Performance of the Xpert™ Mpox PCR assay with oropharyngeal, anorectal, and cutaneous lesion swab specimens

Anorectal and oropharyngeal exposures are implicated in sexual transmission of mpox, but authorized assays in the United States are only validated with cutaneous lesion swabs. Diagnostic assays for anorectal and oropharyngeal swabs are needed to address potential future outbreaks. The Cepheid Xpert® Mpox is the first point-of-care assay to receive FDA emergency use authorization in the United States and would be a valuable tool for evaluating these sample types. Our exploratory study demonstrates 100 % positive agreement with our in-house PCR assay for natural positive anorectal and oropharyngeal specimens and 92 % sensitivity with low-positive spiked specimens. The Xpert® assay detected viral DNA in specimens not detected by our reference PCR assay from four participants with mpox DNA at other sites, suggesting it may be more sensitive at low viral loads. In conclusion, the validation of the Xpert® for oropharyngeal and anorectal sample types can be rapidly achieved if clinical need returns and prospective samples become available.

Comparison of RT-PCR and antigen test sensitivity across nasopharyngeal, nares, and oropharyngeal swab, and saliva sample types during the SARS-CoV-2 omicron variant

Limited data highlight the need to understand differences in SARS-CoV-2 omicron (B.1.1.529) variant viral load between the gold standard nasopharyngeal (NP) swab, mid-turbinate (MT)/anterior nasal swabs, oropharyngeal (OP) swabs, and saliva. MT, OP, and saliva samples from symptomatic individuals in Atlanta, GA, in January 2022 and longitudinal samples from a small familial cohort were tested by both RT-PCR and ultrasensitive antigen assays. Higher concentrations in the nares were observed in the familial cohort, but a dominant sample type was not found among 39 cases in the cross-sectional cohort. The composite of positive MT or OP assay for both RT-PCR and antigen assay trended toward higher diagnostic yield but did not achieve significant difference. Our data did not identify a singular preferred sample type for SARS-CoV-2 testing, but higher levels of saliva nucleocapsid, a trend toward higher yield of composite OP/MT result, and association of apparent MT or OP predominance with symptoms warrant further study.

Multisite Mpox Infection and Viral Dynamics Among Persons With HIV in Metro Atlanta

The 2022 mpox outbreak primarily involved sexual transmission among men who have sex with men and disproportionately affected persons with human immunodeficiency virus (HIV). We examined viral dynamics and clinical features in a cohort evaluated for mpox infection at a comprehensive HIV clinic in Atlanta, Georgia. Viral DNA was found in 8 oropharyngeal and 5 anorectal specimens among 10 mpox cases confirmed by lesion swab polymerase chain reaction. Within-participant anatomic site of lowest cycle threshold (Ct) value varied, and lower Ct values were found in oropharyngeal and anorectal swabs when corresponding symptoms were present. This provides insight into mpox infection across multiple anatomic sites among people with HIV.

Rapid, high throughput, automated detection of SARS-CoV-2 neutralizing antibodies against Wuhan-WT, delta and omicron BA1, BA2 spike trimers

Traditional cellular and live-virus methods for detection of SARS-CoV-2 neutralizing antibodies (nAbs) are labor- and time-intensive, and thus not suited for routine use in the clinical lab to predict vaccine efficacy and natural immune protection. Here, we report the development and validation of a rapid, high throughput method for measuring SARS-CoV-2 nAbs against native-like trimeric spike proteins. This assay uses a blockade of human angiotensin converting enzyme 2 (hACE-2) binding (BoAb) approach in an automated digital immunoassay on the Quanterix HD-X platform. BoAb assays using Wuhan-WT (vaccine strain), delta (B.1.167.2), omicron BA1 and BA2 variant viral strains showed strong correlation with cell-based pseudovirus neutralization activity (PNA) and live-virus neutralization activity. Importantly, we were able to detect similar patterns of delta and omicron variant resistance to neutralization in samples with paired vaccine strain and delta variant BoAb measurements. Finally, we screened clinical samples from patients with or without evidence of SARS-CoV-2 exposure by a single-dilution screening version of our assays, finding significant nAb activity only in exposed individuals. Importantly, this completely automated assay can be performed in 4 h to measure neutralizing antibody titers for 16 samples over 8 serial dilutions or, 128 samples at a single dilution with replicates. In principle, these assays offer a rapid, robust, and scalable alternative to time-, skill-, and cost-intensive standard methods for measuring SARS-CoV-2 nAb levels.

Effect of swab pooling on the Accula point-of-care RT-PCR for SARS-CoV-2 detection

Introduction

Swab pooling may allow for more efficient use of point-of-care assays for SARS-CoV-2 detection in settings where widespread testing is warranted, but the effects of pooling on assay performance are not well described.

Methods

We tested the Thermo-Fisher Accula rapid point-of-care RT-PCR platform with contrived pooled nasal swab specimens.

Results

We observed a higher limit of detection of 3,750 copies/swab in pooled specimens compared to 2,250 copies/swab in individual specimens. Assay performance appeared worse in a specimen with visible nasal mucous and debris, although performance was improved when using a standard laboratory mechanical pipette compared to the transfer pipette included in the assay kit.

Conclusion

Clinicians and public health officials overseeing mass testing efforts must understand limitations and benefits of swab or sample pooling, including reduced assay performance from pooled specimens. We conclude that the Accula RT-PCR platform remains an attractive candidate assay for pooling strategies owing to the superior analytical sensitivity compared to most home use and point-of-care tests despite the inhibitory effects of pooled specimens we characterized.

Pivot, persevere, or perish: how Ellume Health overcame development and regulatory obstacles to become the first authorized over-the-counter COVID-19 test in the United States

The Ellume COVID-19 home test from Ellume Health (Brisbane, Aus) became the first COVID-19 diagnostic tool authorized for home use by the United States FDA in December 2020. This early pandemic success was built on over ten years of work on the Ellume influenza home test. Ellume overcame critical technology challenges during the development of their influenza test. In addition, it faced a recall of its COVID-19 home test in 2021 due to false positive results. While Ellume initially persevered through the recall and restarted sales in the United States, the combination of the recall and the wide availability of competitors' low-cost over the counter tests in the United States led to Ellume entering voluntary administration in September 2022. This paper traces the history of Ellume and how 10 years of experience with a home influenza test allowed the company to quickly develop the Ellume COVID-19 home test. We will also provide to diagnostic developers the key strategies employed by Ellume to succeed while highlighting the pitfalls that have challenged the company's business success.

Investigation of Blood Plasma Viral Nucleocapsid Antigen as a Marker of Active Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variant Infection

Background

Nasopharyngeal qualitative reverse-transcription polymerase chain reaction (RT-PCR) is the gold standard for diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but it is not practical or sufficient in every clinical scenario due to its inability to distinguish active from resolved infection. Alternative or adjunct testing may be needed to guide isolation precautions and treatment in patients admitted to the hospital.

Methods

We performed a single-center, retrospective analysis of residual clinical specimens and medical record data to examine blood plasma nucleocapsid antigen as a candidate biomarker of active SARS-CoV-2. Adult patients admitted to the hospital or presenting to the emergency department with SARS-CoV-2 ribonucleic acid (RNA) detected by RT-PCR from a nasopharyngeal swab specimen were included. Both nasopharyngeal swab and a paired whole blood sample were required to be available for analysis.

Results

Fifty-four patients were included. Eight patients had positive nasopharyngeal swab virus cultures, 7 of whom (87.5%) had concurrent antigenemia. Nineteen (79.2%) of 24 patients with detectable subgenomic RNA and 20 (80.0%) of 25 patients with N2 RT-PCR cycle threshold ≤ 33 had antigenemia.

Conclusions

Most individuals with active SARS-CoV-2 infection are likely to have concurrent antigenemia, but there may be some individuals with active infection in whom antigenemia is not detectable. The potential for high sensitivity and convenience of a blood test prompts interest in further investigation as a screening tool to reduce reliance on nasopharyngeal swab sampling and as an adjunct diagnostic test to aid in clinical decision making during the period after acute coronavirus disease 2019.

SARS-CoV-2 Antigenemia is Associated With Pneumonia in Children But Lacks Sensitivity to Diagnose Acute Infection

BACKGROUND

Nucleocapsid antigenemia in adults has demonstrated high sensitivity and specificity for acute infection, and antigen burden is associated with disease severity. Data regarding SARS-CoV-2 antigenemia in children are limited.

METHODS

We retrospectively analyzed blood plasma specimens from hospitalized children with COVID-19 or MIS-C. Nucleocapsid and spike were measured using ultrasensitive immunoassays.

RESULTS

We detected nucleocapsid antigenemia in 62% (50/81) and spike antigenemia in 27% (21/79) of children with acute COVID-19 but 0% (0/26) and 15% (4/26) with MIS-C from March 2020-March 2021. Higher nucleocapsid levels were associated with radiographic infiltrates and respiratory symptoms in children with COVID-19.

CONCLUSIONS

Antigenemia lacks the sensitivity to diagnose acute infection in children but is associated with signs and symptoms of lower respiratory tract involvement. Further study into the mechanism of antigenemia, its association with specific organ involvement, and the role of antigenemia in the pathogenesis of COVID-19 is warranted.

Nucleocapsid antigenemia in patients receiving anti-CD20 therapy with protracted COVID-19

Immunocompromised patients with prolonged coronavirus disease 2019 symptoms present diagnostic and therapeutic challenges. We measured viral nucleocapsid antigenemia in 3 patients treated with anti-CD20 immunotherapy who acquired severe acute respiratory syndrome coronavirus 2 infection and experienced protracted symptoms. Our results support nucleocapsid antigenemia as a marker of persistent infection and therapeutic response.

Nucleocapsid Antigenemia Is a Marker of Acute SARS-CoV-2 Infection

Detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is essential for diagnosis, treatment, and infection control. Polymerase chain reaction (PCR) fails to distinguish acute from resolved infections, as RNA is frequently detected after infectiousness. We hypothesized that nucleocapsid in blood marks acute infection with the potential to enhance isolation and treatment strategies. In a retrospective serosurvey of inpatient and outpatient encounters, we categorized samples along an infection timeline using timing of SARS-CoV-2 testing and symptomatology. Among 1860 specimens from 1607 patients, the highest levels and frequency of antigenemia were observed in samples from acute SARS-CoV-2 infection. Antigenemia was higher in seronegative individuals and in those with severe disease. In our analysis, antigenemia exhibited 85.8% sensitivity and 98.6% specificity as a biomarker for acute coronavirus disease 2019 (COVID-19). Thus, antigenemia sensitively and specifically marks acute SARS-CoV-2 infection. Further study is warranted to determine whether antigenemia may aid individualized assessment of active COVID-19.

Don't forget about human factors: Lessons learned from COVID-19 point-of-care testing

During the COVID-19 pandemic, the development of point-of-care (POC) diagnostic testing accelerated in an unparalleled fashion. As a result, there has been an increased need for accurate, robust, and easy-to-use POC testing in a variety of non-traditional settings (i.e., pharmacies, drive-thru sites, schools). While stakeholders often express the desire for POC technologies that are "as simple as digital pregnancy tests," there is little discussion of what this means in regards to device design, development, and assessment. The design of POC technologies and systems should take into account the capabilities and limitations of the users and their environments. Such "human factors" are important tenets that can help technology developers create POC technologies that are effective for end-users in a multitude of settings. Here, we review the core principles of human factors and discuss lessons learned during the evaluation process of SARS-CoV-2 POC testing.

Designing for simplicity: lessons from Mesa Biotech for microfluidic entrepreneurs and early-stage companies

The COVID-19 pandemic has proven the need for point-of-care diagnosis of respiratory diseases and microfluidic technology has risen to the occasion. Mesa Biotech (San Diego, CA) originally developed the Accula platform for the diagnosis of influenza A and B and then extended the platform to SARS-CoV-2. Mesa Biotech has experienced tremendous success, culminating in acquisition by Thermo Fisher for up to $550m USD. The Accula microfluidics platform accomplished the leap from the lab to commercial product through clever design and engineering choices. Through information obtained from interviews with key Mesa Biotech leaders and publicly-available documents, we describe the keys to Mesa's success and how they might inform other lab-on-a-chip companies.

Rapid, high throughput, automated detection of SARS-CoV-2 neutralizing antibodies against native-like vaccine and delta variant spike trimers

Traditional cellular and live-virus methods for detection of SARS-CoV-2 neutralizing antibodies (nAbs) are labor- and time-intensive, and thus not suited for routine use in the clinical lab to predict vaccine efficacy and natural immune protection. Here, we report the development and validation of a rapid, high throughput method for measuring SARS-CoV-2 nAbs against native-like trimeric spike proteins. This assay uses a blockade of hACE-2 binding (BoAb) approach in an automated digital immunoassay on the Quanterix HD-X platform. BoAb assays using vaccine and delta variant viral strains showed strong correlation with cell-based pseudovirus and live-virus neutralization activity. Importantly, we were able to detect similar patterns of delta variant resistance to neutralization in samples with paired vaccine and delta variant BoAb measurements. Finally, we screened clinical samples from patients with or without evidence of SARS-CoV-2 exposure by a single-dilution screening version of our assays, finding significant nAb activity only in exposed individuals. In principle, these assays offer a rapid, robust, and scalable alternative to time-, skill-, and cost-intensive standard methods for measuring SARS-CoV-2 nAb levels.

Where is Omicron? Comparison of SARS-CoV-2 RT-PCR and Antigen Test Sensitivity at Commonly Sampled Anatomic Sites Over the Course of Disease

BACKGROUND

Upper respiratory samples for SARS-CoV-2 detection include the gold standard nasopharyngeal (NP) swab, and mid-turbinate (MT) nasal swabs, oropharyngeal (OP) swabs, and saliva. Following the emergence of the omicron (B.1.1.529) variant, limited preliminary data suggest that OP swabs or saliva samples may be more sensitive than nasal swabs, highlighting the need to understand differences in viral load across different sites.

METHODS

MT, OP, and saliva samples were collected from symptomatic individuals presenting for evaluation in Atlanta, GA, in January 2022. Longitudinal samples were collected from a family cohort following COVID-19 exposure to describe detection of viral targets over the course of infection.

RESULTS

SARS-CoV-2 RNA and nucleocapsid antigen measurements demonstrated a nares-predominant phenotype in a familial cohort. A consistent dominant location for SARS-CoV-2 was not found among 54 individuals. Positive percent agreement for virus detection in MT, OP and saliva specimens were 66.7 [54.1-79.2], 82.2 [71.1-93.4], and 72.5 [60.3-84.8] by RT-PCR, respectively, and 46.2 [32.6-59.7], 51.2 [36.2-66.1], and 72.0 [59.6-84.4] by ultrasensitive antigen assay. The composite of positive MT or OP assay was not significantly different than either alone for both RT-PCR and antigen assay (PPA 86.7 [76.7-96.6] and 59.5 [44.7-74.4], respectively).

CONCLUSIONS

Our data suggest that SARS-CoV-2 nucleocapsid and RNA exhibited similar kinetics and diagnostic yield in three upper respiratory sample types across the duration of symptomatic disease. Collection of OP or combined nasal and OP samples does not appear to increase sensitivity versus validated nasal sampling for rapid detection of viral antigen.

Rapid, high throughput, automated detection of SARS-CoV-2 neutralizing antibodies against native-like vaccine and delta variant spike trimers

Traditional cellular and live-virus methods for detection of SARS-CoV-2 neutralizing antibodies (nAbs) are labor- and time-intensive, and thus not suited for routine use in the clinical lab to predict vaccine efficacy and natural immune protection. Here, we report the development and validation of a rapid, high throughput method for measuring SARS-CoV-2 nAbs against native-like trimeric spike proteins. This assay uses a blockade of hACE-2 binding (BoAb) approach in an automated digital immunoassay on the Quanterix HD-X platform. BoAb assays using vaccine and delta variant viral strains showed strong correlation with cell-based pseudovirus and live-virus neutralization activity. Importantly, we were able to detect similar patterns of delta variant resistance to neutralization in samples with paired vaccine and delta variant BoAb measurements. Finally, we screened clinical samples from patients with or without evidence of SARS-CoV-2 exposure by a single-dilution screening version of our assays, finding significant nAb activity only in exposed individuals. In principle, these assays offer a rapid, robust, and scalable alternative to time-, skill-, and cost-intensive standard methods for measuring SARS-CoV-2 nAb levels.

Acanthamoeba castellanii encephalitis in a patient with AIDS: a case report and literature review

Amoebic encephalitis is a rare cause of CNS infection for which mortality exceeds 90%. We present the case of a 27-year-old man with AIDS who presented to a hospital in Atlanta (Georgia, USA) with tonic-clonic seizures and headache. His clinical condition deteriorated over several days. Brain biopsy revealed lymphohistiocytic inflammation and necrosis with trophozoites and encysted forms of amoebae. Immunohistochemical and PCR testing confirmed Acanthamoeba castellanii encephalitis, typically described as granulomatous amoebic encephalitis (GAE). No proven therapy for GAE is available, although both surgical and multiagent antimicrobial treatment strategies are often used. Most recently, these include the antileishmanial agent miltefosine. Here we review all cases of GAE due to Acanthamoeba spp in people with HIV/AIDS identified in the literature and reported to the Centers for Disease Control and Prevention. We describe this case as a reminder to the clinician to consider protozoal infections, especially free-living amoeba, in the immunocompromised host with a CNS infection refractory to traditional antimicrobial therapy.

Clinical Utilization of DiaSorin Molecular Polymerase Chain Reaction in Pneumocystis Pneumonia

BACKGROUND

Pneumocystis jirovecii polymerase chain reaction (PCR) testing is a sensitive diagnostic tool but does not distinguish infection from colonization. Cycle threshold (CT) may correlate with fungal burden and could be considered in clinical decision making. Clinical use of PCR and significance of CT values have not previously been examined with the DiaSorin Molecular platform.

METHODS

Retrospective review of P jirovecii PCR, CT values and clinical data from 18 months in a multihospital academic health system. The diagnostic performance of PCR with respect to pathology and correlation of CT with severity were examined.

RESULTS

Ninety-nine of 1006 (9.8%) assays from 786 patients in 919 encounters were positive. Among 91 (9.9%) encounters in which P jirovecii pneumonia (PJP) was treated, 41 (45%) were influenced by positive PCR. Negative PCR influenced discontinuation of therapy in 35 cases. Sensitivity and specificity of PCR were 93% (95% CI, 68%-100%) and 94% (95% CI, 91%-96%) with respect to pathology. CT values from deep respiratory specimens were significantly different among treated patients (P = .04) and those with positive pathology results (P < .0001) compared to patients not treated and those with negative pathology, respectively, and was highly predictive of positive pathology results (area under the curve = 0.92). No significant difference was observed in comparisons based on indicators of disease severity.

CONCLUSIONS

Pneumocystis jirovecii PCR was a highly impactful tool in the diagnosis and management of PJP, and use of CT values may have value in the treatment decision process in select cases. Further investigation in a prospective manner is needed.

Diagnostic and prognostic capabilities of a biomarker and EMR-based machine learning algorithm for sepsis

Sepsis is a major cause of mortality among hospitalized patients worldwide. Shorter time to administration of broad‐spectrum antibiotics is associated with improved outcomes, but early recognition of sepsis remains a major challenge. In a two‐center cohort study with prospective sample collection from 1400 adult patients in emergency departments suspected of sepsis, we sought to determine the diagnostic and prognostic capabilities of a machine‐learning algorithm based on clinical data and a set of uncommonly measured biomarkers. Specifically, we demonstrate that a machine‐learning model developed using this dataset outputs a score with not only diagnostic capability but also prognostic power with respect to hospital length of stay (LOS), 30‐day mortality, and 3‐day inpatient re‐admission both in our entire testing cohort and various subpopulations. The area under the receiver operating curve (AUROC) for diagnosis of sepsis was 0.83. Predicted risk scores for patients with septic shock were higher compared with patients with sepsis but without shock (p < 0.0001). Scores for patients with infection and organ dysfunction were higher compared with those without either condition (p < 0.0001). Stratification based on predicted scores of the patients into low, medium, and high‐risk groups showed significant differences in LOS (p < 0.0001), 30‐day mortality (p < 0.0001), and 30‐day inpatient readmission (p < 0.0001). In conclusion, a machine‐learning algorithm based on electronic medical record (EMR) data and three nonroutinely measured biomarkers demonstrated good diagnostic and prognostic capability at the time of initial blood culture.

Current Capabilities of Gut Microbiome-Based Diagnostics and the Promise of Clinical Application

There is increasing evidence for the importance of the gut microbiome in human health and disease. Traditional and modern technologies - from cell culture to next generation sequencing - have facilitated these advances in knowledge. Each of the tools employed in measuring the microbiome exhibits unique capabilities that may be leveraged for clinical diagnostics. However, much still needs to be done to standardize the language and metrics by which a microbiome is characterized. Here we review the capabilities of gut microbiome-based diagnostics, review selected examples, and discuss the outlook towards clinical application.

Diagnosis of acute serious illness: the role of point-of-care technologies

Access to rapid diagnostic information is a core value of point-of-care (POC) technology. This is particularly relevant in acute, emergency, and critical care settings where diagnostic speed and precision directly guide the management of patients with potentially life-threatening conditions. Many POC diagnostics described in the literature, however, remain largely unproven and have yet to enter the market entirely. Only a few have traversed the translation and commercialization pathways to reach widespread clinical adoption. Moreover, even technologies that have successfully translated to the patient bedside still frequently lack an evidence base showing improvement of clinical outcomes. In this review, we present aspects of diagnosis of acute life-threatening diseases and describe the potential role of POC technologies, emphasizing the available evidence of clinical outcomes. Finally, we discuss what is needed to identify clinically meaningful new technologies and translate them toward the long-promised goal of better health through rapid POC diagnosis.

Smartphone-imaged microfluidic biochip for measuring CD64 expression from whole blood

Sepsis, a life-threatening syndrome that contributes to millions of deaths annually worldwide, represents a moral and economic burden to the healthcare system. Although no single, or even a combination of biomarkers has been validated for the diagnosis of sepsis, multiple studies have shown the high specificity of CD64 expression on neutrophils (nCD64) to sepsis. The analysis of elevated nCD64 in the first 2-6 hours after infection during the pro-inflammatory stage could significantly contribute to early sepsis diagnosis. Therefore, a rapid and automated device to periodically measure nCD64 expression at the point-of-care (POC) could lead to timely medical intervention and reduced mortality rates. Current accepted technologies for measuring nCD64 expression, such as flow cytometry, require manual sample preparation and long incubation times. For POC applications, however, the technology should be able to measure nCD64 expression with little to no sample preparation. In this paper, we demonstrate a smartphone-imaged microfluidic biochip for detecting nCD64 expression in under 50 min. In our assay, first unprocessed whole blood is injected into a capture chamber to immunologically capture nCD64 along a staggered array of pillars, which were previously functionalized with an antibody against CD64. Then, an image of the capture channel is taken using a smartphone-based microscope. This image is used to measure the cumulative fraction of captured cells (γ) as a function of length in the channel. During the image analysis, a statistical model is fitted to γ in order to extract the probability of capture of neutrophils per collision with a pillar (ε). The fitting shows a strong correlation with nCD64 expression measured using flow cytometry (R² = 0.82). Finally, the applicability of the device to sepsis was demonstrated by analyzing nCD64 from 8 patients (37 blood samples analyzed) along the time they were admitted to the hospital. Results from this analysis, obtained using the smartphone-imaged microfluidic biochip were compared with flow cytometry. Again, a correlation coefficient R² = 0.82 (slope = 0.99) was obtained demonstrating a good linear correlation between the two techniques. Deployment of this technology in ICU could significantly enhance patient care worldwide.

A microfluidic technique to estimate antigen expression on particles

Antigen expression is an important biomarker for cell analysis and disease diagnosis. Traditionally, antigen expression is measured using a flow cytometer which, due to its cost and labor intensive sample preparation, is unsuitable to be used at the point-of-care. Therefore, an automatic, miniaturized assay which can measure antigen expression in the patient could aid in making crucial clinical decisions rapidly. Such a device would also expand the use of such an assay in basic research in biology. In this paper, we present a microfluidic device that can be used to measure antigen expression on cells. We demonstrate our approach using biotin-neutravidin as the binding pair using experimental and computational approaches. We flow beads with varying biotin surface densities (m_r) through a polydimethylsiloxane channel with cylindrical pillars functionalized with neutravidin. We analyze how shear stress and collision angle, the angle at which the beads collide with the pillars, affect the angular location of beads captured on the pillars. We also find that the fraction of captured beads as a function of distance (γ) in the channel is affected by m_r. Using γ, we derive the probability of capture per collision with the pillar (ε). We show that ε is linearly related to m_r, which is analogous to the expression level of proteins on cell surfaces. Although demonstrated with beads, this assay can next be expanded with cells, thus paving the way for a rapid antigen expression test.

Hands-free smartphone-based diagnostics for simultaneous detection of Zika, Chikungunya, and Dengue at point-of-care

Infectious diseases remain the world's top contributors to death and disability, and, with recent outbreaks of Zika virus infections there has been an urgency for simple, sensitive and easily translatable point-of-care tests. Here we demonstrate a novel point-of-care platform to diagnose infectious diseases from whole blood samples. A microfluidic platform performs minimal sample processing in a user-friendly diagnostics card followed by real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) on the same card with pre-dried primers specific to viral targets. Our point-of-care platform uses a commercial smartphone to acquire real-time images of the amplification reaction and displays a visual read-out of the assay. We apply this system to detect closely related Zika, Dengue (types 1 and 3) and Chikungunya virus infections from whole blood on the same pre-printed chip with high specificity and clinically relevant sensitivity. Limit of detection of 1.56e5 PFU/mL of Zika virus from whole blood was achieved through our platform. With the ability to quantitate the target nucleic acid, this platform can also perform point-of-care patient surveillance for pathogen load or select biomarkers in whole blood.

HIV-1 IIIB capture from whole blood on magnetic microparticles

Viral load quantification is a critical need for HIV management worldwide. However, the diagnostic technologies currently available are too limited by their size and expense to reach many remote and resource-limited populations. Toward the development of techniques which can be leveraged for point-of-care assays, we have investigated affinity capture of whole viruses using magnetic microparticles functionalized with antibodies or proteins targeting components of the HIV envelope. Results show the best performance from T-20, a small peptide employed in antiretroviral pharmacotherapy which targets an HIV envelope protein. This demonstration introduces an interesting alternative to antibodies for future affinity-capture applications in HIV diagnostics.

Smartphone-Imaged HIV-1 Reverse-Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) on a Chip from Whole Blood

Viral load measurements are an essential tool for the long-term clinical care of hum an immunodeficiency virus (HIV)-positive individuals. The gold standards in viral load instrumentation, however, are still too limited by their size, cost, and sophisticated operation for these measurements to be ubiquitous in remote settings with poor healthcare infrastructure, including parts of the world that are disproportionately affected by HIV infection. The challenge of developing a point-of-care platform capable of making viral load more accessible has been frequently approached but no solution has yet emerged that meets the practical requirements of low cost, portability, and ease-of-use. In this paper, we perform reverse-transcription loop-mediated isothermal amplification (RT-LAMP) on minimally processed HIV-spiked whole blood samples with a microfluidic and silicon microchip platform, and perform fluorescence measurements with a consumer smartphone. Our integrated assay shows amplification from as few as three viruses in a ~ 60 nL RT-LAMP droplet, corresponding to a whole blood concentration of 670 viruses per µL of whole blood. The technology contains greater power in a digital RT-LAMP approach that could be scaled up for the determination of viral load from a finger prick of blood in the clinical care of HIV-positive individuals. We demonstrate that all aspects of this viral load approach, from a drop of blood to imaging the RT-LAMP reaction, are compatible with lab-on-a-chip components and mobile instrumentation.

Graphene-Based Platform for Infrared Near-Field Nanospectroscopy of Water and Biological Materials in an Aqueous Environment

Scattering scanning near-field optical microscopy (s-SNOM) has emerged as a powerful nanoscale spectroscopic tool capable of characterizing individual biomacromolecules and molecular materials. However, applications of scattering-based near-field techniques in the infrared (IR) to native biosystems still await a solution of how to implement the required aqueous environment. In this work, we demonstrate an IR-compatible liquid cell architecture that enables near-field imaging and nanospectroscopy by taking advantage of the unique properties of graphene. Large-area graphene acts as an impermeable monolayer barrier that allows for nano-IR inspection of underlying molecular materials in liquid. Here, we use s-SNOM to investigate the tobacco mosaic virus (TMV) in water underneath graphene. We resolve individual virus particles and register the amide I and II bands of TMV at ca. 1520 and 1660 cm(-1), respectively, using nanoscale Fourier transform infrared spectroscopy (nano-FTIR). We verify the presence of water in the graphene liquid cell by identifying a spectral feature associated with water absorption at 1610 cm(-1).

Micro- and nanotechnology for HIV/AIDS diagnostics in resource-limited settings

Thirty-four million people are living with HIV worldwide, a disproportionate number of whom live in resource-limited settings. Proper clinical management of AIDS, the disease caused by HIV, requires regular monitoring of both the status of the host's immune system and levels of the virus in their blood. Therefore, more accessible technologies capable of performing a CD4+ T cell count and HIV viral load measurement in settings where HIV is most prevalent are desperately needed to enable better treatment strategies and ultimately quell the spread of the virus within populations. This review discusses micro- and nanotechnology solutions to performing these key clinical measurements in resource-limited settings.

A liposome-based ion release impedance sensor for biological detection

Low-cost detection of pathogens and biomolecules at the point-of-care promises to revolutionize medicine through more individualized monitoring and increased accessibility to diagnostics in remote and resource-limited areas. While many approaches to biosensing are still limited by expensive components or inadequate portability, we present here an ELISA-inspired lab-on-a-chip strategy for biological detection based on liposome tagging and ion-release impedance spectroscopy. Ion-encapsulating dipalmitoylphosphatidylcholine (DPPC) liposomes can be functionalized with antibodies and are stable in deionized water yet permeabilized for ion release upon heating, making them ideal reporters for electrical biosensing of surface-immobilized antigens. We demonstrate the quantification of these liposomes by real-time impedance measurements, as well as the qualitative detection of viruses as a proof-of-concept toward a portable platform for viral load determination which can be applied broadly to the detection of pathogens and other biomolecules.