Agile design and development of a high throughput cobas SARS-CoV-2 RT-PCR diagnostic test.

Diagnostic testing is essential for management of the COVID-19 pandemic. An agile assay design methodology, optimized for the cobas® 6800/8800 system, was used to develop a dual-target, qualitative SARS-CoV-2 RT-PCR test using commercially available reagents and existing sample processing and thermocycling profiles. The limit of detection was 30-52 copies/mL for USA-WA1/2020. Assay sensitivity was confirmed for SARS-CoV-2 variants Alpha, Beta, Gamma, Delta and Kappa. The coefficients of variation of the cycle threshold number (Ct) were between 1.1 and 2.2%. There was no difference in Ct using nasopharyngeal compared to oropharyngeal swabs in universal transport medium (UTM). A small increase in Ct was observed with specimens collected in cobas PCR medium compared to UTM. In silico analysis indicated that the dual-target test is capable of detecting all >1,800,000 SARS-CoV-2 sequences in the GISAID database. Our agile assay design approach facilitated rapid development and deployment of this SARS-CoV-2 RT-PCR test.

Implementation of an mHealth App to Promote Engagement During HIV Care and Viral Load Suppression in Johannesburg, South Africa (iThemba Life): Pilot Technical Feasibility and Acceptability Study.

BACKGROUND: South Africa has the largest HIV treatment program worldwide. Retention in care and medication adherence remain problematic necessitating innovative solutions for improving HIV care. The increasing availability and use of mobile technology can support positive clinical outcomes for persons living with HIV. iThemba Life is a mobile health app designed with input from South African health professionals and patients, promoting engagement with HIV care through access to medical results. OBJECTIVE: This study aimed to test the feasibility and acceptability of receiving HIV viral load (VL) results through the app and compare the time to HIV VL result return for study participants before and after app use. METHODS: Using convenience sampling, adults having routine VL phlebotomy were recruited from 2 Johannesburg health facilities. After signed consent, the app was downloaded on their Android smartphones, phlebotomy was performed, and the sample barcode was scanned through their phone to link the sample and app. Participants received a notification of the result availability and logged into the app to view results, their explanation and recommended action. RESULTS: Overall, 750 people were screened to enroll 500 participants. Of 750, 113 (15.1%) failed eligibility screening. 21.5% (137/637) had smartphone technical limitations preventing enrollment. Results were released to 92.2% (461/500) of participants' phones. App technical issues and laboratory operational issues limited the number of released results. Approximately 78.1% (360/461) results were viewed in the app. Median time from notification of availability to result viewed being 15.5 hours (0.6; range 0-150 days). Turnaround time from phlebotomy to the result being received was 6 (range 1-167) days for users versus 56 days (range 10-430 days; P<.001) before app use. Overall, 4% (20/500) of participants received unsuppressed results (VL>1000 copies/mL). Turnaround time for unsuppressed results was 7 days for participants versus 37.5 days before app use (P<.001). The difference before and after app use in the suppressed and unsuppressed users for time from sample collection to result delivery was statistically significant. Of 20 participants, 12 (60%) returned for a confirmatory VL during the study period. The time from an unsuppressed VL to a confirmatory VL was 106 days for app users versus 203 days before app use (P<.001). Overall, 52.4% (262/500) of participants completed an exit survey; 23.2% (58/250) reported challenges in viewing their VL results. Moreover, 58% (35/60) reported that they overcame challenges with technical assistance from others, and 97.3% (255/262) wanted to continue using the app for VL results. CONCLUSIONS: Using iThemba Life for VL results was well-received despite limited smartphone access for some participants. App users received results 10 times sooner than before the app and 5 times sooner if their VL >1000 copies/mL. This increased notification speed led to participants wanting to continue using iThemba Life.

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.

High-volume workflow and performance comparisons for Chlamydia trachomatis and Neisseria gonorrhoeae testing using automated molecular platforms.

BACKGROUND: The global burden of sexually transmitted infections (STIs) is high and there have been reports of increasing chlamydial and gonorrheal infections. High-volume screening programs for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are an important component of STI control. This study evaluated the high-volume workflow and performance of the cobas® CT/NG assay for use on the automated Roche cobas® 6800 system, with the cobas p 480 instrument for pre-analytics, compared with the Aptima Combo 2 assay on the Hologic Panther system. METHODS: High-volume workflow and performance were evaluated using paired female urine specimens. Workflow analysis (n = 376) included hands-on time (HoT), number of manual interventions, and time to first and last results. For performance assessment, paired results from the cobas CT/NG and Aptima Combo 2 assays, for both CT and NG, were compared and two-sided 95% confidence intervals calculated to provide estimates of positive percent agreement (PPA), negative percent agreement (NPA), and overall percent agreement (OPA) between the tests. McNemar's test was used for significance testing. RESULTS: Pre-analytical preparations and system start-up on the cobas 6800 system required 00:27:38 (hr:min:sec) HoT whilst the Panther system required 00:30:43. The cobas 6800 system required eight interactions and 00:43:59 HoT to process 376 samples. The Panther system required six interactions and 00:39:10 HoT. Time to first results was 02:53:00 on the cobas c6800 system for 96 samples and 03:28:29 on the Panther system for five samples. The cobas 6800 system delivered all 376 results 3 h faster than the Panther system (07:45:26 and 10:47:30, respectively). The performance correlation between both assays was high (PPA, NPA and OPA > 99% for both CT and NG). McNemar's test revealed no statistically significant difference between the assays. CONCLUSION: For high-volume automated CT/NG testing, both the cobas 6800 system and Panther system provided accurate results. Although less manual intervention steps were needed for the Panther system, improved turnaround time was obtained with the cobas 6800 system with less risk for contamination. The additional testing capacity on the cobas 6800 system would allow a growing service to deliver more results in a single shift.

Diagnosis and antibiotic treatment of group a streptococcal pharyngitis in children in a primary care setting: impact of point-of-care polymerase chain reaction.

BACKGROUND: To compare the sensitivity and specificity of the recommended 2-step rapid antigen detection test (RADT) with confirmatory culture vs the point-of-care (POC) polymerase chain reaction (PCR) Roche cobas® Liat® Strep A test for detection of group A Streptococcus (GAS) in pediatric patients with pharyngitis, and to investigate the impact of these tests on antibiotic use in a large pediatric clinic. METHODS: This prospective, open-label study was conducted at a single site during fall/winter 2016-2017. A total of 275 patients aged 3 to 18 years with symptoms of pharyngitis had a throat-swab specimen analyzed using RADT, POC PCR, and culture. The sensitivity, specificity, and percentage agreement (95% CI) between assays and a laboratory-based nucleic acid amplification test were calculated. DNA sequencing was used to adjudicate discrepancies. The RADT or POC PCR result was provided to clinicians on alternating weeks to compare the impact on antibiotic use. RESULTS: A total of 255 samples were evaluated; 110 (43.1%) were GAS positive. Sensitivities (95% CI) for POC PCR, RADT, and culture were 95.5% (89.7-98.5%), 85.5% (77.5-1.5%), and 71.8% (62.4-80.0%), respectively. Specificities (95% CI) for POC PCR, RADT, and culture were 99.3% (96.2-99.98%), 93.7% (88.5-97.1%), and 100% (97.5-100%), respectively. Compared with RADT, POC PCR resulted in significantly greater appropriate antibiotic use (97.1% vs 87.5%; P = .0065). CONCLUSION: Under real-world conditions, RADT results were less specific and culture results were less sensitive than found in established literature and led to increased rates of inappropriate antibiotic use. POC PCR had high sensitivity and specificity and rapid turnaround times, and led to more appropriate antibiotic use. TRIAL REGISTRATION: ID number ISRCTN84562679 . Registered October 162,018, retrospectively registered.

Beyond early infant diagnosis: case finding strategies for identification of HIV-infected infants and children.

There are 3.4 million children infected with HIV worldwide, with up to 2.6 million eligible for treatment under current guidelines. However, roughly 70% of infected children are not receiving live-saving HIV care and treatment. Strengthening case finding through improved diagnosis strategies, and actively linking identified HIV-infected children to care and treatment is essential to ensuring that these children benefit from the care and treatment available to them. Without attention or advocacy, the majority of these children will remain undiagnosed and die from complications of HIV. In this article, we summarize the challenges of identifying HIV-infected infants and children, review currently available evidence and guidance, describe promising new strategies for case finding, and make recommendations for future research and interventions to improve identification of HIV-infected infants and children.

Antifreeze on a freezing morning: ethylene glycol poisoning in a 2-year-old.

This case report describes the presentation and management of a 2-year-old child who ingested a potentially fatal amount of ethylene glycol (EG). There are few published cases worldwide of EG poisoning in children managed with fomepizole. All cases described in the literature were managed in a paediatric intensive care unit. In this case, the child presented irritable, pale and confused with high anion gap metabolic acidosis. As there were no paediatric intensive care beds available in the region, the child was successfully managed in a high dependency area in our district general hospital. The child fully recovered and was discharged home in 7 days. The authors believe that multi-disciplinary team management and the use of fomepizole contributed to the positive outcome and this case raised many useful learning points.

Contraception among HIV concordant and discordant couples in Zambia: a randomized controlled trial.

OBJECTIVES: This study examines the impact of an intervention to promote dual-method contraceptive use among HIV concordant and discordant couples already using condoms for HIV prevention. METHODS: A three-armed randomized, controlled trial was conducted at a voluntary HIV testing and counseling clinic in Lusaka, Zambia; 251 couples were randomized. Control couples received family planning education and referral to an outside clinic for nonbarrier contraceptives, intervention 1 couples received education and offer of contraceptives at the research clinic, and intervention 2 couples received intervention 1 plus a presentation designed to reduce outside pressures to conceive. RESULTS: There was a 3-fold higher contraceptive initiation rate in both intervention arms compared with the control arm. The interventions had no impact on incident pregnancy, largely due to high levels of contraceptive discontinuation and user failure. HIV-positive women who initially selected injectable contraception were less likely to abandon the method and significantly less likely to conceive than other study participants. CONCLUSIONS: Improving access to nonbarrier contraceptives among couples already using condoms for HIV prevention increased dual-method use. Selection of longer-acting injectable contraception was associated with lower pregnancy rates among HIV-positive women. Further research is needed to identify ways to help couples in this population continue to correctly use nonbarrier contraceptives.