A retrospective analysis of the application of the Elecsys® HIV combi PT assay in southern China.

BACKGROUND: Fourth-generation HIV assays have been implemented worldwide as a screening test for many years. Understanding the performance of fourth-generation assay in low HIV prevalence region is pivotal to interpret the test result correctly. In this study, retrospective analysis was used to evaluate application of the Elecsys® HIV combi PT assay. METHODS: A total of 85 043 specimens from a low prevalence setting were detected between June 2013 and October 2015. We evaluated the false-positive rate (FPR), specificity, and positive predictive value (PPV). RESULTS: The specificity between male and female were 99.85% and 99.82%, respectively. The PPV on male (50.75%) was higher than female (17.05%) significantly, while the FPR was 0.15% and 0.18%. The gap between false-positive (median: 1.83, [IQR]: 1.30, 3.38) and confirmed-positive (median: 407.5, [IQR]: 184.2, 871.7) is enormous. The highest s/co ratio for false-positive cases was 85.45, while the lowest s/co ratio for confirmed-positive cases was 59.68. Various reasons were attributed to false-positive cases. CONCLUSION: Optimal cutoff value is needed to be set to reduce the false-positive cases and predict the final status of HIV infection reliably. Retrospective analysis will help us to understand more about diagnosis of HIV.

Can Analysis of Routine Viral Testing Provide Accurate Estimates of Respiratory Syncytial Virus Disease Burden in Adults?

Respiratory syncytial virus (RSV) is increasingly recognized as a significant cause of adult respiratory illness. We evaluated routine viral testing and discharge diagnoses for identifying RSV and influenza burden. Polymerase chain reaction results performed in adults during emergency room visits or hospitalizations were reviewed. Peak RSV activity preceded influenza activity by 8 weeks. The ratio of total number of viral tests performed divided by total number of respiratory visits was higher during influenza than RSV peaks (1.31 vs 0.72; P = .0001). Influenza and RSV were listed primary diagnoses in 56 (30%) vs 7 (6%), respectively (P < .0001). Routine viral testing to estimate adult RSV disease burden has limitations.

Should We Be Testing for Baseline Integrase Resistance in Patients Newly Diagnosed With Human Immunodeficiency Virus?

Background: Current guidelines recommend genotype resistance testing at diagnosis to guide initial selection of antiretroviral therapy (ART). Many standard resistance genotypes exclude testing for resistance to integrase inhibitors ("IR testing"), although this class of drugs is a component of most recommended first-line regimens. Methods: We compared the 96-week clinical outcomes and cost-effectiveness of 2 strategies: no IR testing vs IR testing performed at human immunodeficiency virus (HIV) diagnosis. The base case prevalence of transmitted integrase strand transfer inhibitor (INSTI)-resistant (INSTI-R) virus is estimated at 0.1%. With no IR testing, all patients start dolutegravir (DTG)-based ART after genotype; 12-week suppression rates are 90% (INSTI-susceptible [INSTI-S] virus) and 35% (INSTI-R virus). Those not suppressed at 12 weeks undergo IR testing; if diagnosed with INSTI-R virus, they change to ritonavir-boosted darunavir (DRV/r)-based ART. With IR testing, all patients are diagnosed with INSTI-S/INSTI-R virus prior to ART initiation and start DTG- or DRV/r-based regimens, respectively. Costs include IR tests (175 US dollars [USD]) and ART (41100-44900 USD/year). We examined the impact of key parameters in sensitivity analyses. Results: IR testing resulted in worse clinical outcomes compared to no IR testing and increased costs by 200 USD/person/year. Prevalence of transmitted INSTI-R virus did not affect the favored strategy. No IR testing remained clinically preferred unless DTG suppression of INSTI-R virus was <20% or 96-week DRV/r suppression was >92%. If quality of life was worse with DRV/r- than DTG-based ART, no IR testing was clinically preferred over an even broader range of parameters. Conclusions: In patients with newly diagnosed HIV, IR testing is projected to result in worse outcomes and is not cost-effective. Pretreatment assessment for INSTI resistance should not be recommended in treatment guidelines.

Categorical data analysis in experimental biology.

The categorical data set is an important data class in experimental biology and contains data separable into several mutually exclusive categories. Unlike measurement of a continuous variable, categorical data cannot be analyzed with methods such as the Student's t-test. Thus, these data require a different method of analysis to aid in interpretation. In this article, we will review issues related to categorical data, such as how to plot them in a graph, how to integrate results from different experiments, how to calculate the error bar/region, and how to perform significance tests. In addition, we illustrate analysis of categorical data using experimental results from developmental biology and virology studies.

Survey of diagnostic services for genital herpes in fourteen countries in Eastern Europe.

This paper reports survey-based data on the diagnosis and management of genital herpes simplex virus (HSV) infection in 14 countries of the Eastern European Network for Sexual and Reproductive Health (EE SRH). Only 43% of the countries could provide the number of genital HSV cases recorded at national level. Eighty-six percent of countries employed syndromic management in cases of genital ulcer disease. Most countries performed type-specific and/or non-type-specific enzyme immunoassays to detect HSV antibodies. Non-type-specific serology for diagnostic purposes should be actively discouraged. Direct detection methods for HSV, such as PCR, antigen detection and culture, are available in the region, but their usage was extremely low. Their use in Eastern European countries should be actively promoted. The availability of laboratory services must be improved, and countries in the region should implement consensus recommendations for the laboratory diagnosis of genital HSV infections in order to improve clinical practice.

Completion of national laboratory inventories for wild poliovirus containment --- region of the Americas, March 2010.

In May 1988, the World Health Assembly resolved to eradicate wild poliovirus (WPV) transmission globally. By 2006, transmission of indigenous WPV was eliminated in all but four countries (Afghanistan, India, Nigeria, and Pakistan). In May 1999, the World Health Assembly urged member states to begin the process leading to laboratory containment of WPV. Containment of infectious and potentially infectious WPV materials after eradication is essential to minimize the risk for reintroducing WPV into poliomyelitis-free communities. The staged containment approach begins with a national survey of all biomedical facilities, which alerts facilities to the need for containment, encourages reduction of WPV materials, and develops a national inventory of facilities holding such materials (Phase I). In May 2008, the World Health Assembly reiterated the need for progress in containment and urged polio-free states to complete Phase I. This report describes completion of Phase I by the countries and territories in the World Health Organization (WHO) Region of the Americas during 2001-2010. Of 67,362 biomedical facilities, all 15,541 (23.1%) that were classified as high-risk or medium-risk facilities were surveyed. Of the remaining 51,821 (76.9%) facilities, all classified as low-risk, 44,077 (85.1%) were surveyed; sampling ranged from 12.8% to 100% among countries. After voluntary destruction of some materials during Phase I, a total of 215 facilities in nine countries of the Region of the Americas reported retaining WPV materials as of March 2010. The survey provides a facility registry for use in subsequent steps that will lead to global poliovirus containment.

Effect of Antiviral Therapy on the Outcome of Mechanically Ventilated Patients With Herpes Simplex Virus Type 1 in BAL Fluid: A Retrospective Cohort Study.

BACKGROUND: Herpes simplex virus type 1 (HSV-1) is frequently detected in the BAL fluid of patients on mechanical ventilation. RESEARCH QUESTION: The aim of the study was to investigate whether antiviral therapy is associated with improved overall survival within 30 days. STUDY DESIGN AND METHODS: This was a retrospective cohort study in four ICUs between January 2011 and December 2017. All adult patients on mechanical ventilation with a respiratory tract infection with positive polymerase chain reaction testing for HSV-1 in the BAL were included. Patients already receiving antiviral agents on the day BAL was performed were excluded. We performed uni- and multivariable Cox and logistic regression modeling. RESULTS: Overall, 306 patients were included in the analysis. Among them, 177 patients (57.8%) received antiviral therapy (90.9% acyclovir, 6.2% ganciclovir, 2.9% both). The overall 30-day mortality rate was 42.4% (n = 75) in the antiviral treatment group and 50.4% (n = 65) in the control group. The adjusted hazard ratio (HR) for the primary outcome was 0.62 (95% CI, 0.44-0.87; P = .005), indicating better overall survival within 30 days for the antiviral-treated group than for the untreated group. This benefit was also present in the subgroup of patients without immunosuppression (n = 246; adjusted HR, 0.53; 95% CI, 0.36-0.78; P = .001). Overall, the median lengths of hospital stay (31 vs 24 days, P = .002) and ICU stay (24 vs 17 days, P < .001), and the duration of mechanical ventilation (18 vs 11 days, P < .001), were longer for patients with therapy. No evidence for the treatment-related deterioration of renal function was observed. INTERPRETATION: These data suggest that detection of HSV-1 in the BAL of patients on mechanical ventilation may be of clinical significance and that specific antiviral treatment may improve clinical outcomes. However, this needs to be proven in multicenter randomized controlled trials before implementation into the clinical routine.

National laboratory inventories for wild poliovirus containment--Western Pacific region, 2008.

In the future, when wild poliovirus (WPV) transmission is interrupted worldwide, facilities holding WPV materials will represent the only remaining repository of the virus. Maintaining the number of such facilities at a minimum and at an appropriate biosafety standard (laboratory containment) reduces the risk for a facility-associated reintroduction of WPV. In May 1999, the World Health Assembly (WHA) urged all member states to begin the process leading to laboratory containment of WPV. The World Health Organization (WHO) global action plan for laboratory containment of WPV issued in 1999 indicated a staged approach that begins with a national survey of all biomedical facilities (Phase I); the purpose of the survey is to alert institutions and facilities to the need for containment, encourage reduction of WPV materials, and develop a national inventory of facilities holding such materials. The survey and inventory provide a facility database for use in all subsequent steps toward global poliovirus containment. In May 2008, WHA urged all WHO member states to complete Phase I activities outlined in the WHO Global Action Plan for Laboratory Containment of Wild Polioviruses. In the WHO Western Pacific Region (WPR), Phase I surveys of 77,260 laboratories in the 37 countries and areas of WPR were conducted during 1999--2008. A total of 45 laboratories were identified as holding WPV materials in 2008. This report describes completion of Phase I containment activities by WPR countries, and updates a previous report on Phase I completion in the European Region and global progress.

International standard reagents for HPV detection.

Human papillomavirus is the commonest genital viral infection in healthy sexually active subjects, and the presence of chronic or persistent HPV types in genital cells may constitute a prognostic marker of underlying, or predict future HPV-associated diseases. A variety of novel tests for detecting the presence of oncogenic HPV types in biological specimens have been reported. These are based on the various stages of infection and viral life cycle. HPV infects squamous epithelium with expression of various gene products intimately linked to epithelial cell differentiation. Hence, there are basically three classes of detectable markers directly derived from HPVs: molecular markers based on detection of nucleic acid sequences, serological markers based on detection of antibodies against viral proteins, and cellular markers based on detection of proteins expressed intracellularly, upon either infection or carcinogenesis. The nature of various assays and the development of international standard reagents for qualitative and quantitative assessment of assay performance are outlined. There is an increasing demand to develop standard tools to assess the quality of HPV detection systems, for regulatory and clinical management purposes. International standard reagents for HPV will help defining the analytical sensitivity and specificity of various detection methods, and will allow assuring that laboratory services used to evaluate disease burden, HPV vaccines, and cancer prevention strategies are accurate and comparable worldwide. The advancement of prophylactic vaccine candidates against HPV infections and related diseases stresses the increasing importance of HPV assays in monitoring the impact of HPV vaccination on disease burden.

HPV detection methods.

Given the causal relation between a persistent high-risk human papillomavirus (hrHPV) infection and the development of high-grade cervical intraepithelial neoplasia (CIN) and cervical cancer, hrHPV testing has been advocated in addition to cytology for the detection of clinically relevant cervical lesions. HrHPV testing is thought to improve cervical screening algorithms, the management of women with cytologically equivocal smears, and the management of women treated for high grade CIN. In this chapter we discuss different methods for HPV detection and genotyping and their respective applications.

Diagnostic virology practices for respiratory syncytial virus and influenza virus among children in the hospital setting: a national survey.

A survey was sent to the emergency room and laboratory directors of 400 randomly selected US hospitals to assess the diagnostic testing practices for respiratory syncytial virus and influenza virus in children. The results demonstrate that the majority of hospitals routinely perform viral testing for both viruses and use virology testing practices appropriate for the reasons reported for testing.

The analysis and regulation for the dynamics of a temperate bacteriophage model.

The purpose of this paper is to study the asymptotical behavior of a temperate bacteriophage model in chemostat, which was first proposed by Levin et al. [B.R. Levin, F.M. Stewart, L. Chao, Resource-limited growth, competition and predation: A model and experiment studies with bacteria and bacteriophage, Am. Nat. 125 (1977) 3]. Firstly, a classification for the equilibria of the model and their stability are obtained; secondly, sufficient conditions for uniform persistence are obtained; thirdly, sufficient conditions for the global asymptotic behavior are given, and simulations for the model are presented. The theoretical results show that there are more than eight cases for the classification of the model, and that the decrease (increase) of the nutrient concentration or average lytic time (flow rate) is beneficial to the survival of the sensitive cells. Both the simulated and theoretical results show that there is a possibility of switch phenomena or a periodical outburst of the phages and the lysogens, which is caused by the internal factors rather than by some external environment. Finally, the simulation and regulation of the dynamics of the model with experimental data are presented.

Factors influencing the virological testing of cornea donors.

To assess the influence of donor, environment, and logistical factors on the results of virological testing of blood samples from cornea donors.Data from 670 consecutive cornea donors were analyzed retrospectively. Logistic regression analysis was used to assess the influence of different factors on the results of virological testing of blood samples from cornea donors.The mean annual rate of donors with serology-reactive or not evaluable result was 14.8% (99 of 670) (range 11.9%-16.9%). The cause of donor death by cancer increased the risk of serology-reactive or not evaluable result (P = .0300). Prolonged time between death and post mortem blood removal was associated with a higher rate of serology-reactive or not evaluable result (P < .0001). Mean monthly temperature including warmer months, differentiating between septic and aseptic donors, sex, and donor age had no significant impact on the results of virological testing of blood samples from cornea donors.The cause of donor death by cancer and a prolonged time between death and post mortem blood removal seem to be mainly responsible for serology-reactive or not evaluable result of blood samples from cornea donors. The percentage of discarded corneas caused by serology-reactive or not evaluable result may be reduced by shortening the period of time between death and post mortem blood removal.

National laboratory inventory for global poliovirus containment--European Region, June 2006.

In May 1999, the World Health Assembly reaffirmed the commitment of the World Health Organization (WHO) to eradicate poliomyelitis and urged all member states to begin the process leading to the laboratory containment of wild poliovirus (WPV). The WHO global action plan for laboratory containment of WPV begins with a survey of all biomedical facilities (Phase I). The purpose of the survey is to alert institutions and facilities to the need for containment, encourage reduction of WPV materials, and develop a national inventory of facilities holding such materials. The objective of Phase I is to provide a facility database for use in all subsequent steps toward global poliovirus containment. This report describes completion of Phase I containment by the European Region, the first of the six WHO regions to accomplish this goal.

Clinical performance of the LCx HCV RNA quantitative assay.

This study was conducted to assess the performance of the Abbott laboratories LCx HCV RNA Quantitative Assay (LCx assay) in the clinical setting. Four clinical laboratories measured LCx assay precision, specificity, and linearity. In addition, a method comparison was conducted between the LCx assay and the Roche HCV Amplicor Monitor, version 2.0 (Roche Monitor 2.0) and the Bayer VERSANT HCV RNA 3.0 Assay (Bayer bDNA 3.0) quantitative assays. For precision, the observed LCx assay intra-assay standard deviation (S.D.) was 0.060-0.117 log IU/ml, the inter-assay S.D. was 0.083-0.133 log IU/ml, the inter-lot S.D. was 0.105-0.177 log IU/ml, the inter-site S.D. was 0.099-0.190 log IU/ml, and the total S.D. was 0.113-0.190 log IU/ml. The specificity of the LCx assay was 99.4% (542/545; 95% CI, 98.4-99.9%). For linearity, the mean pooled LCx assay results were linear (r=0.994) over the range of the panel (2.54-5.15 log IU/ml). A method comparison demonstrated a correlation coefficient of 0.881 between the LCx assay and Roche Monitor 2.0, 0.872 between the LCx assay and Bayer bDNA 3.0, and 0.870 between Roche Monitor 2.0 and Bayer bDNA 3.0. The mean LCx assay result was 0.04 log IU/ml (95% CI, -0.08, 0.01) lower than the mean Roche Monitor 2.0 result, but 0.57 log IU/ml (95% CI, 0.53, 0.61) higher than the mean Bayer bDNA 3.0 result. The mean Roche Monitor 2.0 result was 0.60 log IU/ml (95% CI, 0.56, 0.65) higher than the mean Bayer bDNA 3.0 result. The LCx assay quantitated genotypes 1-4 with statistical equivalency. The vast majority (98.9%, 278/281) of paired LCx assay-Roche Monitor 2.0 specimen results were within 1 log IU/ml. Similarly, 86.6% (240/277) of paired LCx assay and Bayer bDNA 3.0 specimen results were within 1 log, as were 85.6% (237/277) of paired Roche Monitor 2.0 and Bayer specimen results. These data demonstrate that the LCx assay may be used for quantitation of HCV RNA in HCV-infected individuals.

Commercial immunoassay kits for the detection of influenza virus type A: evaluation of their use with poultry.

Five antigen capture immunoassay test kits, Directigen Flu A (Becton Dickinson), QuickVue Influenza test kit (Quidel), FLU OIA (ThermoBiostar), Zstat Flu (ZymeTx, Inc.) and NOW FLU A Test (Binax) were used to detect avian influenza virus (AIV) in clinical specimens as per manufacturers' protocols. Each kit was shown to be specific for AIV propagated in embryonating chicken eggs (ECE); other respiratory viruses of poultry tested gave negative results. The Directigen Flu A kit proved to be 10-fold more sensitive than the other kits, capable of detecting 10(4.7) mean embryo lethal dose (ELD50)/ml in allantoic fluid; this is more sensitive than the hemagglutination test using chicken erythrocytes. None of the kits proved to be sufficiently sensitive to reliably detect AIV in oropharyngeal and cloacal swabs collected from chickens experimentally infected with AIV subtype H6N2. In two different experiments, individual swabs and pools of five or six swabs were tested. By virus isolation, 39 individual oropharyngeal swabs tested positive for AIV, but Directigen and Flu OIA only detected 2/39 and NOW FLU A 1/39. Zstat and QuickVue did not detect any. Five individual cloacal swabs positive by virus isolation were negative with all five kits. In a second experiment using pools of five swabs, 26 swab pools were positive by virus isolation and 5/26 were positive by Directigen, the only kit to provide any positive results. Five cloacal swab pools were also positive by virus isolation and 1/5 was positive by Directigen; all other test kits were negative. All of these experiments were performed using the H6N2 subtype of AIV. The results are disappointing, as the kits have proven to be insensitive for detecting AIV when compared with the gold standard, virus isolation. This limits their use in diagnostic field investigations. Individual or groups of chickens could be assumed to be positive for AIV if positive by any of the kits, but a negative result with any of the kits would not prove that birds were AIV free.

Qualitative and quantitative detection of HIV-1 RNA by nucleic acid sequence-based amplification.

AIM: To develop a method to detect HIV-1 viral RNA by amplifying a specific nucleic acid sequence. METHOD: The nucleic acid sequence-based amplification (NASBA) method uses the simultaneous activity of avian myeloblastosis virus reverse transcriptase, T7 RNA polymerase and RNase H to amplify a specific nucleic acid target sequence. VALIDATION: An in vitro cultured HIV-1 stock solution was used to validate the NASBA method and determine the variation in RNA measurement. CONCLUSION: Although NASBA is theoretically capable of specific amplification of RNA or DNA, it is most suitable for amplification of RNA, and therefore for detection of HIV-1 viral RNA.

Direct and quantitative detection of HIV-1 RNA in human plasma with a branched DNA signal amplification assay.

AIM: To determine the relative effect of sample matrix on the quantitation of HIV RNA in plasma. METHOD: Two HIV-positive specimens were diluted into five and 10 different HIV-negative plasma samples, respectively. Branched DNA signal amplification technology and reverse-transcriptase polymerase chain reaction were used to measure the viral load. RESULTS: In one sample the viral load by polymerase chain reaction ranged from undetectable to 1.9 x 10(5) copies/ml, and the branched DNA results ranged from 2.6 x 10(4) to 4.2 x 10(4) HIV RNA equivalent/ml. In the other sample the corresponding figures were 6.3 x 10(4) to 5.5 x 10(5) copies/ml and 5.7 x 10(4) to 7.5 x 10(4) HIV RNA equivalents/ml. CONCLUSION: In contrast to reverse-transcriptase polymerase chain reaction the branched DNA signal amplification assay does not require a separate extraction step or enzymatic amplification of the target. Therefore this measurement is less affected by the sample matrix and the signal generated is directly proportional to the viral load.

Global progress toward laboratory containment of wild polioviruses--July 2001-August 2002.

Since the World Health Assembly launched the Global Poliomyelitis Eradication Initiative in 1988 (see box), the number of countries in which wild poliovirus is endemic has decreased from 125 to 10 in 2001. Three of the six World Health Organization (WHO) regions (Americas, European, and Western Pacific) have been certified as free of wild poliovirus transmission. The Global Commission for the Certification of the Eradication of Poliomyelitis will declare the world polio-free when all regions have documented the absence of wild poliovirus transmission for at least 3 consecutive years and when laboratories with wild poliovirus-containing materials have implemented appropriate containment conditions. This report describes preparations for laboratory containment and the creation of a global inventory of laboratories and institutions retaining wild poliovirus and summarizes global progress since July 2001. The data indicate that substantial progress has been made in identifying laboratories with wild poliovirus-containing materials and in conducting national wild poliovirus inventories.

Viral bioinformatics: computational views of host and pathogen.

Wherever cellular life occurs, viruses are also found. As a result, complex organism and cellular antiviral responses co-evolve with virally encoded countermeasures. Since viruses co-opt or interfere with specific cellular pathways during their replication, knowledge of viral genome sequences has helped fundamental understanding of host biology. During viral infection, shifts in the balance between host and viral biological processes result in acute or chronic viral disease pathology accompanied with either active viral replication, viral containment/persistence or viral clearance. Studying host-virus interactions at the level of single gene effects, however, fails to produce a global systems-level understanding. This should now be achievable in the context of complete host and pathogen genome sequences. New experimental methods and computational approaches are rapidly developing, allowing global views of dynamic viral and cellular molecular mechanisms. Systems level virology using DNA microarrays and specific viral data resources will reveal the detailed cellular context in which viruses replicate, highlighting common and distinct antiviral mechanisms, the effect of different host cell gene expression programs, and the response of cells to similar or diverse virus types. Ultimately, microbiology and immunology will tend towards a systems-level view of how host and pathogen interact.