NSE and SCC appear to be very useful to improve the diagnosis of malignant pleural effusions.

Evaluation of alpha-fetoprotein assay in ascitic fluid for the diagnosis of hepatocellular carcinoma.

Ascites and hepatocellular carcinoma are frequently associated. We evaluated the usefulness of alpha-fetoprotein assay in ascitic fluid versus the serum assay, for the diagnosis of hepatocellular carcinoma, in 125 patients with peritoneal effusions (31 patients with hepatocellular carcinoma, 14 with extra-hepatic malignancies and 80 with a benign effusion). Albumin and total protein were also assayed and cytological analysis of the ascitic fluid performed. Alpha-fetoprotein appeared to be lower in ascitic fluid than in serum. For a diagnostic specificity of 95%, the thresholds were 18.9 microg/l in serum and 4 microg/l in ascitic fluid and the diagnostic sensitivity of alpha-fetoprotein was identical in serum and ascitic fluid (67.7%). Various ratios between alpha-fetoprotein and albumin or total protein did not enhance the diagnostic performance. Thus alpha-fetoprotein concentration in ascitic fluid reflected the serum concentration and proved to be of similar value for the diagnosis of hepatocellular carcinoma, providing that the appropriate thresholds are considered.

Evaluation of pleural CYFRA 21-1 and carcinoembryonic antigen in the diagnosis of malignant pleural effusions.

CYFRA 21-1 assay, measuring cytokeratin 19 fragments, was compared with carcinoembryonic antigen (CEA) assay, as an addition to cytological analysis for the diagnosis of malignant effusions. Both markers were determined with commercial enzyme immunoassays in pleural fluid from 196 patients. Cytological analysis and/or pleural biopsy confirmed the malignant origin of the effusion in 99 patients (76 carcinomas, nine pleural mesotheliomas and 14 non-epithelial malignancies). Effusions were confirmed as benign in 97 patients (33 cardiac failures, 39 infectious diseases--including 12 tuberculosis-- and 25 miscellaneous effusions). Both markers were significantly higher in malignant than in benign effusions. All the patients with non-epithelial malignancies presented CYFRA and CEA values lower than the 95% diagnostic specificity thresholds (100 and 6 ng ml(-1) respectively). The diagnostic sensitivity in the group of carcinomas and mesotheliomas was similar for CYFRA (58.8%) and CEA (64.7%). However, CEA had a significantly higher sensitivity in carcinomas (72.4% vs 55.3%), while CYFRA had a clearly higher sensitivity in mesotheliomas (89.9% vs 0%). Interestingly, 12 out of the 16 malignant effusions with a negative cytology were CEA and/or CYFRA positive. Regarding their high diagnostic sensitivity and their complementarity, CEA and CYFRA appear to be very useful for the diagnosis of malignant pleural effusions when cytology is negative.

Influence of digital rectal massage on urinary prostate-specific antigen: interest for the detection of local recurrence after radical prostatectomy.

BACKGROUND: Following radical prostatectomy, urinary prostate-specific antigen (uPSA) may originate from periurethral glands or from recurrent carcinomatous prostatic cells. We evaluated massage of the urethro-vesical anastomosis as a uPSA-releasing method for the detection of local recurrence. METHODS: PSA was assessed (PSA IMx, Abbott Diagnostic, Rungis, France) in serum and in the first voided urine before and after massage in 59 patients: 7 after cystoprostatectomy for bladder cancer, 22 with prostate in situ, and 30 after radical prostatectomy for prostate cancer. RESULTS: No significant changes of uPSA were induced by the massage in cystoprostatectomy patients and in 4 radical prostatectomy patients with a negative biopsy of the anastomosis. In contrast, a significant increase of uPSA was observed after massage in the patients with prostate in situ and in 6 radical prostatectomy patients with biopsy-proven local relapse. CONCLUSIONS: uPSA before and after massage of the prostatic fossa may constitute a new and efficient tool for the detection of local recurrence, if these preliminary results are confirmed on a larger scale.