Routine, Cost-Effective SARS-CoV-2 Surveillance Testing Using Pooled Saliva Limits Viral Spread on a Residential College Campus.

Routine testing for SARS-CoV-2 is rare for institutes of higher education due to prohibitive costs and supply chain delays. During spring 2021, we routinely tested all residential students 1 to 2 times per week using pooled, RNA-extraction-free, reverse transcription quantitative PCR (RT-qPCR) testing of saliva at a cost of $0.43/sample with same-day results. The limit of detection was 500 copies/ml on individual samples, and analysis indicates 1,000 and 2,500 copies/ml in pools of 5 and 10, respectively, which is orders of magnitude more sensitive than rapid antigen tests. Importantly, saliva testing flagged 83% of semester positives (43,884 tests administered) and was 95.6% concordant with nasopharyngeal diagnostic results (69.0% concordant on the first test when the nucleocapsid gene (N1) cycle threshold (CT) value was >30). Moreover, testing reduced weekly cases by 59.9% in the spring despite far looser restrictions, allowing for more normalcy while eliminating outbreaks. We also coupled our testing with a survey to clarify symptoms and transmissibility among college-age students. While only 8.5% remained asymptomatic throughout, symptoms were disparate and often cold-like (e.g., only 37.3% developed a fever), highlighting the difficulty with relying on symptom monitoring among this demographic. Based on reported symptom progression, we estimate that we removed 348 days of infectious individuals by routine testing. Interestingly, viral load (CT value) at the time of testing did not affect transmissibility (R2 = 0.0085), though those experiencing noticeable symptoms at the time of testing were more likely to spread the virus to close contacts (31.6% versus 14.3%). Together, our findings support routine testing for reducing the spread of SARS-CoV-2. Implementation of cost- and resource-efficient approaches should receive strong consideration in communities that lack herd immunity. IMPORTANCE This study highlights the utility of routine testing for SARS-CoV-2 using pooled saliva while maintaining high sensitivity of detection (under 2,500 copies/ml) and rapid turnaround of high volume (up to 930 samples in 8 h by two technicians and one quantitative PCR [qPCR] machine). This pooled approach allowed us to test all residential students 1 to 2 times per week on our college campus during the spring of 2021 and flagged 83% of our semester positives. Most students were asymptomatic or presented with symptoms mirroring common colds at the time of testing, allowing for removal of infectious individuals before they otherwise would have sought testing. To our knowledge, the total per-sample consumable cost of $0.43 is the lowest to date. With many communities still lagging in vaccination rates, routine testing that is cost-efficient highlights the capacity of the laboratory's role in controlling the spread of SARS-CoV-2.

Optimized and scalable synthesis of magnetic nanoparticles for RNA extraction in response to developing countries' needs in the detection and control of SARS-CoV-2.

Ecuador is one of the most affected countries, with the coronavirus disease 2019 (COVID-19) infection, in Latin America derived from an ongoing economic crisis. One of the most important methods for COVID-19 detection is the use of techniques such as real time RT-PCR based on a previous extraction/purification of RNA procedure from nasopharyngeal cells using functionalized magnetic nanoparticles (MNP). This technique allows the processing of ~ 10,000 tests per day in private companies and around hundreds per day at local Universities guaranteeing to reach a wide range of the population. However, the main drawback of this method is the need for specialized MNP with a strong negative charge for the viral RNA extraction to detect the existence of the SARS-CoV-2 virus. Here we present a simplified low cost method to produce 10 g of nanoparticles in 100 mL of solution that was scaled to one litter by parallelizing the process 10 times in just two days and allowing for the possibility of making ~ 50,000 COVID-19 tests. This communication helps in reducing the cost of acquiring MNP for diverse biomolecular applications supporting developing country budgets constraints and chemical availability specially during the COVID-19 International Health Emergency.

Optimising triage procedures for patients with cancer needing active anticancer treatment in the COVID-19 era.

BACKGROUND: Immunosuppression induced by anticancer therapy in a COVID-19-positive asymptomatic patient with cancer may have a devastating effect and, eventually, be lethal. To identify asymptomatic cases among patients receiving active cancer treatment, the Federico II University Hospital in Naples performs rapid serological tests in addition to hospital standard clinical triage for COVID-19 infection. METHODS: From 6 to 17 April 2020, all candidates for chemotherapy, radiotherapy or target/immunotherapy, if negative at the standard clinical triage on the day scheduled for anticancer treatment, received a rapid serological test on peripheral blood for COVID-19 IgM and IgG detection. In case of COVID-19 IgM and/or IgG positivity, patients underwent a real-time PCR (RT-PCR) SARS-CoV-2 test to confirm infection, and active cancer treatment was delayed. RESULTS: Overall 466 patients, negative for COVID-19 symptoms, underwent serological testing in addition to standard clinical triage. The average age was 61 years (range 25-88 years). Most patients (190, 40.8%) had breast cancer, and chemotherapy with or without immunotherapy was administered in 323 (69.3%) patients. Overall 433 (92.9%) patients were IgG-negative and IgM-negative, and 33 (7.1%) were IgM-positive and/or IgG-positive. Among the latter patients, 18 (3.9%), 11 (2.4%) and 4 (0.9%) were IgM-negative/IgG-positive, IgM-positive/IgG-negative and IgM-positive/IgG-positive, respectively. All 33 patients with a positive serological test, tested negative for RT-PCR SARS-CoV-2 test. No patient in our cohort developed symptoms suggestive of active COVID-19 infection. CONCLUSION: Rapid serological testing at hospital admission failed to detect active asymptomatic COVID-19 infection. Moreover, it entailed additional economic and human resources, delayed therapy administrationand increased hospital accesses.

Pooled RNA sample reverse transcriptase real time PCR assay for SARS CoV-2 infection: A reliable, faster and economical method.

BACKGROUND: Corona virus disease 2019 (COVID-19) which initially started as a cluster of pneumonia cases in the Wuhan city of China has now become a full-blown pandemic. Timely diagnosis of COVID-19 is the key in containing the pandemic and breaking the chain of transmission. In low- and middle-income countries availability of testing kits has become the major bottleneck in testing. Novel methods like pooling of samples are the need of the hour. OBJECTIVE: We undertook this study to evaluate a novel protocol of pooling of RNA samples/elutes in performance of PCR for SARS CoV-2 virus. STUDY DESIGN: Extracted RNA samples were randomly placed in pools of 8 on a 96 well plate. Both individual RNA (ID) and pooled RNA RT-qPCR for the screening E gene were done in the same plate and the positivity for the E gene was seen. RESULTS: The present study demonstrated that pool testing with RNA samples can easily detect even up to a single positive sample with Ct value as high as 38. The present study also showed that the results of pool testing is not affected by number of positive samples in a pool. CONCLUSION: Pooling of RNA samples can reduce the time and expense, and can help expand diagnostic capabilities, especially during constrained supply of reagents and PCR kits for the diagnosis of SARS-CoV-2 infection.

Development and evaluation of a multiplex conventional reverse-transcription polymerase chain reaction assay for detection of common viral pathogens causing acute gastroenteritis.

Timely identification of etiological agents of enteric infections is necessary to reduce the burden of infantile diarrheal mortality. Nucleic acid amplification-based detection methods offer a quick, reliable way for diagnosis of microbes in clinical specimens. This study was undertaken to evaluate an easy-to-use, cost-effective multiplex conventional reverse-transcription polymerase chain reaction (RT-PCR) assay developed at the Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases virology laboratory to identify 4 common enteric viruses (rotavirus, norovirus, adenovirus, astrovirus) in stool samples from patients who were being evaluated for acute diarrhea. On comparison with a commercially available real-time PCR method, significant agreement in sensitivity and specificity was observed. Though the turnaround time for RT-PCR was 6-8 h compared to 5-6 h for real-time PCR, the real-time PCR has high test cost (approximately 28 USD/2000 INR) for Fast-Track Diagnostics kit-based quantitative RT-PCR versus 6 USD or 400 INR for conventional multiplex RT-PCR/sample. Thus, the conventional RT-PCR method is expected to be adaptable at local hospitals and health cares in resource-poor settings.

Probabilistic cost-utility analysis and expected value of perfect information for the Oncotype multigenic test: a discrete event simulation model.

OBJECTIVE: To carry out a cost-utility analysis of the application of the Oncotype genomic test to inform the decision to use or not to use chemotherapy in the Basque Country (Spain). METHOD: The cost-utility study was carried out using a discrete event simulation model representing the natural history of breast cancer. The decision of treatment with chemotherapy based on Oncotype was compared with the standard of treatment based on clinical-pathological criteria. The model included clinical data from Basque hospitals and the literature and was processed by deterministic and probabilistic analysis to calculate the incremental cost-effectiveness ratio (ICER), the cost-effectiveness plane, the acceptability curve and the expected value of perfect information. The study adopted both a health and societal perspective. RESULTS: From a health perspective, the deterministic analysis estimated an ICER for Oncotype of 17,453 euros/quality-adjusted life year (QALY), discount included, and 9,613 euros/QALY without the discount. Eighty five percent (85%) of the simulations were below the efficiency threshold for Spain. The parametric variability associated with the Oncotype results was the main uncertainty factor in the decision. CONCLUSIONS: Oncotype is a cost-effective intervention from a health system perspective since each QALY gained costs less than 25,000 euros. From a societal perspective, it is dominant since it provides greater health and is accompanied by cost savings.

Economic value of regular monitoring of response to treatment among US patients with chronic myeloid leukemia based on an economic model.

BACKGROUND: Regular molecular monitoring with reverse-transcription quantitative PCR (RT-qPCR) analysis of BCR-ABL1 transcripts is associated with reduced disease progression among patients with chronic myeloid leukemia (CML). Molecular monitoring assists in the timely detection of primary or secondary resistance to tyrosine kinase inhibitor (TKI) therapy and is a recommended practice by the National Comprehensive Cancer Network guidelines. An economic model was developed to estimate the potential impact of CML monitoring vs lack of monitoring on patient healthcare costs. METHODS: An Excel-based decision-analytic economic model was developed from a US payer perspective. The model was used to estimate the expected healthcare cost differences between regular molecular monitoring of CML patients and lack of monitoring. CML progression rates among patients with vs without monitoring, the annual cost of CML progression, the average number of monitoring tests per year, and the average cost per RT-qPCR monitoring test were incorporated into the model. Univariate and multivariable sensitivity analyses were conducted. RESULTS: Based on estimates in published literature, disease progression to the accelerated/blast phase occurs among 0.35% of patients with monitoring and 5.12% of patients without monitoring, and the annual cost of CML progression is $136,308 per patient year. The analysis found that total healthcare costs, including the costs associated with CML progression and RT-qPCR monitoring tests (three tests per year), were $1,142 for patients with monitoring and $6,982 for patients without monitoring (difference = $5,840). In a hypothetical cohort of 100 patients with CML, achieving a 100% monitoring rate was associated with a total cost-savings of $584,005 compared to a 0% monitoring rate. This cost-savings remained consistent under both univariate and multivariable sensitivity analyses. CONCLUSION: Regular CML monitoring was associated with improved outcomes among CML patients and, consequently, reduced healthcare costs.

Development of a One-Step Duplex RT-PCR Method for the Simultaneous Detection of VP3/VP1 and VP1/P2B Regions of the Hepatitis A Virus.

The simultaneous detection and accurate identification of hepatitis A virus (HAV) is critical in food safety and epidemiological studies to prevent the spread of HAV outbreaks. Towards this goal, a one-step duplex reverse-transcription (RT)-PCR method was developed targeting the VP1/P2B and VP3/VP1 regions of the HAV genome for the qualitative detection of HAV. An HAV RT-qPCR standard curve was produced for the quantification of HAV RNA. The detection limit of the duplex RT-PCR method was 2.8 × 10(1) copies of HAV. The PCR products enabled HAV genotyping analysis through DNA sequencing, which can be applied for epidemiological investigations. The ability of this duplex RT-PCR method to detect HAV was evaluated with HAV-spiked samples of fresh lettuce, frozen strawberries, and oysters. The limit of detection of the one-step duplex RT-PCR for each food model was 9.4 × 10(2) copies/20 g fresh lettuce, 9.7 × 10(3) copies/20 g frozen strawberries, and 4.1 × 10(3) copies/1.5 g oysters. Use of a one-step duplex RT-PCR method has advantages such as shorter time, decreased cost, and decreased labor owing to the single amplification reaction instead of four amplifications necessary for nested RT-PCR.

Combined multiplex and monoplex RT-PCR as a reliable and cost-effective method for molecular diagnostics of pediatric acute lymphoblastic leukemia.

The precise diagnosis of acute lymphoblastic leukemia is essential for correct prognosis assessment and therapy regimen selection. At present, immunophenotyping, cytogenetics and molecular screening are major and complementary methods utilized in a routine leukemia diagnostics. The aim of this study was to validate the application of multiplex reverse transcription-polymerase chain reaction (RT-PCR) assay for molecular diagnosis of the most common pediatric acute lymphoblastic leukemia-associated fusion transcripts. Our data show that screening of bone marrow and/or peripheral blood by RT-PCR, consisting of multiplex and monoplex PCR, confirmed results of real-time quantitative PCR (RT qPCR). This screening may provide a reliable, specific and sensitive method amenable to standard laboratory practice and a cost-effective alternative to more complex and expensive RT qPCR techniques.

[Economic assessment of the routine use of Oncotype DX® assay for early breast cancer in Franche-Comte region]. / Évaluation économique de l'utilisation en routine du test Oncotype DX® dans la prise en charge des cancers du sein en Franche-Comté.

Oncotype DX® has been validated as quantifying the likelihood of distant recurrence at 10 years and overall chemotherapy benefit in patients with estrogen-receptor-positive and HER-2-negative early breast cancer. In 2012, this genomic signature was routinely available for patients in Franche-Comté, France. Patients eligible for Oncotype DX(®) testing had a ER-positive, HER-2-négative early breast cancer with a nodal involvement limited to 0 or 1 positive-node without extracapsular spread; an adjuvant chemotherapy was indicated based on usual prognostic factors. The aim was to assess the economic impact of Oncotype DX(®) testing in a French region. A cost-minimisation analysis from the French Public Healthcare System perspective was performed. The availability of Oncotype DX(®) in Franche-Comté, France, and its use in clinical routine allowed a decrease of 73 % of adjuvant chemotherapy without increase of the cost of the patients' management and with a potential reduction of the cost for the French Public Healthcare System. This strategy was successful and may allow the reimbursement of this test in France for patients with early breast cancer.

A Combined Fabrication and Instrumentation Platform for Sample Preparation.

While potentially powerful, access to molecular diagnostics is substantially limited in the developing world. Here we present an approach to reduced cost molecular diagnostic instrumentation that has the potential to empower developing world communities by reducing costs through streamlining the sample preparation process. In addition, this instrument is capable of producing its own consumable devices on demand, reducing reliance on assay suppliers. Furthermore, this instrument is designed with an "open" architecture, allowing users to visually observe the assay process and make modifications as necessary (as opposed to traditional "black box" systems). This open environment enables integration of microfluidic fabrication and viral RNA purification onto an easy-to-use modular system via the use of interchangeable trays. Here we employ this system to develop a protocol to fabricate microfluidic devices and then use these devices to isolate viral RNA from serum for the measurement of human immunodeficiency virus (HIV) viral load. Results obtained from this method show significantly reduced error compared with similar nonautomated sample preparation processes.

[Comparative cost analysis of molecular biology methods in the diagnosis of sarcomas]. / Analyse comparative des coûts de techniques de biologie moléculaire dans le diagnostic de sarcomes.

Sarcomas represent a complex and heterogeneous group of rare malignant tumors and their correct diagnosis is often difficult. Recent molecular biological techniques have been of great diagnostic use and there is a need to assess the cost of these procedures in routine clinical practice. Using prospective and observational data from eight molecular biology laboratories in France, we used "microcosting" method to assess the cost of molecular biological techniques in the diagnosis of five types of sarcoma. The mean cost of fluorescence in situ hybridization (FISH) was 318 € (273-393) per sample; mean reverse transcription polymerase chain reaction (RT-PCR) cost ranged from 300 € (229-481) per formalin-fixed, paraffin-embedded specimen to 258 € (213-339) per frozen specimen; mean quantitative polymerase chain reaction (Q-PCR) cost was 184 € (112-229) and mean CGH-array cost was 332 € (329-335). The cost of these recently implemented techniques varied according to the type of sarcoma; the method of tissue collection and local organizational factors including the level of local expertise and investment. The cost of molecular diagnostic techniques needs to be balanced against their respective performance.

Molecular staging individualizing cancer management.

Although the most important prognostic and predictive marker in colorectal cancer is tumor cells in lymph nodes, approximately 30% of patients who are node-negative die from occult metastases. Molecular staging employing specific markers and sensitive detection technologies has emerged as a powerful platform to assess prognosis in node-negative colon cancer. Integrating molecular staging into algorithms that individualize patient management will require validation and the definition of relationships between occult tumor cells, prognosis, and responses to chemotherapy.

Mass scale screening of common arboviral infections by an affordable, cost effective RT-PCR method.

OBJECTIVE: To develop a rapid, cost effective RT-PCR method for the mass scale diagnosis of such diseases at the viremia stage to find out the actual disease burden in that area. METHODS: For this purpose, cases with the history of only short febrile illness were considered. Thus 157 samples with the history of dengue/chikungunya like illness and only 58 samples with a history of acute encephalitis syndrome (AES) were selected. RESULTS: Out of 157 samples, 42 and 74 were detected as dengue and chikungunya, respectively and out of 58 AES cases only 23 could be detected as Japanese encephalitis by this RT-PCR method. CONCLUSIONS: This cost effective RT-PCR method can detect the total positive cases that remain undetected by ELISA method. Moreover, this method is capable to detect the viral RNA from patients' sera even after the appearance of IgM antibody at one fifth costs as compared with the other commercially available kits.

Cost-effectiveness of 21-gene assay in node-positive, early-stage breast cancer.

OBJECTIVE: To assess impact on health outcomes and healthcare expenditures of adopting a 21-gene assay for women with early-stage, minimally node-positive, estrogen receptor-positive (N (1-3)/ER) HER2-negative breast cancer. STUDY DESIGN: We adapted a deterministic decision-analytic model to estimate costs and quality-of-life outcomes associated with chemotherapy, adverse events, supportive care, recurrence, and second primary cancers for usual care compared with care determined by the 21-gene assay recurrence score, where 71% and 54% of women, respectively, were treated with adjuvant chemotherapy. Model input data were based on national statistics, published literature, physician surveys, and Medicare Part B prices. METHODS: Annual numbers of events were multiplied by quality-adjusted life-years (QALYs) lost and costs to estimate net health and economic impacts of each strategy. Analyses were from a managed care payer perspective for the US population. RESULTS: Patients receiving the assay were predicted to gain 0.127 QALY and save $4359 annually from avoiding chemotherapy, adverse events, supportive care, and secondary primary tumors. For a 2-million member plan, net gains were 4.44 QALYs/year and savings were $13,476/year. Cost savings were greater for the Medicare population. Although overall results were sensitive only to reduced impact of testing and chemotherapy costs, they were still highly cost-effective (incremental cost-effectiveness ratio <$20,000/QALY). CONCLUSIONS: Use of a 21-gene assay in patients with early-stage N (1-3)/ER HER2-negative breast cancer may improve health outcomes and add no incremental cost, thereby providing valuable insight for health plans, the Centers for Medicare and Medicaid Services, and clinicians regarding coverage policies and treatment decisions.

Costo-efectividad en la detección de influenza H1N1: datos clínicos versus pruebas rápidas / Cost-effectiveness in the detection of influenza H1N1: clinical data versus rapid tests

OBJETIVO: Evaluar el desempeño de los datos clínicos y la prueba rápida (PR) en el diagnóstico de influenza H1N1, y analizar el costo-beneficio que representa el uso de esta herramienta diagnóstica. MÉTODOS: Se aplicó la PR a pacientes que acudieron a cuatro hospitales en la ciudad de México con sintomatología similar a influenza (SSI) durante el período octubre y noviembre de 2009. Se comparó el desempeño diagnóstico de la SSI más la PR contra el de la reacción en cadena de la polimerasa en transcripción reversa en tiempo real (rRT-PCR). La rRT-PCR fue procesada en un laboratorio de referencia y cegado al resultado de la PR. Además, se llevó a cabo una evaluación económica a partir de la cual se estimó el impacto presupuestal relacionado con la utilización de la PR RESULTADOS: Se incluyó a 78 pacientes, de los cuales 39 fueron positivos para influenza H1N1 y 6 para influenza A estacional, de acuerdo al resultado de la rRT-PCR. La SSI mostró una sensibilidad de 96 por ciento y una especificidad de 21 por ciento, la PR de 76 por ciento y 82 por ciento y el conjunto de SSI más PR de 96 por ciento y 100 por ciento, respectivamente. El Cociente de Verosimilitud positivo de la SSI-cefalea fue de 31,5 y el de SSI-odinofagia fue de 330. El uso de PR mostró un ahorro de US$ 12,6 por cada caso sospechoso. CONCLUSIONES: El uso de la PR como auxiliar en el diagnóstico de influenza H1N1 incrementa la certeza y reduce el costo promedio por paciente sospechoso e infectado.

OBJECTIVE: Evaluate the performance of clinical data and the rapid influenza diagnostic test (RIDT) in diagnosing influenza H1N1, and analyze the cost-benefit of using this diagnostic tool. METHODS: The RIDT was used for patients who came to four hospitals in Mexico City with an influenza-like illness (ILI) in October and November 2009. The diagnostic performance of the ILI clinical data and the RIDT was compared to that of the real-time reverse transcription polymerase chain reaction (rRT-PCR) test. The rRT-PCR test was conducted in a reference laboratory and blinded to the results of the RIDT. An economic evaluation also was conducted to estimate the budgetary impact of using the RIDT. RESULTS: The study included 78 patients, 39 of whom tested positive for influenza H1N1 and 6 tested positive for seasonal influenza A, according to the results of the rRT-PCR. The ILI clinical data yielded a sensitivity of 96 percent and specificity of 21 percent; the RIDT yielded a sensitivity of 76 percent and specificity of 82 percent; and the ILI clinical data and RIDT together yielded a sensitivity of 96 percent and specificity of 100 percent. The positive likelihood quotient for ILI-headaches was 31.5 and that of ILI-odynophagia, 330. The use of RIDT yielded savings of US$12.6 per each suspected case. CONCLUSIONS: Use of the RIDT to aid in the diagnosis of influenza H1N1 increases certainty and lowers the average cost per suspected and infected patient.

Twenty-four mini-pool HCV RNA screening in a routine clinical virology laboratory setting: a six-year prospective study.

The usefulness of combined anti-HCV and 24 mini-pool HCV RNA screening strategy was re-evaluated after a six-year continuous routine use in a clinical virology laboratory, at which more than half of newly diagnosed hepatitis C patients are intravenous drug users. Pools of 24 samples were prepared from 20,448 anti-HCV negative serum samples and tested using an automated commercial PCR assay with a lower limit of detection of 50 IU/ml. After detection of anti-HCV negative/HCV RNA positive patients, responsible physicians provided follow-up samples. Thirty-eight (0.19%) anti-HCV negative/HCV RNA positive samples from 30 patients (28 intravenous drug users) were detected. Follow-up samples were available for 27/30 patients. Twenty, six and one patient seroconverted in the second, third and fourth available samples, respectively. The interval between the first HCV RNA positive and the first available anti-HCV positive sample was 17-517 days. The costs of detecting a single anti-HCV negative/HCV RNA positive patient were 1227 Euros. Combined anti-HCV and 24 mini-pool HCV RNA screening is a useful and cost effective strategy, not only in blood-transfusion settings but also in a routine clinical virology laboratory, at which a significant proportion of the tested population belongs to a high-risk population.

Detection of poliovirus by ICC/qPCR in concentrated water samples has greater sensitivity and is less costly using BGM cells in suspension as compared to monolayers.

The integrated cell culture quantitative reverse transcriptase PCR (ICC/qRT-PCR) method is used in our lab to detect enteroviruses in environmental waters. Typically we utilize monolayers of 3 cell lines; buffalo green monkey kidney (BGM), human colonic carcinoma (CACO-2) and African rhesus monkey kidney (MA104) with the intent of providing one or more permissive hosts to a wide range of enteroviruses. In this study the BGM cell line was used to compare poliovirus infectivity in conventional monolayer cultures to BGM cells in suspensions. Propagated virus was subsequently amplified by qRT-PCR. Our PCR data showed lower cycle threshold (Ct) values in the suspensions which corresponded to a higher rate of infectivity than that observed in the monolayers. The difference in Ct values was determined statistically significant by One-way ANOVA (0.000). Infecting BGM cells in suspensions required less hands-on time, less chance of contamination and was more cost effective than utilizing the conventional monolayer technique.