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International audience; The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the resulting disease COVID-19 has killed over 2 million people as of 22 January 2021. We have used a modified susceptible, infected, recovered epidemiological model to predict how the spread of the virus in France will vary depending on the public health strategies adopted, including anti-COVID-19 vaccination. Our prediction model indicates that the French authorities' adoption of a gradual release from lockdown could lead in March 2021 to a virus prevalence similar to that before lockdown. However, a massive vaccination campaign initiated in January 2021 and the continuation of public health measures over several months could curb the spread of virus and thus relieve the load on hospitals.

Resume La prise en ompte et le calcul des incertitudes font partie des exigences d’accreditation des laboratoires de biologie medicale selon la norme NF EN ISO 15 189. Les examens de serologie infectieuse sont assimiles dans leur grande majorite a des tests quantitatifs et il est donc logique de s’interesser a l’incertitude analytique. Le niveau le plus pertinent ou elle merite d’etre prise en compte est le seuil de positivite qui permet de determiner la presence ou l’absence de l’anticorps ou de l’antigene recherches. L’incertitude finale se calcule en faisant la somme quadratique des deux composantes principales que sont la justesse et la fidelite intermediaire. Le controle interne de qualite proche du seuil permet d’estimer la fidelite intermediaire. Pour la justesse, le biais sera determine, le cas echeant, en utilisant les standards de l’Organisation mondiale de la sante (OMS) pour les resultats rendus en unites internationales. L’incertitude totale elargie permet ainsi d’optimiser la zone douteuse en fonction des performances reelles de la methode. A cote de l’incertitude analytique, la specificite diagnostique et la limite de detection ont un impact tout aussi important sur la valeur predictive du resultat et elles ne doivent pas etre negligees. En l’absence de standards internationaux pour l’ensemble des parametres de serologie, le choix du controle externe de qualite apparait comme un element particulierement critique.

The SARS-CoV-2 virus has spread world-wide since December 2019, killing more than 2.9 million of people. We have adapted a statistical model from the SIR epidemiological models to predict the spread of SARS-CoV-2 in France. Our model is based on several parameters and assumed a 4.2% seroprevalence in Occitania after the first lockdown. The recent use of serological tests to measure the effective seroprevalence of SARS-CoV-2 in the population of Occitania has led to a seroprevalence around 2.4%. This implies to review the parameters of our model to conclude at a lower than expected virus transmission rate, which may be due to infectivity varying with the patient’s symptoms or to a constraint due to an uneven population geographical distribution.

International audience; The spread of SARS-CoV-2 and the resulting disease Covid-19 has killed over 2 million people as of January 22, 2021. We have designed a model and used it to quantify the effect of a 6 p.m curfew on the SARS-CoV-2 epidemic in Toulouse, France. The data show that this measure can lead to the opposite effect from that intended due to larger groups of people on the authorized hours.

International audience; Contents lists available at ScienceDirect Journal of Clinical Virology journal homepage: www.elsevier.com/locate/jcv Clinical performance of a rapid test compared to a microplate test to detect total anti SARS-CoV-2 antibodies directed to the spike protein The recent emergence of the SARS-CoV-2 pandemic has posed for-midable challenges for clinical laboratories. While immunoassays are already available, their diagnostic accuracy and optimal use remain undefined. Serologic tests could be used as complements to assays for virus nucleic acid in the diagnosis of COVID-19 [1–3]. Serologic assays that accurately assess prior infection and immunity to SARS–CoV-2 are essential for retrospective diagnosis, epidemiologic studies, ongoing surveillance and vaccine studies

International audience; Recent reports of SARS-CoV-2 reinfection have raised questions as to whether and to what degree a first infection protects against reinfection. This is particularly important for healthcare workers (HCW) as they are always in the front line combatting both the present epidemic and any new waves of SARS-CoV-2 infection. These workers can also transmit the virus to co-workers and hospitalized susceptible patients. In their recent study, Lumley et al presented 6 months of data from a longitudinal seroprevalence study of UK HCW and showed that SARS-CoV-2 anti-nucleocapsid antibodies wane within months.

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.

International audience; Hepatitis E virus is an emerging concern in immunocompromised patients, who may become chronically infected. This prompted us to assess the performance of two anti-HEV IgG and IgM assays for diagnosing acute HEV infections. The specificities of the assays were estimated by testing samples from 2 to 3 year-old French children and blood donors and their sensitivities by testing 40 immunocompromised patients acutely infected. Both anti-HEV IgM assays were highly specific (99.6% and 100%). The sensitivity of the Adaltis was 87.5%, and that of Wantai was 85%. The specificities of anti-HEV IgG Wantai (97.8%) and Adaltis tests (89.5%, p=0.1) were similar but the Wantai test was more sensitive (45%) than the Adaltis test (15%, p

Background The Common Technical Specifications for HIV-1 p24 assays published in 2009 fixed the lower limit of detection for obtaining C.E. approval at 2 IU/ml against the WHO standard (first international reference, code NIBSC 90/636); it was previously 50 pg/ml. Some recent fourth generation HIV assays that simultaneously detect antigen and antibody are equivalent to p24 assays, but they were mainly evaluated using p24 antigen standards in pg/ml and little is known of their performance with the IU/ml standard. Objectives To evaluate four of the combined serological assays most commonly used for HIV diagnosis in France against the WHO standard in IU/ml. Study design The analytical sensitivity of four combined p24 antigen and antibody assays (ARCHITECT HIV Ag/Ab Combo, AxSYM HIV Ag/Ab Combo, VIDAS HIV DUO Quick and VIDAS HIV DUO Ultra) and of one p24 assay (VIDAS HIV p24 II) were determined using dilutions of the WHO standard. Results Four of the five assays had a lower limit of detection below 2 IU/ml: 1.24 for ARCHITECT Combo, 0.66 for VIDAS DUO Ultra, 0.43 for VIDAS DUO Quick and 0.73 to 1.15 for VIDAS p24, while that of AxSYM was close to 2 (1.94-2.25). Conclusions We have provided the first data on the lower limit of detection of HIV combined assays using the IU/ml WHO standard and demonstrated the need for a single international standard for comparing assays. We recommend the use of this approach in medical laboratory to validate on site their methods.

Background A variety of epidemiological data provide evidence for the nosocomial transmission of hepatitis C virus (HCV) infections to haemodialysis patients. We conducted a multicentric study to determine the prevalence and incidence of HCV infection in French haemodialysis units. Methods Patients undergoing chronic haemodialysis in 56 French units (4718 patients) were systematically screened for anti-HCV antibodies using third-generation tests. The incidence was estimated by detecting HCV RNA in seronegative patients using a standardized real-time PCR assay on pooled samples. Results Testing for HCV antibodies identified 361 patients with anti-HCV antibodies, giving a prevalence of 7.7%. Multivariate analysis demonstrated that anti-HCV status was linked to the time on haemodialysis, previous kidney transplantation and the presence of anti-HBc antibodies, whereas erythropoietin therapy and carrying out dialysis in dedicated spaces seem to protect against HCV infection. Only two of the 4357 patients without anti-HCV antibodies tested positive for HCV RNA, giving an estimated incidence of 0.05% new HCV infections/year. Molecular analyses indicated that the two patients probably acquired HCV outside the haemodialysis unit. Conclusion This decreased prevalence and incidence emphasizes the importance of adhering to the recommended universal infection-control precautions. Virological follow-up based on detecting anti-HCV antibodies with sensitive, specific new-generation serological tests could be adequate for dialysis units with few HCV infections. However, new infections in haemodialysis units should be identified by determining the HCV RNA status of seronegative patients. Standardized real-time PCR assays, plus pooling serum samples, make this a promising method for large-scale epidemiological studies.

Resume Le laboratoire de virologie du CHU de Toulouse a decide en 2003 de prioriser l’accreditation du laboratoire selon la norme ISO 15189 « Laboratoires d’analyses de biologie medicale – Exigences particulieres concernant la qualite et la competence ». Une premiere phase d’optimisation de l’organisation et d’analyse des processus a debouche sur une refonte de la gestion documentaire sous l’impulsion du responsable assurance qualite, d’une equipe de referents et de l’ensemble des biologistes. L’installation d’un logiciel de gestion de la qualite a permis d’accelerer le processus et de finaliser la demarche. Les dossiers de validation des methodes ont ete transmis au Cofrac en juillet 2006 et un audit « a blanc » sur l’ensemble de la norme (partie qualite et partie competence technique) a ete realise en decembre 2006. L’audit du Cofrac a eu lieu en fevrier 2007 et a conduit a l’accreditation du laboratoire en avril 2007. Au dela de la gestion documentaire, les aspects les plus critiques et/ou les plus lourds a gerer ont ete : la gestion des ressources humaines, l’amelioration continue de la qualite, le suivi metrologie, le manuel de prelevement, les dossiers de validation des methodes, la gestion des controles de qualite et l’estimation des incertitudes.

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.

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.

Prospective nucleic acid tests were carried out for human immunodeficiency virus (HIV) and hepatitis C virus (HCV) using the COBAS Amplicor HIV-1 and HCV tests (Roche Diagnostics, Meylan, France) on potential organ (n=113) and cornea (n=368) donors in France to evaluate their performance and suitability for use as a complement to routine serological tests. Blood samples were collected from organ donors with preserved cardiac function after verification of cerebral death. Blood samples were collected from cornea donors post-mortem within 48 hr after death. An internal control was added to the samples before extraction to monitor each individual polymerase chain reaction (PCR). The nucleic acid tests were always interpretable in organ donors and negative in all except in 2 anti-HCV positive patients. One had an indeterminate HIV p24 antigen but was negative for HIV RNA. HIV and HCV RNA were not found in cornea donors with a negative serology but indeterminate molecular results were frequent in this group (17.6%). Cornea donors also gave significantly more (14.4%) indeterminate serological results than organ donors (1.8%) (P

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. Images Figure 1

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.

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.

Background It is important to diagnose a hepatitis C virus infection in the acute phase in order to reduce the incidence of this infection in high-risk populations like haemodialysis patients. But detection systems for serum HCV antibodies are insensitive in the acute phase because of the long serological window. Previous studies showed that the HCV core antigen (HCV Ag) may be an alternative to HCV RNA in this context. Objectives To evaluate the performances of the new Abbott ARCHITECT® HCV Ag test and its usefulness in screening for HCV infections in haemodialysis patients. Study design The serum HCV Ag titre was compared to the HCV RNA viral load in 98 samples from HCV-infected patients to determine the correlation between the two markers and the influence of genotype. We screened 2752 patients from 37 French haemodialysis units who tested negative for HCV antibodies using the HCV Ag and RNA assays. Results The HCV Ag titre was correlated with the HCV RNA (Spearman test coefficient 0.9041, p

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.

Background Due to their high prevalence, hepatitis B virus (HBV) and hepatitis C virus (HCV) infections need accurate and rapid diagnosis tools. Objectives Technical performances of the UniCel DxI 800 analyser (Beckman Coulter) and a comparison with the Vitros ECi (Ortho Clinical Diagnostics) were performed for five serological markers: HBsAg, total anti-HBc, anti-HBc IgM, anti-HBs and anti-HCV. Study design Reproducibility was determined by repeated tests on the manufacturers’ controls. The performance of the UniCel DxI 800 was assessed by testing negative and positive samples previously analysed with the Vitros ECi. The accuracy and linearity of anti-HBs assay were evaluated using the WHO international standard (W1042). Results The intra-assay and inter-assay coefficients of variation were: 0.8% and 4.4% for HBsAg, 2.4% and 6.2% for anti-HBc, 5% and 8.7% for anti-HBc IgM, 2.1% and 5.1% for anti-HBs and 3.7% and 7.4% for anti-HCV. The two methods were concordant: 100% agreement for the five markers except for the negative HBsAg sera (99%). The anti-HBs results correlated well with the Vitros ECi (r = 0.925 with p Conclusion The high throughput, specificity and sensitivity make UniCel DxI 800 assays useful for routine diagnoses of HCV and HBV infections.

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.

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. © 1999 Cancer Research Campaign

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. Prostate 34:23–28, 1998. © 1998 Wiley-Liss, Inc.