Rapid detection of monkeypox virus using a CRISPR-Cas12a mediated assay: a laboratory validation and evaluation study

BACKGROUND

The 2022 outbreak of mpox (formerly known as monkeypox) led to the spread of monkeypox virus (MPXV) in over 110 countries, demanding effective disease management and surveillance. As current diagnostics rely largely on centralised laboratory testing, our objective was to develop a simple rapid point-of-care assay to detect MPXV in clinical samples using isothermal amplification coupled with CRISPR and CRISPR-associated protein (Cas) technology.

METHODS

In this proof-of-concept study, we developed a portable isothermal amplification CRISPR-Cas12a-based assay for the detection of MPXV. We designed a panel of 22 primer-guide RNA sets using pangenome and gene-agnostic approaches, and subsequently shortlisted the three sets producing the strongest signals for evaluation of analytical sensitivity and specificity using a fluorescence-based readout. The set displaying 100% specificity and the lowest limit of detection (LOD) was selected for further assay validation using both a fluorescence-based and lateral-flow readout. Assay specificity was confirmed using a panel of viral and bacterial pathogens. Finally, we did a blind concordance study on genomic DNA extracted from 185 clinical samples, comparing assay results with a gold-standard quantitative PCR (qPCR) assay. We identified the optimal time to detection and analysed the performance of the assay relative to qPCR using receiver operating characteristic (ROC) curves. We also assessed the compatibility with lateral-flow strips, both visually and computationally, where strips were interpreted blinded to the fluorescence results on the basis of the presence or absence of test bands.

FINDINGS

With an optimal run duration of approximately 45 min from isothermal amplification to CRISPR-assay readout, the MPXV recombinase polymerase amplification CRISPR-Cas12a-based assay with the selected primer-guide set had an LOD of 1 copy per μL and 100% specificity against tested viral pathogens. Blinded concordance testing of 185 clinical samples resulted in 100% sensitivity (95% CI 89·3-100) and 99·3% specificity (95% CI 95·7-100) using the fluorescence readout. For optimal time to detection by fluorescence readout, we estimated the areas under the ROC curve to be 0·98 at 2 min and 0·99 at 4 min. Lateral-flow strips had 100% sensitivity (89·3-100) and 98·6% specificity (94·7-100) with both visual and computational assessment. Overall, lateral-flow results were highly concordant with fluorescence-based readouts (179 of 185 tests, 96·8% concordant), with discrepancies associated with low viral load samples.

INTERPRETATION

Our assay for the diagnosis of mpox displayed good performance characteristics compared with qPCR. Although optimisation of the assay will be required before deployment, its usability and versatility present a potential solution to MPXV detection in low-resource and remote settings, as well as a means of community-based, on-site testing.

FUNDING

Victorian Medical Research Accelerator Fund and the Australian Government Department of Health.

Aneurysmal growth in type-B aortic dissection: assessing the impact of patient-specific inlet conditions on key haemodynamic indices

Type-B aortic dissection is a cardiovascular disease in which a tear develops in the intimal layer of the descending aorta, allowing pressurized blood to delaminate the layers of the vessel wall. In medically managed patients, long-term aneurysmal dilatation of the false lumen (FL) is considered virtually inevitable and is associated with poorer disease outcomes. While the pathophysiological mechanisms driving FL dilatation are not yet understood, haemodynamic factors are believed to play a key role. Computational fluid dynamics (CFD) and 4D-flow MRI (4DMR) analyses have revealed correlations between flow helicity, oscillatory wall shear stress and aneurysmal dilatation of the FL. In this study, we compare CFD simulations using a patient-specific, three-dimensional, three-component inlet velocity profile (4D IVP) extracted from 4DMR data against simulations with flow rate-matched uniform and axial velocity profiles that remain widely used in the absence of 4DMR. We also evaluate the influence of measurement errors in 4DMR data by scaling the 4D IVP to the degree of imaging error detected in prior studies. We observe that oscillatory shear and helicity are highly sensitive to inlet velocity distribution and flow volume throughout the FL and conclude that the choice of IVP may greatly affect the future clinical value of simulations.

Laboratory assessment of a multi-target assay for the rapid detection of viruses causing vesicular diseases

BACKGROUND

The recent mpox outbreak has highlighted the need to rapidly diagnose the causative agents of viral vesicular disease to inform treatment and control measures. Common causes of vesicular disease include Monkeypox virus (MPXV), clades I and II, Herpes simplex viruses Type 1 and Type 2 (HSV-1, HSV-2), human herpes virus 6 (HHV-6), Varicella-zoster virus (VZV) and Enteroviruses (EVs). Here, we assessed a syndromic viral vesicular panel for rapid and simultaneous detection of these 7 targets in a single cartridge.

OBJECTIVE

The aim of this study was to evaluate the QIAStat-Dx ® viral vesicular (VV) panel and compare with laboratory developed tests (LDTs). Limit of detection, inter-run variability, cross-reactivity and specificity were assessed. Positive and negative percent agreement, and correlation between assays was determined using 124 clinical samples from multiple anatomical sites.

RESULTS

The overall concordance between the QIAstat and LDTs was 96%. Positive percent agreement was 82% for HHV-6, 89% for HSV-1 and 100% for MPXV, HSV-2, EV and VZV. Negative percent agreement was 100% for all targets assessed. There was no cross-reactivity with Vaccinia, Orf, Molluscum contagiosum viruses, and a pooled respiratory panel.

CONCLUSION

The QIAstat VV multi-target syndromic panel combine ease of use, rapid turnaround, good sensitivity and specificity for enhanced diagnosis, clinical care and public health responses.

Evaluation of 16 molecular assays for the detection of orthopox and mpox viruses

BACKGROUND

The current global mpox virus (MPXV) outbreak has been declared a Public Health Emergency of International Concern by WHO, with more than 80,000 cases confirmed across multiple continents. Diagnosis is confirmed by PCR of viral DNA from vesicle and other swabs.

OBJECTIVE

The aim of this study was to assess commercial RT PCR assays for Orthopoxvirus (OPX) and MPXV for analytical sensitivity, and percent agreements and compare them to primer/probe sets employed at the Victorian Infectious Diseases Reference Laboratory (VIDRL), Centers for Disease Control andPrevention (CDC) and US Army Medical Research Institute of Infectious Diseases (USAMRIID). Limits of detection (LOD), intra-run variability, cross-reactivity and performance on forty clinical samples was assessed on eleven commercial assays and five primer/probe combinations used at VIDRL, CDC and USAMRIID.

RESULTS

All assays were able to detect OPX and MPXV (LOD 57 to 14,495 copies/mL) with intra-run coefficients of variation between Cycle thresholds of 0.58 and 3.44, and there was no unexpected cross-reactivity. All assays demonstrated 100% negative percent agreement with clinical samples and all but one yielded 100% positive percent agreement.

CONCLUSIONS

Variations in LOD between assays may be dependent on the platform used and sample type. Despite the overall comparable performance of the assays assessed, it is important that routine laboratories perform in-house validations before implementing RT PCR for OPX and/or MPXV as reliable and accurate laboratory diagnosis of MPXV and isolation is crucial to containing the spread of this current outbreak and informing public health interventions and response.

Monkeypox infection presenting as genital rash, Australia, May 2022

Rapid diagnosis and whole genome sequencing confirmed a case of monkeypox in an HIV-positive individual receiving antiretroviral therapy. The patient had a normal CD4+ T-cell count and suppressed HIV viral load and presented with a genital rash in Melbourne, Australia after return from Europe in May 2022. He subsequently developed systemic illness and disseminated rash and 11 days after symptom onset, he was hospitalised to manage painful bacterial cellulitis of the genital area.

Safety and efficacy of absorbable and non-absorbable fixation systems for intraperitoneal mesh fixation: an experimental study in swine

PURPOSE

Choice of the best possible fixation system in terms of safety and effectiveness for intraperitoneal mesh placement in hernia surgery remains controversial. The aim of the present study was to compare the performance of four fixation systems in a swine model of intraperitoneal mesh fixation.

METHODS

Fourteen Landrace swine were utilized in the study. The experiment included two stages. Initially, four pieces of mesh (Ventralight ™ ST) sizing 10 × 5 cm were placed and fixed intraperitoneally to reinforce 4 small full thickness abdominal wall defects created with diathermy. These defects were repaired primarily with absorbable suture before mesh implantation. Each mesh was anchored with a different tack device between Absorbatack™, Protack™, Capsure™, or Optifix™. The second stage took place after 60 days and included euthanasia, laparoscopy, and laparotomy via U-shaped incision to obtain the measurements for the outcome parameters. The primary endpoint of the study was to compare the peel strength of the compound tack/mesh from the abdominal wall. Secondary parameters were the extent and quality of visceral adhesions to the mesh, the degree of mesh shrinkage and the histological response around the tacks.

RESULTS

Thirteen out of 14 animals survived the experiment and 10 were included in the final analysis. Capsure™ tacks had higher peel strength when compared to Absorbatack™ (p = 0.028); Protack™ (p = 0.043); and Optifix™ (p = 0.009). No significant differences were noted regarding the extent of visceral adhesions (Friedman's test p value 0.854), the adhesion quality (Friedman's test p value 0.506), or the mesh shrinkage (Friedman's test p value = 0.827). Four out of the ten animals developed no adhesions at all 2 months after implantation.

CONCLUSION

Capsure™ fixation system provided higher peel strength that the other tested devices in our swine model of intraperitoneal mesh fixation. Our findings generate the hypothesis that this type of fixation may be superior in a clinical setting. Clinical trials with long-term follow-up are required to assess the safety and efficacy of mesh fixation systems in hernia surgery.

Portable real-time colorimetric LAMP-device for rapid quantitative detection of nucleic acids in crude samples

Loop-mediated isothermal amplification is known for its high sensitivity, specificity and tolerance to inhibiting-substances. In this work, we developed a device for performing real-time colorimetric LAMP combining the accuracy of lab-based quantitative analysis with the simplicity of point-of-care testing. The device innovation lies on the use of a plastic tube anchored vertically on a hot surface while the side walls are exposed to a mini camera able to take snapshots of the colour change in real time during LAMP amplification. Competitive features are the rapid analysis (< 30 min), quantification over 9 log-units, crude sample-compatibility (saliva, tissue, swabs), low detection limit (< 5 copies/reaction), smartphone-operation, fast prototyping (3D-printing) and ability to select the dye of interest (Phenol red, HNB). The device’s clinical utility is demonstrated in cancer mutations-analysis during the detection of 0.01% of BRAF-V600E-to-wild-type molecules from tissue samples and COVID-19 testing with 97% (Ct < 36.8) and 98% (Ct < 30) sensitivity when using extracted RNA and nasopharyngeal-swabs, respectively. The device high technology-readiness-level makes it a suitable platform for performing any colorimetric LAMP assay; moreover, its simple and inexpensive fabrication holds promise for fast deployment and application in global diagnostics.

High-grade blunt traumatic rupture of kidney transplant: is conservative management an option?

Road traffic accidents are the most common cause of blunt native kidney injuries. Transplanted kidneys are more exposed to such injuries due to the common positioning in the iliac fossa compared with the relatively protected position of the native kidneys. The small number of cases identified in the literature describe grade II and III transplant kidney injuries that were treated surgically. In our case a grade IV injury was managed conservatively giving the necessary time to appropriately plan the future renal replacement therapy options for the patient.

Prolonged Detection of Japanese Encephalitis Virus in Urine and Whole Blood in a Returned Short-term Traveler

We describe a fatal case of Japanese encephalitis virus infection following short-term travel to Thailand. Viral RNA was detected in urine and whole blood out to 26 and 28 days, respectively, after the onset of symptoms. Live virus was isolated from a urine specimen from day 14.

Molecular-Level Simulations of Turbulence and Its Decay

We provide the first demonstration that molecular-level methods based on gas kinetic theory and molecular chaos can simulate turbulence and its decay. The direct simulation Monte Carlo (DSMC) method, a molecular-level technique for simulating gas flows that resolves phenomena from molecular to hydrodynamic (continuum) length scales, is applied to simulate the Taylor-Green vortex flow. The DSMC simulations reproduce the Kolmogorov -5/3 law and agree well with the turbulent kinetic energy and energy dissipation rate obtained from direct numerical simulation of the Navier-Stokes equations using a spectral method. This agreement provides strong evidence that molecular-level methods for gases can be used to investigate turbulent flows quantitatively.

Parechovirus Genotype 3 Outbreak among Infants, New South Wales, Australia, 2013-2014

Syndromic surveillance was useful for outbreak monitoring, and public health response helped reduce hospitalization times.

From October 2013 through February 2014, human parechovirus genotype 3 infection was identified in 183 infants in New South Wales, Australia. Of those infants, 57% were male and 95% required hospitalization. Common signs and symptoms were fever >38°C (86%), irritability (80%), tachycardia (68%), and rash (62%). Compared with affected infants in the Northern Hemisphere, infants in New South Wales were slightly older, both sexes were affected more equally, and rash occurred with considerably higher frequency. The New South Wales syndromic surveillance system, which uses near real-time emergency department and ambulance data, was useful for monitoring the outbreak. An alert distributed to clinicians reduced unnecessary hospitalization for patients with suspected sepsis.

Plasma nanotextured polymeric lab-on-a-chip for highly efficient bacteria capture and lysis

We describe the design, fabrication, and successful demonstration of a sample preparation module comprising bacteria cell capture and thermal lysis on-chip with potential applications in food sample pathogen analysis. Plasma nanotexturing of the polymeric substrate allows increase of the surface area of the chip and the antibody binding capacity. Three different anti-Salmonella antibodies were directly and covalently linked to plasma treated chips without any additional linker chemistry or other treatment. Then, the Ab-modified chips were tested for their capacity to bind bacteria in the concentration range of 10(2)-10(8) cells per mL; the module exhibited 100% efficiency in Salmonella enterica serovar Typhimurium bacteria capture for cell suspensions below 10(5) cells per mL (10(4) cells injected with a 100 μL sample volume) and efficiency higher than 50% for 10(7) cells per mL. Moreover, thermal lysis achieved on-chip from as low as 10 captured cells was demonstrated and shown to compare well with off-chip lysis. Excellent selectivity (over 1 : 300) was obtained in a sample containing, in addition to S. Typhimurium and E. coli bacteria.

Laboratory identification of donor-derived coxsackievirus b3 transmission

Unexpected donor-to-recipient infectious disease transmission is an important, albeit rare, complication of solid organ transplantation. Greater work and understanding about the epidemiology of these donor-derived transmissions is continually required to further mitigate this risk. Herein we present the first reported case of proven donor-derived transmission of coxsackievirus serogroup-3, an enterovirus, following solid organ transplant. Swift and effective communication between the organ donation agency, treating physicians, laboratory testing and notification ensured a coordinated approach. The resulting clinical syndromes in the organ recipients were mild. This case highlights the requirement for ongoing surveillance over a broad range of infecting pathogens that may present as a donor-derived infection.

Acoustic detection of DNA conformation in genetic assays combined with PCR

Application of PCR to multiplexing assays is not trivial; it requires multiple fluorescent labels for amplicon detection and sophisticated software for data interpretation. Alternative PCR-free methods exploiting new concepts in nanotechnology exhibit high sensitivities but require multiple labeling and/or amplification steps. Here, we propose to simplify the problem of simultaneous analysis of multiple targets in genetic assays by detecting directly the conformation, rather than mass, of target amplicons produced in the same PCR reaction. The new methodology exploits acoustic wave devices which are shown to be able to characterize in a fully quantitative manner multiple double stranded DNAs of various lengths. The generic nature of the combined acoustic/PCR platform is shown using real samples and, specifically, during the detection of SNP genotyping in Anopheles gambiae and gene expression quantification in treated mice. The method possesses significant advantages to TaqMan assay and real-time PCR regarding multiplexing capability, speed, simplicity and cost.

Influenza vaccine effectiveness during the 2012 influenza season in Victoria, Australia: influences of waning immunity and vaccine match

Vaccine effectiveness may wane with increasing time since vaccination. This analysis used the Victorian sentinel general practitioner (GP) network to estimate vaccine effectiveness for trivalent inactivated vaccines in the 2012 season. A test-negative design was used where patients presenting to GPs with influenza-like illness who tested positive for influenza were cases and noncases were those who tested negative. Vaccination status was recorded by GPs. Vaccine effectiveness was calculated as (1-odds ratio) × 100%. Estimates were compared early versus late in the season and by time since vaccination. Virus isolates were assessed antigenically by hemagglutination inhibition assay in a selection of positive samples and viruses from healthy adults who experienced a vaccine breakthrough were analyzed genetically. The adjusted vaccine effectiveness estimate for any type of influenza was 45% (95% CI: 8,66) and for influenza A(H3) was 35% (95% CI: -11,62). A non-significant effect of waning effectiveness by time since vaccination was observed for A(H3). For those vaccinated <93 days of presentation vaccine effectiveness was 37% (95% CI: -29,69), while for those vaccinated ≥93 days before presentation it was 18% (95% CI: -83,63). Comparison of early versus late in the season estimates was very sensitive to the cut off week chosen for analysis. Antigenic data suggested that low vaccine effectiveness was not associated with poor vaccine match among the A(H3) viruses. However, genetic analysis suggested nucleotide substitutions in antigenic sites. In 2012, the trivalent influenza vaccine provided moderate protection against influenza and showed limited evidence for waning effectiveness. Antigenic and genetic data can provide additional insight into understanding these estimates.

Estimation of type- and subtype-specific influenza vaccine effectiveness in Victoria, Australia using a test negative case control method, 2007-2008

BACKGROUND

Antigenic variation of influenza virus necessitates annual reformulation of seasonal influenza vaccines, which contain two type A strains (H1N1 and H3N2) and one type B strain. We used a test negative case control design to estimate influenza vaccine effectiveness (VE) against influenza by type and subtype over two consecutive seasons in Victoria, Australia.

METHODS

Patients presenting with influenza-like illness to general practitioners (GPs) in a sentinel surveillance network during 2007 and 2008 were tested for influenza. Cases tested positive for influenza by polymerase chain reaction and controls tested negative for influenza. Vaccination status was recorded by sentinel GPs. Vaccine effectiveness was calculated as [(1--adjusted odds ratio) × 100%].

RESULTS

There were 386 eligible study participants in 2007 of whom 50% were influenza positive and 19% were vaccinated. In 2008 there were 330 eligible study participants of whom 32% were influenza positive and 17% were vaccinated. Adjusted VE against A/H3N2 influenza in 2007 was 68% (95% CI, 32 to 85%) but VE against A/H1N1 (27%; 95% CI, -92 to 72%) and B (84%; 95% CI, -2 to 98%) were not statistically significant. In 2008, the adjusted VE estimate was positive against type B influenza (49%) but negative for A/H1N1 (-88%) and A/H3N2 (-66%); none was statistically significant.

CONCLUSIONS

Type- and subtype-specific assessment of influenza VE is needed to identify variations that cannot be differentiated from a measure of VE against all influenza. Type- and subtype-specific influenza VE estimates in Victoria in 2007 and 2008 were generally consistent with strain circulation data.

Higher than expected seasonal influenza activity in Victoria, 2007

In 2007, the Victorian influenza season exceeded normal seasonal activity thresholds. The average rate of influenza-like illness (ILI) reported by general practitioners (GPs) participating in sentinel surveillance was 9.0 cases per 1,000 consultations, peaking at 22 cases per 1,000 consultations in mid-August. The average ILI rate reported by the Melbourne Medical Locum Service (MMLS) was 11.5 per 1,000 consultations over the season. The MMLS ILI rate peaked at 30 per 1,000 consultations at the same time as peak rates were reported by GPs, with a secondary peak observed three weeks later (22 cases per 1,000 consultations). Influenza cases notified to the Victorian Department of Human Services peaked in mid-August with a secondary peak of influenza A in early September. Of the influenza positive swabs collected by GPs and among those collected throughout the state, 92% were type A and 8% were type B. The most common strains identified in Victoria in the 2007 influenza season were A/ Brisbane/10/2007-like followed by A/Solomon Islands/3/2006-like. While neither virus strain was specifically included in the 2007 Australian influenza vaccine, reasonable cross protection was afforded by the strains in the vaccine.

Investigation of the mechanism of action of prostaglandin synthesis inhibitors on renin and aldosterone secretion and sodium excretion

Mean blood pressure (MBP) was found to be lower, while renal plasma flow (RPF), glomerular filtration rats (GFR), sodium excretion rate (U(Na)V), potassium excretion rate (U(k)V) and urinary prostaglandin E (PGE) concentration were higher in 15 normotensive subjects (15NS) compared with the values obtained in 15 essential hypertensive patients (15EHP) of the same mean age. After volume expansion of the 15HP with isotonic saline infusion, RPF, U(Na)V, U(k)V, urine volume (UV) and urinary PGE increased significantly while plasma renin activity (PRA) decreased significantly. Urinary aldosterone concentration and MBP decreased also but not significantly. After oral administration of 75 mg of indomethacin, in the same loaded group of 15 EHP, urinary PGE, urinary aldosterone and PRA decreased significantly while RPF, GRF, U(Na)V remained unaltered and MBP increased. When these values obtained in saline loaded and indomethacin treated 15EHP were compared to those obtained in the same group before volume expansion, it was found that RPF, U(NaV, U(k)V and UV were higher after indomethacin-saline administration while MBP, GRF and urinary PGE did not differ significantly and PRA and urinary aldosterone were significantly lower. These findings argue against the suggestion that PGE increases sodium reabsorption at the distal tubule and indicate that the unaltered sodium excretion rate in saline loaded and indomethacin treated unanaesthetized subjects, results from the simultaneous decrease of renomedullary PGE, Renin and aldosterone secretion.

Hydatid cyst of the liver with intrathoracic rupture

In the last 10 years we have operated on 33 cases of hydatid cyst of the liver with intrathoracic rupture. Twenty-one out of 33 cases ruptured into bronchi, in seven the rupture affected the pleural cavity, and in six simultaneous rupture into the bronchus and pleural cavity occurred. Laboratory tests were not carried out in all cases. The Casoni intradermal test was carried out in 23 cases and was positive in 18. A liver scan was performed in 10 and was positive in all. Conservative operations were carried out in 22 patients. In these the hepatic cavity was evacuated and separately drained. This was followed by suturing the diaphragmatic rupture and also closing the bronchial opening if present. Lung resections were performed in 11 out of 33 cases. In eight lobectomy was carried out and in three segmental resections. Resection was necessary when suppuration and bronchiectatic changes affected the lung. Ruptured cyst into the pleural cavity requires emergency thoracotomy after the anaphylactic shock is over. Removal of the parasite, re-expansion of the lung, and drainage of the pleural and hepatic cavities is necessary. Immediate and late complications occurred in 13 patients. In two postoperative haemorrhage occurred and in two postoperative empyema developed. Recurrent haemoptysis was seen in five, persistent bile fistula in one, and dissemination of hydatid cyst in three. In the remaining 20 cases there was no complication. Operative mortality was nil.

HLA-B27 frequency in Greek patients with acute anterior uveitis

The histocompatibility antigen HLA-B27 was identified in 12 out of 33 patients with acute non-granulomatous anterior uveitis. This is a frequency of 36.36%, compared with 4.72% in controls. Seven patients had in addition evidence of systemic disease, including ankylosing spondylitis, sacroiliitis, Reiter's disease, Still's disease, and rheumatoid arthritis. Five of these were HLA-B27 positive, which suggests that the uveitis in many of these cases has a similar aetiology to the uveitis in those with rheumatic disease. It appears that the more severe cases of acute anterior uveitis are related more frequently to the presence of HLA-B27.