Number, type and cost of microbiological tests during HIV Pre-Exposure Prophylaxis: The experience of a French hospital.

BACKGROUND: Microbiological tests are required for individuals on HIV Pre-Exposure Prophylaxis (PrEP), but their real-life numbers, types and cost are poorly described. METHODS: Number, type, and results of microbiological tests performed in a Besançon Hospital-associated laboratory, France, from 2016 to 2019, in the setting of PrEP consultations were retrospectively collected. Costs were estimated by the current reimbursement rate set by the French national protection system. RESULTS: 756 consultations for PrEP initiation or follow-up of 135 persons were performed over 4 years. Among 3434 tests performed in the institution-associated laboratory, 1083 and 2351 were virological and bacteriological tests, respectively. Serology was predominant in virology (98% of virological tests), with HIV, HCV, and HBV screening as the 3 more frequent assays, whereas molecular biology was predominant in bacteriology (63.1% of bacteriological tests) with N. gonorrhoeae and C. trachomatis screening as leader assays. Agar-based culture accounted for 1% of bacterial tests. The global cost of microbiological tests was 45,983.20 euros, corresponding to a mean cost of 60.80 euros per consultation. Virological and bacteriological tests accounted for 37.7% and 62.3% of this budget, respectively. No seroconversion was observed for HIV or HCV. N. gonorrhoeae and C. trachomatis were detected at least once in 39.3% and 22.4% of individuals, respectively, with 15% of symptomatic episodes in both cases. Active syphilis infection was detected in 15.4% of individuals. CONCLUSIONS: Since numerous microbiological tests are required during PrEP, the availability of specific technical platforms should not be neglected by centers wishing to set up PrEP consultations.

Laboratory diagnosis of COVID-19 in Africa: availability, challenges and implications.

The COVID-19 infection has been a matter of urgency to tackle around the world today, there exist 200 countries around the world and 54 countries in Africa that the COVID-19 infection cases have been confirmed. This situation prompted us to look into the challenges African laboratories are facing in the diagnosis of novel COVID-19 infection. A limited supply of essential laboratory equipment and test kits are some of the challenges faced in combatting the novel virus in Africa. Also, there is inadequate skilled personnel, which might pose a significant danger in case there is a surge in COVID-19 infection cases. The choice of diagnostic method in Africa is limited as there are only two available diagnostic methods being used out of the six methods used globally, thereby reducing the opportunity of supplementary diagnosis, which will further lead to inappropriate diagnosis and affect the accuracy of diagnostic reports. Furthermore, challenges like inadequate power supply, the method used in sample collection, storage and transportation of specimens are also significant as they also pose their respective implication. From the observations, there is an urgent need for more investment into the laboratories for proper, timely, and accurate diagnosis of COVID-19.

A Simple and Cost-Effective DNA Preparation Method Suitable for High-Throughput PCR Quantification of Hepatitis B Virus Genomes.

Hepatitis B virus (HBV) is a para-retrovirus that reverse transcribes its pregenomic RNA into relaxed circular DNA inside viral nucleocapsids. The number of HBV genomes produced in vitro is typically quantified using commercial silica-membrane-based nucleic acid purification kits to isolate total DNA followed by HBV-specific quantitative PCR (qPCR). However, despite the convenience of commercial kits, this procedure is costly and time-consuming due to multiple centrifugation steps, which produce unnecessary waste. Here, we report a rapid, cost-effective, and environmentally friendly total DNA preparation method. The assay is based on the simple incubation of detergent and proteinase K with cells or cell-free supernatants to permeabilize cells and disrupt viral particles. After heat inactivation and subsequent centrifugation to clear the lysates, DNA samples are directly subjected to qPCR to quantify HBV genomes. As a proof of concept, the assay was developed in 12-well plates to assess intra- and extracellular HBV genome equivalents (GEqs) of stably viral-replicating cell lines (e.g., HepAD38) and HBV-infected HepG2-NTCP cells, both treated with lamivudine (LMV), an HBV replication inhibitor. Viral DNA was also prepared from the serum of patients chronically infected with HBV. To validate the assay, a representative commercial DNA isolation kit was used side-by-side to isolate intra- and extracellular HBV DNA. Both methods yielded comparable amounts of HBV GEqs with comparable LMV 50% efficient concentration (EC50) values. The assay was subsequently adapted to 96- and 384-well microtiter plates using HepAD38 cells. The EC50 values were comparable to those obtained in 12-well plates. In addition, the calculated coefficient of variation, Z' values, and assay window demonstrated high reproducibility and quality. We devised a novel, robust, reproducible, high-throughput microtiter plate DNA preparation method suitable for quantifying HBV GEqs by qPCR analysis. This strategy enables rapid and convenient quantitative analysis of multiple viral DNA samples in parallel to investigate intracellular HBV replication and the secretion of DNA-containing viral particles.

Virology Tests in Brain-Dead Donors: Let the Bills Run Up?

OBJECTIVES: In the organ donation process, screening for serologic markers for a selection of agents is essential to prevent infection transmission. The screening of donors for specific potential infections can never absolutely exclude the risk of transmission. For reevaluation of serology tests, we analyzed results of tests requested for all brain-dead donors. MATERIALS AND METHODS: Our study included all actual brain-dead donors who were seen from January 2017 to February 2018, received ancillary tests, and had final confirmation of brain death at our organ procurement unit. RESULTS: Most candidates for organ and tissue donation were seronegative for intended agents. We found that 14.4% of the samples were suspicious for infectious and needed further evaluation; 12.2% of donors had positive results corresponding to hepatitis B, and only 1.9% were rejected from donation. Requisiteness to DNA detection for hepatitis B virus infection was mainly related to age over 50 years. CONCLUSIONS: The process of donor screening must systemically assess the donor. At the final stage, essential biomarkers must be investigated. Application of more caution in evaluation of older donors, including more screening tests before transfer to the operating room, remains mandatory.

Simple drop cast method for enumeration of bacteriophages.

Phage enumeration is a basic prerequisite for application of phages in industrial, medical and other processes. Double layer agar (DLA) plaque assay is the classical method employed for isolation, detection as well as enumeration of phage particles in a solution. However, DLA method is considered cumbersome due to its specific temperature requirements and need for one petriplate with two agar layers for each phage sample. We are proposing a drop cast method for enumeration of phages which is comparatively easier and cost effective than classical DLA method as single layer of agar without any specific temperature condition is required. Added advantage of this method is that 7-10 dilutions of phage suspension can be enumerated on a single agar plate in contrast to one dilution per plate as required in DLA method. Although standard deviation in phage count was higher in the proposed method than DLA method, still drop cast method provided first-approximation phage titer which can be further validated by DLA method for more accuracy. Hence, the present method can be considered reliable, easy and cost effective for determining approximate phage count in an unknown phage suspension.

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.

Assessment of a New Lower-Cost Real-Time PCR Assay for Detection of High-Risk Human Papillomavirus: Useful for Cervical Screening in Limited-Resource Settings?

Inexpensive and easy-to-perform human papillomavirus (HPV) tests are needed for primary cervical cancer screening in lower-resource regions. In a convenience sample of 516 residual exfoliative cervical specimens from the Kaiser Permanente Northern California and U.S. National Cancer Institute Persistence and Progression Study, we assessed the agreement and clinical performance of a simple, inexpensive real-time PCR assay for the detection of 13 carcinogenic HPV types (the H13 assay; Hybribio, Hong Kong) that is marketed in limited-resource settings compared to previous testing by the Hybrid Capture 2 assay (HC2; Qiagen, Germantown, MD) and the Onclarity assay (BD Diagnostics, Sparks, MD). The test set was chosen to include many HPV-positive specimens. The reference standard was a combination of HC2 and Onclarity results for HPV detection and histologic diagnosis of controls (less than cervical intraepithelial neoplasia grade 2 [

A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses.

BACKGROUND: Next-generation sequencing (NGS) allows ultra-deep sequencing of nucleic acids. The use of sequence-independent amplification of viral nucleic acids without utilization of target-specific primers provides advantages over traditional sequencing methods and allows detection of unsuspected variants and co-infecting agents. However, NGS is not widely used for small RNA viruses because of incorrectly perceived cost estimates and inefficient utilization of freely available bioinformatics tools. METHODS: In this study, we have utilized NGS-based random sequencing of total RNA combined with barcode multiplexing of libraries to quickly, effectively and simultaneously characterize the genomic sequences of multiple avian paramyxoviruses. Thirty libraries were prepared from diagnostic samples amplified in allantoic fluids and their total RNAs were sequenced in a single flow cell on an Illumina MiSeq instrument. After digital normalization, data were assembled using the MIRA assembler within a customized workflow on the Galaxy platform. RESULTS: Twenty-eight avian paramyxovirus 1 (APMV-1), one APMV-13, four avian influenza and two infectious bronchitis virus complete or nearly complete genome sequences were obtained from the single run. The 29 avian paramyxovirus genomes displayed 99.6% mean coverage based on bases with Phred quality scores of 30 or more. The lower and upper quartiles of sample median depth per position for those 29 samples were 2984 and 6894, respectively, indicating coverage across samples sufficient for deep variant analysis. Sample processing and library preparation took approximately 25-30 h, the sequencing run took 39 h, and processing through the Galaxy workflow took approximately 2-3 h. The cost of all steps, excluding labor, was estimated to be 106 USD per sample. CONCLUSIONS: This work describes an efficient multiplexing NGS approach, a detailed analysis workflow, and customized tools for the characterization of the genomes of RNA viruses. The combination of multiplexing NGS technology with the Galaxy workflow platform resulted in a fast, user-friendly, and cost-efficient protocol for the simultaneous characterization of multiple full-length viral genomes. Twenty-nine full-length or near-full-length APMV genomes with a high median depth were successfully sequenced out of 30 samples. The applied de novo assembly approach also allowed identification of mixed viral populations in some of the samples.

The cost-effectiveness of testing for NS5a resistance-associated polymorphisms at baseline in genotype 1a-infected (treatment-naïve and treatment-experienced) subjects treated with all-oral elbasvir/grazoprevir regimens in the United States.

BACKGROUND: The presence of baseline NS5A resistance-associated variants (RAVs) impacted treatment response in HCV genotype 1a (GT1a)-infected patients treated with elbasvir/grazoprevir (EBR/GZR) for 12 weeks, but not patients treated with EBR/GZR and ribavirin (RBV) for 16 weeks. AIMS: To assess the cost-effectiveness of baseline testing for NS5A RAVs in EBR/GZR-treated patients compared without testing, and with current treatments for GT1a patients. METHODS: We simulated the course of treatment with EBR/GZR, ledipasvir/sofosbuvir (LDV/SOF) and ombitasvir/paritaprevir/ritonavir+dasabuvir (3D) with or without RBV and natural history of disease of GT1a patients. Treatment-related data from clinical trials were used in a state-transition model of the natural history of chronic HCV GT1a infection and liver disease to project lifetime costs (US$2015) and quality-adjusted life years (QALY). Other clinical and economic inputs were estimated from published sources. We conducted base case and sensitivity analyses. RESULTS: RAVs testing-guided treatment with EBR/GZR resulted in more QALYs than EBR/GZR without testing, 3D+RBV, or LDV/SOF8. This strategy was cost-saving relative to 3D+RBV or LDV/SOF8 and was cost-effective compared with EBR/GZR without testing. LDV/SOF12 was not cost-effective compared with the EBR/GZR RAVs testing-based strategy. Treatment with EBR/GZR guided by RAVs testing is the most effective regimen among treatment-experienced patients without cirrhosis and cirrhotic patients. In sensitivity analysis, RAVs testing was cost-effective in 48-55% and 63-85% among noncirrhotic and cirrhotic patients respectively. CONCLUSIONS: RAVs testing before treatment with EBR/GZR is likely to be a cost-effective alternative to the use of EBR/GZR without testing, LDV/SOF, or 3D among GT1a treatment-naïve or treatment-experienced patients.

Simple and efficient ultrafiltration method for purification of rotavirus VP6 oligomeric proteins.

Bacterial endotoxins, DNA, live viruses, and viral proteins derived from bacterial and baculovirus (BV) expression vectors employed in recombinant protein production contaminate the final product. Density gradient centrifugation is commonly used to partially purify oligomeric proteins, but impurities from the expression system still remain. We describe a simple and rapid ultrafiltration method for final purification of rotavirus VP6 oligomeric nanotubes and nanospheres. Contamination originating from the BV vector used in VP6 production was undetectable. The method is highly efficient, fast and inexpensive and can be used for a small-scale laboratory purification of VP6 protein to replace technically demanding multi-step chromatographic procedures.

Cost-Effectiveness Analysis of Different Management Strategies for Detection CIN2+ of Women with Atypical Squamous Cells of Undetermined Significance (ASC-US) Pap Smear in Thailand.

BACKGROUND: To identify the optimal cost effective strategy for the management of women having ASC-US who attended at King Chulalongkorn Memorial Hospital (KMCH). DESIGN: An Economical Analysis based on a retrospective study. SUBJECT: The women who were referred to the gynecological department due to screening result of ASC-US at King Chulalongkorn Memorial Hospital, a general and tertiary referral center in Bangkok Thailand, from Jan 2008 - Dec 2012. MATERIALS AND METHODS: A decision tree-based was constructed to evaluate the cost effectiveness of three follow up strategies in the management of ASC-US results: repeat cytology, triage with HPV testing and immediate colposcopy. Each ASC-US woman made the decision of each strategy after receiving all details about this algorithm, advantages and disadvantages of each strategy from a doctor. The model compared the incremental costs per case of high-grade cervical intraepithelial neoplasia (CIN2+) detected as measured by incremental cost-effectiveness ratio (ICER). RESULTS: From the provider's perspective, immediate colposcopy is the least costly strategy and also the most effective option among the three follow up strategies. Compared with HPV triage, repeat cytology triage is less costly than HPV triage, whereas the latter provides a more effective option at an incremental cost-effectiveness ratio (ICER) of 56,048 Baht per additional case of CIN 2+ detected. From the patient's perspective, the least costly and least effective is repeat cytology triage. Repeat colposcopy has an incremental cost-effectiveness (ICER) of 2,500 Baht per additional case of CIN2+ detected when compared to colposcopy. From the sensitivity analysis, immediate colposcopy triage is no longer cost effective when the cost exceeds 2,250 Baht or the cost of cytology is less than 50 Baht (1USD = 31.58 THB). CONCLUSIONS: In women with ASC-US cytology, colposcopy is more cost-effective than repeat cytology or triage with HPV testing for both provider and patient perspectives.

A real time genotyping PCR assay for polyomavirus BK.

BACKGROUND: Polyomavirus BK (BKV) may cause nephropathy in renal transplant recipients and hemorrhagic cystitis in bone marrow recipients. We developed real-time PCRs (RT-PCR) to determine easily and rapidly the different BKV genotypes (BKGT) (I-IV). METHODS: On the VP1 gene a duplex of RT-PCRs was developed and validated to differentiate the four main BKGT. 212 BKV positive samples (21 plasma, 191 urine) were tested with these specific PCRs. Of these 212 samples, 55 PCR results were additionally confirmed by sequencing a VP1 gene fragment (nucleotide 1630-1956). RESULTS: For every genotype, a highly specific, precise and internally controlled assay was developed with a limit of detection of log 3 copies per ml. In 18 (8.5%) of these samples genotyping was not successful due to a low viral load. By sequence analysis, the genotype of 46 out of 55 and 2 out of 4 samples with double infection could be confirmed. CONCLUSIONS: This study describes RT-PCRs for detection of the main BKGT. It proved to be rapid, cheap and sensitive compared to sequencing. Double infections can also be detected. This method will be of value to investigate the role of BKV infection in relation to the genotype.

A flow-through chromatography process for influenza A and B virus purification.

Vaccination is still the most efficient measure to protect against influenza virus infections. Besides the seasonal wave of influenza, pandemic outbreaks of bird or swine flu represent a high threat to human population. With the establishment of cell culture-based processes, there is a growing demand for robust, economic and efficient downstream processes for influenza virus purification. This study focused on the development of an economic flow-through chromatographic process avoiding virus strain sensitive capture steps. Therefore, a three-step process consisting of anion exchange chromatography (AEC), Benzonase(®) treatment, and size exclusion chromatography with a ligand-activated core (LCC) was established, and tested for purification of two influenza A virus strains and one influenza B virus strain. The process resulted in high virus yields (≥68%) with protein contamination levels fulfilling requirements of the European Pharmacopeia for production of influenza vaccines for human use. DNA was depleted by ≥98.7% for all strains. The measured DNA concentrations per dose were close to the required limits of 10ng DNA per dose set by the European Pharmacopeia. In addition, the added Benzonase(®) could be successfully removed from the product fraction. Overall, the presented downstream process could potentially represent a simple, robust and economic platform technology for production of cell culture-derived influenza vaccines.

Rapid and sensitive detection of human astrovirus in water samples by loop-mediated isothermal amplification with hydroxynaphthol blue dye.

BACKGROUND: The aim of this paper was to develop a reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for rapid, sensitive and inexpensive detection of astrovirus. RESULTS: The detection limit of LAMP using in vitro RNA transcripts was 3.6 × 10 copies·µL⁻¹, which is as sensitive as the presently used PCR assays. However, the LAMP products could be identified as different colors with the naked eye following staining with hydroxynaphthol blue dye (HNB). No cross-reactivity with other gastroenteric viruses (rotavirus and norovirus) was observed, indicating the relatively high specificity of LAMP. The RT-LAMP method with HNB was used to effectively detect astrovirus in reclaimed water samples. CONCLUSIONS: The LAMP technique described in this study is a cheap, sensitive, specific and rapid method for the detection of astrovirus. The RT-LAMP method can be simply applied for the specific detection of astrovirus and has the potential to be utilized in the field as a screening test.

Cost-effectiveness analysis of 2 surveillance options for cervical intraepithelial neoplasia 1.

OBJECTIVE: We aim to determine the difference in cost between 2 accepted surveillance strategies for women diagnosed with cervical intraepithelial neoplasia 1 (CIN 1): repeat cytology at 6 and 12 months versus human papillomavirus (HPV) DNA testing at 12 months. MATERIALS AND METHODS: Extracting data from the literature regarding the natural history of HPV infection and CIN 1, we estimated regression, persistence, and progression rates during a 2-year interval. Costs were based on 2011 Medicaid reimbursements for cytology, biopsy interpretation, HPV testing, and the associated office visit or procedure fee. We constructed a decision tree model to estimate the potential cost benefits of using HPV testing, and sensitivity analyses were performed. Treatment costs for high-grade disease were not included because of equal occurrence in both groups. RESULTS: In a hypothetical cohort of 100 women with CIN 1 (assumed compliant with 2 y of follow-up), the total cost for cytology-based follow-up was $89,969, whereas the total cost for HPV-based follow-up was $37,357. This indicates an average cost savings of $526 per patient in favor of HPV testing. If we then consider the 234,603 incident cases of CIN 1 in the United Sates per year, preferential use of HPV-based follow-up would save $123,429,305. CONCLUSIONS: Although both cytology and HPV testing are sound methods for surveillance of CIN 1, it is more cost-effective to use HPV testing.

Rapid molecular detection of Lujo virus RNA.

Lujo virus is an emerging arenavirus circulating in Southern Africa. Although to date there has only been a single outbreak of the novel haemorrhagic disease resulting from human infection with this virus, the case-fatality rate of exposed individuals, including nosocomial transmission, was 80%. The ability to identify viral haemorrhagic fevers accurately, especially those capable of nosocomial transmission, is of critical importance. Timely identification of these diseases allow medical professionals to isolate patients and implement barrier nursing techniques in order to prevent onward transmission of the virus. While rapid diagnostic methods are published for most viral haemorrhagic fevers, at present there are no such virus specific protocols for Lujo haemorrhagic fever. This report details the first set of diagnostic molecular assays designed to identify Lujo viral RNA rapidly, and demonstrates the potential functionality of these assays for use in the clinical setting. Although these assays have been designed and validated against a solitary isolate of Lujo virus, this represents the entirety of strains detected to date, and offer quick, cheap and easy methods for use in diagnostic laboratories.

Detection of Papaya leaf distortion mosaic virus by reverse-transcription loop-mediated isothermal amplification.

Papaya leaf distortion mosaic virus (PLDMV) can infect transgenic papaya resistant to a related pathogen, Papaya ringspot virus (PRSV), posing a substantial threat to papaya production in China. Current detection methods, however, are unable to be used for rapid detection in the field. Here, a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of PLDMV, using a set of four RT-LAMP primers designed based on the conserved sequence of PLDMV CP. The RT-LAMP method detected specifically PLDMV and was highly sensitive, with a detection limit of 1.32×10(-6) µg of total RNA per reaction. Indeed, the reaction was 10 times more sensitive than one-step RT-PCR, while also requiring significantly less time and equipment. The effectiveness of RT-LAMP and one-step RT-PCR in detecting the virus were compared using 90 field samples of non-transgenic papaya and 90 field samples of commercialized PRSV-resistant transgenic papaya from Hainan Island. None of the non-transgenic papaya tested positive for PLDMV using either method. In contrast, 19 of the commercialized PRSV-resistant transgenic papaya samples tested positive by RT-LAMP assay, and 6 of those tested negative by RT-PCR. Therefore, the PLDMV-specific RT-LAMP is a simple, rapid, sensitive, and cost-effective tool in the field diagnosis and control of PLDMV.

Rapid detection of duck hepatitis A virus genotype C using reverse transcription loop-mediated isothermal amplification.

A one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was used and optimized to develop a rapid and sensitive detection system for duck hepatitis A virus genotype C (DHAV-C) RNA. A set of four specific primers was designed against highly conserved sequences located within the 3D gene from DHAV (strain GX1201). Under optimal reaction conditions, the sensitivity of DHAV-C-specific RT-LAMP was 100-fold higher than that of reverse transcriptase-polymerase chain reaction (RT-PCR), with a detection limit of 0.3pg (6.59×10(4) copies) per reaction. No cross-reactivity was observed from the samples of other duck viruses, which is in good accordance with RT-PCR. Furthermore, a positive reaction can be visually inspected by observing turbidity or color change after the addition of SYBR green I dye. The DHAV-C-specific RT-LAMP assay was applied to the samples and compared with RT-PCR. The positive-sample ratios were 26.7% (12 of 45) by RT-LAMP and 20% (9 of 45) by RT-PCR. Therefore, the newly developed RT-LAMP assay is a rapid, specific, sensitive, and cost-effective method of DHAV-C detection. This assay has potential applications in both clinical diagnosis and field surveillance of DHAV-C infection.