Evaluation of Lyme serologic quantitative test indexes: High first-tier test index values predict positive second-tier result in standard and modified 2-tier Lyme testing algorithms.

OBJECTIVES: In this study, we evaluated the potential utility of reporting a quantitative Lyme serologic test index to improve the utility of results from first-tier Lyme assays. METHODS: Serum from consecutive samples sent to our laboratory for Lyme testing were tested on 2 commercial first-tier Lyme assays and evaluated to determine the probability of second-tier confirmation based on the serologic index value. RESULTS: For both assays, we identified an index value above which 100% of samples confirmed on second-tier testing using both standard and modified 2-tier testing algorithms. Lower rates of confirmation were observed for positive or equivocal samples with lower index values. CONCLUSION: The use of a Lyme test index value may eliminate the need for confirmatory testing on many positive first-tier samples, providing more rapid turnaround time to a definitive result. This practice would also increase efficiency in the clinical laboratory.

Lessons learnt from assessing and improving accuracy and positive predictive value of the national HIV testing algorithm in Nigeria.

Background: HIV testing remains an entry point into HIV care and treatment services. In 2007, Nigeria adopted and implemented a two-test rapid HIV testing algorithm of three HIV rapid test kits, following the sequence: Alere Determine (first test), UnigoldTM (second test), and STAT-PAK® as the tie-breaker. Sub-analysis of the 2018 Nigeria HIV/AIDS Indicator and Impact Survey data showed significant discordance between the first and second tests, necessitating an evaluation of the algorithm. This manuscript highlights lessons learnt from that evaluation. Intervention: A two-phased evaluation method was employed, including abstraction and analysis of retrospective HIV testing data from January 2017 to December 2019 from 24 selected sites supported by the United States President's Emergency Plan for AIDS Relief programme. A prospective evaluation of HIV testing was done among 2895 consecutively enrolled and consented adults, aged 15-64 years, accessing HIV testing services from three selected sites per state across the six geopolitical zones of Nigeria between July 2020 and September 2020. The prospective evaluation was performed both in the field and at the National Reference Laboratory under controlled laboratory conditions. Stakeholder engagements, strategic selection and training of study personnel, and integrated supportive supervision were employed to assure the quality of evaluation procedures and outcomes. Lessons learnt: The algorithm showed higher sensitivity and specificity in the National Reference Laboratory compared with the field. The approaches to quality assurance were integral to the high-quality study outcomes. Recommendations: We recommend comparison of testing algorithms under evaluation against a gold standard. What this study adds: This study provides context-specific considerations in using World Health Organization recommendations to evaluate the Nigerian national HIV rapid testing algorithm.

Clinical performance evaluation of an HIV Duo assay: From HIV screening to acute and non-acute HIV infection detection.

BACKGROUND: Evaluating the clinical performance of Elecsys HIV Duo assay for primary human immunodeficiency virus (HIV) screening and acute HIV infection detection. METHODS: This study was conducted from April 2022 to April 2023 and involved two distinct populations. For the HIV screening population, three HIV Duo results [HIV Duo, HIV antigen (Ag), and HIV antibody (Ab)] in primary screening were obtained (January 2021 to June 2021). In the diagnosed HIV population, retrospective samples from November 2016 to March 2023 were measured. RESULTS: The HIV screening population included 111,383 samples from a real-world screening program. The assay demonstrated a specificity of 99.91 % (95 % CI: 99.89 %, 99.93 %) and a PPV of 0.8516 (95 % CI: 0.8225, 0.8776). Regarding the diagnosed HIV population, 836 HIV patients were enrolled, including 14 acute HIV infectious patients with only HIV Ag + and a Western Blot (WB) confirmation rate of 0 %. The median (IQR) of the numeric cut-off index (COI) ratios of HIV Duo Ab and Ag significantly differed among the Ag + Ab-, Ag-Ab+, and Ag + Ab + subgroups. CONCLUSION: The Elecsys HIV Duo assay is suitable for primary HIV screening and can be integrated into a novel laboratory HIV testing algorithm to improve acute HIV detection in Chinese clinical practice. ABBREVIATIONS: HIV, Human immunodeficiency virus; AIDS, acquired immunodeficiency syndrome; Ag, antigen; Ab, antibody; WB, Western Blot; COI, numeric cut-off index; CI, confidence interval; NAT, nucleic acid tests; EDC, electronic data capture systems; CDC, Chinese Centers for Disease Control and Prevention; IQR, interquartile range; PPV, positive predictive value; HCV, hepatitis C virus; HBV, hepatitis B virus; CI, confidence interval; ND, not able to define; F, female; M, male.

A vulnerability detection method for IoT protocol based on parallel fuzzy algorithm.

The Internet of Things communication protocol is prone to security vulnerabilities when facing increasing types and scales of network attacks, which can affect the communication security of the Internet of Things. It is crucial to effectively detect these vulnerabilities in order to improve the security of IoT communication protocols and promptly fix them. Therefore, this study proposes a distributed IoT communication protocol vulnerability detection method based on an improved parallelized fuzzy testing algorithm. Firstly, based on design principles and by comparing different communication protocols, a communication architecture for the distribution network's Internet of Things was constructed, and the communication protocols were formalized and decomposed. Next, preprocess the vulnerability detection samples, and then use genetic algorithm to improve the parallelized fuzzy testing algorithm to perform vulnerability detection. Through this improved algorithm, the missed detection rate and false detection rate can be effectively reduced, thereby improving the security of IoT communication protocols. The experimental results show that the highest missed detection rate of this method is only 4.0 %, and the false detection rate is low, with high detection efficiency. This indicates that the method has good performance and reliability in detecting vulnerabilities in IoT communication protocols.

Aetiological profile of acute encephalitis syndrome in Assam, India, during a 4-year period from 2019 to 2022.

Acute encephalitis syndrome (AES) is a major public health concern in India as the aetiology remains unknown in the majority of cases with the current testing algorithm. We aimed to study the incidence of Japanese encephalitis (JE) and determine the aetiology of non-JE AES cases to develop an evidence-based testing algorithm. Cerebrospinal fluid (CSF) samples were tested for Japanese encephalitis virus by ELISA and polymerase chain reaction (PCR). Multiplex real-time PCR was done for Dengue, Chikungunya, West Nile, Zika, Enterovirus, Epstein Barr Virus, Herpes Simplex Virus, Adenovirus, Cytomegalovirus, Herpesvirus 6, Parechovirus, Parvovirus B19, Varicella Zoster Virus, Scrub typhus, Rickettsia species, Leptospira, Salmonella species, Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, Plasmodium species and by ELISA for Mumps and Measles virus. Of the 3173 CSF samples, 461 (14.5%) were positive for JE. Of the 334 non-JE AES cases, 66.2% viz. Scrub typhus (25.7%), Mumps (19.5%), Measles (4.2%), Parvovirus B19 (3.9%) Plasmodium (2.7%), HSV 1 and 2 (2.4%), EBV and Streptococcus pneumoniae (2.1% each), Salmonella and HHV 6 (1.2% each) were predominant. Hence, an improved surveillance system and our suggested expanded testing algorithm can improve the diagnosis of potentially treatable infectious agents of AES in India.

Assessment of the performance regarding confirmatory diagnosis and initiation of antiretroviral therapy under a modified national HIV testing algorithm and pay-for-performance program in Taiwan.

BACKGROUND: A pay-for-performance plan for rapid antiretroviral therapy (ART) commencement was initiated in 2018, while a modified testing algorithm offers immunochromatographic test (ICT) to replace Western blot (WB), and simultaneous testing with ICT and Nucleic Acid Amplification Test (NAAT) for HIV-positive sera was adopted in 2019 in Taiwan. METHODS: Serum specimens collected from 1117 suspected or confirmed HIV infection cases in 2016-2019 were reassessed the performance of WB, ICT, and NAAT. We reviewed the medical records of 10,732 individuals diagnosed with HIV in 2015-2021 to determine the time from screening to confirmatory diagnosis, followed by ART commencement. RESULTS: All 860 WB-positives were also positive by ICT and NAAT. The positive detection percentages were 37.0% by ICT and 51.4% by NAAT for 257 WB-indeterminate and -negative sera. The sensitivity for WB and ICT was 93.8% and 95.5%, respectively. In the people living with HIV (PLHIV) cohort, the median time from initial positive to confirmatory diagnosis decreased from 5 to 6 days before 2019 to 1 day in 2021. The median time from initial positive to ART initiation decreased from 37 days in 2015, 14 days in 2018, to 6 days in 2021. Compared to 2015-2017, the time to ART initiation was 91.48 days lower in 2018 (P < 0.001) and 100.66 days lower in 2019-2021 (P < 0.001) by the adjusted linear regression model. CONCLUSION: A significant decrease in the time to ART initiation was observed after initiation of the pay-for-performance program and optimized testing algorithm in Taiwan.

HIV rapid test performance among health facilities enrolled in HIV rapid test quality improvement initiative (RTQII) in Ethiopia.

BACKGROUND: As the Human Immunodeficiency Virus (HIV) rapid testing services expanded to reach the global target that 95% of people living with the virus will know their status by 2030, ensuring the quality of those services becomes critical. This study was conducted to assess the performance of HIV Rapid testing at sites in health facilities that were enrolled in the Rapid Test Quality Improvement Initiative (RTQII) in Ethiopia. METHODS: Characterized HIV proficiency testing (PT) panels of Dried Tube Specimen (DTS) were prepared, verified, and distributed to testing sites from August to December 2019. In addition on-site evaluation of HIV testing sites (HTSs) was conducted using a checklist to assess testing conditions. For proficiency testing, the study included 159 HIV testing sites (HTSs) in 41 Health facilities (HFs) in five administrative regions and two city administrations. The collected data was analyzed by SPSS version 20 and chi-square test was applied to identify the association between acceptable performance and contributing factors. Testing sites with 100% PT score as well as conducting the test with adherence to the National HIV Testing Algorithm were considered acceptable. RESULTS: The overall acceptable performance (100% PT score with the correct algorithm followed) was found to be 62% while 12% scored 80% and 11% scored between 20 and 60%. The rest 15% were not considered as acceptable due to failure to adhere to the National HIV Testing Algorithm. Testing sites that participated in External Quality Assessment/Proficiency Testing schemes have shown better performance than those that did not participate with 70% and 56% performance respectively (p = 0.057).

A systematic review of limiting antigen avidity enzyme immunoassay for detection of recent HIV-1 infection to expand supported applications.

Introduction: The need for detection of new and recent HIV infections is essential for surveillance and assessing interventions in controlling the epidemic. HIV recency assays are one way of providing reliable incidence estimates by determining recent versus non-recent infection. The objective of this study was to review the current body of knowledge of the limiting antigen avidity enzyme immunoassay to expand supported applications through an assessment of what is known and the gaps. Methods: A search for peer-reviewed literature in PubMed, Embase, and Web of Science Core Collection was conducted using the search term "human immunodeficiency virus and avidity". Non-peer reviewed published reports from the Population-based HIV Impact Assessment Project were also included. These were limited to literature published in English between January 2010 and August 2021. Results: This search resulted in 2080 publications and 14 reports, with 137 peer-reviewed studies and 14 non-peer reviewed reports that met the inclusion criteria, yielding a total of 151 studies for the final review. There were similar findings among studies that compared the performances of assay manufacturers and sample types. Studies that evaluated various assay algorithms and thresholds were heterogeneous, illustrating the need for context-specific test characteristics for classifying recent infections. Most studies estimated subtype-specific test characteristics for HIV subtypes A, B, C, and D. This was further illustrated when looking only at studies that compared HIV incidence estimates from recency assay algorithms and longitudinal cohorts. Conclusions: These findings suggest that the current body of knowledge provides important information that contributes towards distinguishing recent and non-recent infection and incidence estimation. However, there are knowledge gaps with respect to factors that influence the test characteristics (e.g., HIV-1 subtype, population characteristics, assay algorithms and thresholds). Further studies are needed to estimate and establish context-specific test characteristics that consider these influencing factors to improve and expand the use of this assay for detection of recent HIV infection.

Circular Whole-Transcriptome Amplification (cWTA) and mNGS Screening Enhanced by a Group Testing Algorithm (mEGA) Enable High-Throughput and Comprehensive Virus Identification.

Metagenomic next-generation sequencing (mNGS) offers a hypothesis-free approach for pathogen detection, but its applicability in clinical diagnosis, in addition to other factors, remains limited due to complicated library construction. The present study describes a PCR-free isothermal workflow for mNGS targeting RNA, based on a multiple displacement amplification, termed circular whole-transcriptome amplification (cWTA), as the template is circularized before amplification. The cWTA approach was validated with clinical samples and nanopore sequencing. Reads homologous to dengue virus 2 and chikungunya virus were detected in clinical samples from Bangladesh and Brazil, respectively. In addition, the practicality of a high-throughput detection system that combines mNGS and a group testing algorithm termed mNGS screening enhanced by a group testing algorithm (mEGA) was established. This approach enabled significant library size reduction while permitting trackability between samples and diagnostic results. Serum samples of patients with undifferentiated febrile illnesses from Vietnam (n = 43) were also amplified with cWTA, divided into 11 pools, processed for library construction, and sequenced. Dengue virus 2, hepatitis B virus, and parvovirus B19 were successfully detected without prior knowledge of their existence. Collectively, cWTA with the nanopore platform opens the possibility of hypothesis-free on-site comprehensive pathogen diagnosis, while mEGA contributes to the scaling up of sample throughput. IMPORTANCE Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the available tests being highly specific to a certain pathogen. Recent developments in sequencing technology have introduced mNGS as an alternative that provides detection of a wide-range of pathogens by detecting the presence of their nucleic acids in the sample. However, sequencing library preparation is still a bottleneck, as it is complicated, costly, and time-consuming. In our studies, alternative approaches to optimize library construction for mNGS were developed. This included isothermal nucleic acid amplification and expansion of sample throughput with a group testing algorithm. These methods can improve the utilization of mNGS as a diagnostic tool and can serve as a high-throughput screening system aiding infectious disease surveillance.

Developing and validating SARS-CoV-2 assays for nonhuman primate surveillance.

INTRODUCTION: In early 2020, the California National Primate Research Center implemented surveillance to address the threat of SARS-CoV-2 infection in its nonhuman primate colony. MATERIALS/METHODS: To detect antiviral antibodies, multi-antigen assays were developed and validated on enzyme immunoassay and multiplex microbead immunofluorescent assay (MMIA) platforms. To detect viral RNA, RT-PCR was also performed. RESULTS/CONCLUSION: Using a 4plex, antibody was identified in 16/16 experimentally infected animals; and specificity for spike, nucleocapsid, receptor binding domain, and whole virus antigens was 95.2%, 93.8%, 94.3%, and 97.1%, respectively on surveillance samples. Six laboratories compared this MMIA favorably with nine additional laboratory-developed or commercially available assays. Using a screen and confirm algorithm, 141 of the last 2441 surveillance samples were screen-reactive requiring confirmatory testing. Although 35 samples were reactive to either nucleocapsid or spike; none were reactive to both. Over 20 000 animals have been tested and no spontaneous infections have so far been confirmed across the NIH sponsored National Primate Research Centers.

Transition to PCR diagnosis of cryptosporidiosis and giardiasis in the Norwegian healthcare system: could the increase in reported cases be due to higher sensitivity or a change in the testing algorithm?

Cryptosporidiosis has been a notifiable infection in Norway since 2012 and giardiasis since 1977. For both infections, there has been an increase in notified cases. We used a questionnaire to explore whether this may be associated with implementation of molecular diagnostic methods. We received responses from 14 of 16 laboratories, most of which had implemented molecular diagnostic methods for these parasites. Algorithms for testing had also been modified, and several laboratories now test more faecal samples than previously for both parasites. The increase in reported cases may reflect not only higher sensitivity of diagnostic methods, but also more sample testing.

Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants.

OBJECTIVES: To evaluate a testing algorithm for the rapid identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that includes the use of PCR-based targeted single nucleotide polymorphism (SNP) detection assays preceded by a multiplex PCR sensitive to S-Gene Target Failure (SGTF). METHODS: PCR SNP assays targeting SARS-CoV-2 S-gene mutations ΔH69-V70, L452R, E484K, N501Y, H655Y and P681R using melting curve analysis were performed on 567 samples in which SARS-CoV-2 viral RNA was detected by a multiplex PCR. Viral whole-genome sequencing (WGS) was performed to confirm the presence of SNPs and to identify the Pangolin lineage. Additionally, 1133 SARS-CoV-2 positive samples with SGTF were further assessed by WGS to determine the presence of ΔH69-V70. RESULTS: The N501Y-specific assay (n = 567) had an overall percentage agreement (OPA) of 98.5%. The ΔH69-V70-specific (n = 178) and E484K-specific (n = 401) assays had OPA of 96.6% and 99.7%, respectively. Assessment of H655Y (n = 139) yielded a 100.0% concordance when applied in the proposed algorithm. The L452R-specific (n = 67) and P681R-specific (n = 62) assays had an OPA of 98.2% and 98.1%, respectively. The proposed algorithm identified six variants of concern/interest (VOC/VOI)-Alpha (n = 149), Beta (n = 65), Gamma (n = 86), Delta (n = 49), Eta (n = 6), Kappa (n = 6)-and 205 non-VOC/VOI strains-including the variants under monitoring B.1.214.2 (n = 43) and B.1.1.318 (n = 18) and Epsilon (n = 1). An excellent concordance was observed for the identification of all SARS-CoV-2 lineages evaluated. CONCLUSIONS: We present a flexible testing algorithm for the rapid detection of current and emerging SARS-CoV-2 VOC/VOIs, which can be easily adapted based on the local endemicity of specific variants.

Recommended testing algorithms for NTRK gene fusions in pediatric and selected adult cancers: Consensus of a Singapore Task Force.

The occurrence of neurotrophic tyrosine receptor kinase (NTRK) gene fusions in a wide range of tumor types presents an attractive opportunity for using a tropomyosin receptor kinase (TRK) inhibitor as cancer therapy. Recent clinical studies have demonstrated highly efficacious outcomes associated with the use of TRK inhibitors, such as larotrectinib and entrectinib in NTRK fusion-bearing cancers, in both adult and pediatric populations. While NTRK gene fusions are commonly found in some uncommon adult and pediatric malignancies, they are also found, albeit rarely, in a wide range of more common malignancies. The potential value of testing for NTRK gene fusions in practically all advanced malignancies is underpinned by the remarkable therapeutic outcomes that TRK inhibitors offer. This requirement presents practical and financial challenges in real-world oncological practice. Furthermore, different testing platforms exist to detect NTRK gene fusions, each with its advantages and disadvantages. It is, therefore, imperative to develop strategies for NTRK gene fusion testing in an attempt to optimize the use of limited tissue specimen and financial resources, and to minimize the turnaround time. A multidisciplinary task force of Singapore medical experts in both public and private sectors was convened in late 2020 to propose testing algorithms for adult colorectal tumors, sarcomas, non-small cell lung cancer, and pediatric cancers, with particular adaptation to the Singapore oncological practice. The recommendations presented here highlight the heterogeneity of NTRK-fusion positive cancers, and emphasize the need to customize the testing methods to each tumor type to optimize the workflow.

Reduction in Health Care Facility-Onset Clostridioides difficile Infection: A Quality Improvement Initiative.

OBJECTIVE: To reduce health care facility-onset (HCFO) Clostridioides difficile infection (CDI) incidence by improving diagnostic stewardship and reducing the inappropriate testing of C difficile assays. PATIENTS AND METHODS: A multidisciplinary team conducted a quality improvement initiative from January 1, 2020, through March 31, 2021. Clostridioides difficile infection and inappropriate testing were identified via electronic health records using predefined criteria related to stool quantity/caliber, confounding medications, and laboratory data. An intervention bundle was designed including (1) provider education, (2) implementation of an appropriate testing algorithm, (3) expert review of C difficile orders, and (4) batch testing of assays to facilitate review and cancellation if inappropriate. RESULTS: Compared with a baseline period from January to September 2020, implementation of our intervention bundle from December 2020 to March 2021 resulted in an 83.6% reduction in inappropriate orders tested and a 41.7% reduction in HCFO CDI incidence. CONCLUSION: A novel prevention bundle improved C difficile diagnostic stewardship and HCFO CDI incidence by reducing testing of inappropriate orders. Such initiatives targeting HCFO CDI may positively affect patient safety and hospital reimbursement.

Prospective multi-centric study to analyze pre-transplant compatibility algorithm for live-related donor kidney transplant in Indian setting: the "Delhi approach"!

BACKGROUND: Since no single test is always accurate and sensitive, two or more tests are used to increase the precision of evaluation. Different algorithms have been proposed by centers in Leiden, Basel, Vienna and Minnesota, etc. With an intention to develop an optimal algorithm for India, we evaluated pre-transplant compatibility tests for live-donor kidney transplants. Three tests complement dependent cyto-toxicity cross-match (CDCXM), flow-cytometry cross-match (FCXM) and anti-HLA antibody screening (HAS) were performed and confirmed by the anti-HLA antibody identification (HAI) assay in a multi-centric trial (three transplant centers) in India. MATERIALS AND METHODS: All prospective recipients (and their potential donors) underwent low-resolution HLA typing as well as CDCXM, FCXM and HAS assays. In addition, HAI {single antigen bead assay; (SAB)} was done for all recipients to identify possible anti-HLA antibodies. In a virtual cross-match (VXM), antibody specificity was mapped to donor HLA type to determine donor-specific antibodies (DSA). Only patients without DSA were cleared for the transplant. Alternatively, patients with DSA were offered an exchange in the kidney paired donation (KPD) program. The screening results (CDCXM, FCXM, and HAS) were analyzed, individually as well as in combination of screening assays (CDCXM+HAS, CDCXM+FCXM, and FCXM+HAS) and the results were compared with those from the HAI test. RESULTS: Out of 100 patients, 69 were males and 31 were females; 85 recipients (85%) underwent a kidney transplant. The sensitivity of CDCXM was only 12.1% and the specificity of CDCXM was 100%; whereas the sensitivity of FCXM was 84.8% and the specificity of FCXM was 89.6%. The sensitivity and specificity of class I HAS was 88.2% and 84.3%, respectively. The sensitivity and specificity class II HAS was 88.0% and 80.0%, respectively. However, when both class I/II HAS were tested together the sensitivity increased to 97.0% and the specificity to 82.1%. Similarly, the sensitivity of combined FCXM+HAS had the sensitivity of 100% and the specificity of 76.1%; CDCXM+FCXM had the sensitivity of 84.8% and the specificity of 89.6% and CDCXM+HAS assays reached 97% with the specificity of 82.1%. CONCLUSIONS: Our results showed that the algorithm of FCXM with HAS produced the best sensitivity of 100%. The specificity of 76.1% indicate that the combined FCXM+HAS assays may detect up to 24.9% false positive results. We suggest that these false-positives may be easily resolved by performing the virtual crossmatch based on HAI (SAB) results. In our reflex testing algorithmic approach only 49% patients needed HAI (SAB). Finally, our results suggested that the CDCXM assay may be discontinued in pre-transplant workup owing to its very low sensitivity (12.1%).

The evolving HIV epidemic and its impact on the HIV testing algorithm: Is it time to change the HIV testing algorithm in South Africa?

HIV-1/2 testing is the first step in ensuring HIV-infected individuals are diagnosed and appropriately managed. The impact of suboptimal HIV-1/2 testing algorithms significantly contributes to the increased rates of misdiagnosis of HIV infection. Recently, the World Health Organization (WHO) recommended that high burden countries revise their testing algorithm from a 2 to 3-test testing strategy in the context of an evolving HIV epidemic. Implementation of a new HIV-testing algorithm must be tailor-made within a national framework and must be balanced out with operational feasibility, patient outcomes, and cost-effectiveness. In this review, we provide an overview of the current state of the HIV epidemic and its impact on HIV testing, further we highlight areas of concern in changing from a 2-step to a 3-step test algorithm in the context of South Africa's HIV epidemic and public health program.

An HIV Diagnostic Testing Algorithm Using the cobas HIV-1/HIV-2 Qualitative Assay for HIV Type Differentiation and Confirmation.

Human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) diagnostic testing algorithms recommended by the Centers for Disease Control involve up to three tests and rely mostly on detection of viral antigen and host antibody responses. HIV-1 p24 antigen/HIV-1/HIV-2 antibody-reactive specimens are confirmed with an immunochromatographic HIV-1/HIV-2 antibody differentiation assay, and negative or indeterminate results from the differentiation assay are resolved by an HIV-1-specific nucleic acid amplification test (NAT). The performance of a proposed alternative algorithm using the cobas HIV-1/HIV-2 qualitative NAT as the differentiation assay was evaluated in subjects known to be infected with HIV-1 (n = 876) or HIV-2 (n = 139), at low (n = 6,017) or high (n = 1,020) risk of HIV-1 infection, or at high-risk for HIV-2 infection (n = 498) (study A). The performance of the cobas HIV-1/HIV-2 qualitative test was also evaluated by comparison to an HIV-1 or HIV-2 alternative NAT (study B). The HIV-1 and HIV-2 overall percent agreements (OPA) in study A ranged from 95% to 100% in all groups. The positive percent agreements (PPA) for HIV-1 and HIV-2 were 100% (876/876) and 99.4% (167/168), respectively, for known positive groups. The negative percent agreement in the HIV low-risk group was 100% for both HIV-1 and HIV-2. In study B, the HIV-1 and HIV-2 OPA ranged from 99% to 100% in all groups evaluated (n = 183 to 1,030), and the PPA for HIV-1 and HIV-2 were 100% and 99.5%, respectively, for known positive groups. The cobas HIV-1/HIV-2 qualitative assay can discriminate between HIV-1 and HIV-2 based on HIV RNA and can be included in an alternative diagnostic algorithm for HIV.

SARS-CoV-2 surveillance for a non-human primate breeding research facility.

BACKGROUND: The emergence of SARS-CoV-2 and the ensuing COVID-19 pandemic prompted the need for a surveillance program to determine the viral status of the California National Primate Research Center non-human primate breeding colony, both for reasons of maintaining colony health and minimizing the risk of interference in COVID-19 and other research studies. METHODS: We collected biological samples from 10% of the rhesus macaque population for systematic testing to detect SARS-CoV-2 virus by RT-PCR and host antibody response by ELISA. Testing required the development and validation of new assays and an algorithm using in laboratory-developed and commercially available reagents and protocols. RESULTS AND CONCLUSIONS: No SARS-CoV-2 RNA or antibody was detected in this study; therefore, we have proposed a modified testing algorithm for sentinel surveillance to monitor for any future transmissions. As additional reagents and controls become available, assay development and validation will continue, leading to the enhanced sensitivity, specificity, accuracy, and efficiency of testing.

Serology Is More Sensitive Than Urea Breath Test or Stool Antigen for the Initial Diagnosis of Helicobacter pylori Gastritis When Compared With Histopathology.

OBJECTIVES: To assess the concordance and performance characteristics of Helicobacter pylori laboratory tests compared with histopathology and to propose algorithms for the diagnosis of H pylori that minimize diagnostic error. METHODS: H pylori diagnostics were reviewed from a 12-year period within a health system (2,560 cases). Analyses were performed to adjust diagnostic performance based on treatment and consensus histopathologic diagnoses among pathologists. Markers of access to care, including test cancellation frequency and turnaround time, were assessed. Costs and performance of candidate noninvasive testing algorithms were modeled as a function of disease prevalence. RESULTS: Serum H pylori IgG demonstrated a higher sensitivity (0.94) than urea breath and stool antigen tests (0.64 and 0.61, respectively). Evidence of an advantage in access to care for serology included a lower cancellation rate. Interobserver variability was higher (κ = 0.34) among pathologists for cases with a discordant laboratory test than concordant cases (κ = 0.56). A model testing algorithm utilizing serology for first-time diagnoses minimizes diagnostic error. CONCLUSIONS: Although H pylori serology has modestly lower specificity than other noninvasive tests, the superior sensitivity and negative predictive value in our population support its use as a noninvasive test to rule out H pylori infection. Reflexive testing with positive serology followed by either stool antigen or urea breath test may optimize diagnostic accuracy in low-prevalence populations.