A new multiplex RT-qPCR method for the simultaneous detection and discrimination of Zika and chikungunya viruses

Rapid and sensitive detection of chikungunya virus using one-tube, reverse transcription, semi-nested multi-enzyme isothermal rapid amplification, and lateral flow dipstick assays

Chikungunya fever is an acute infectious disease caused by chikungunya virus (CHIKV), which is transmitted by Aedes mosquitoes. Simple, rapid, and sensitive detection of CHIKV is critical for its prevention and spread. To address this issue, we combined one-tube, reverse transcription semi-nested, multi-enzyme isothermal rapid amplification, and lateral flow dipstick strips assay to detect CHIKV RNA. The study used a 318-bp gene fragment of CHIKV NSP4 as the target of the assay. This method of amplification takes 30 min for two-step amplification at 39°C. The dilution of amplification products was added to the LFD strip with results visible to the naked eye after 10 min. The method has a sensitivity of 1 copy/μL for the detection of CHIKV RNA, which is 100-fold higher than the conventional reverse transcription-multi-enzyme isothermal rapid amplification and 10-fold higher than the reverse transcription quantitative PCR (RT-qPCR) method. In addition, the method demonstrated good specificity and a better detection rate (85.7%, 18 of 21) than RT-qPCR (80.9%, 17 of 21) in clinically confirmed patient plasma samples. Thus, the rapid CHIKV RNA assay developed in this study will be an important tool for the rapid and accurate screening of patients for chikungunya fever.

IMPORTANCE

This study presents a new one-tube, reverse transcription semi-nested, multi-enzyme isothermal rapid amplification assay combined with lateral flow dipstick strips for the detection of CHIKV. This technique significantly improves sensitivity and outperforms RT-qPCR for the detection of CHIKV, especially in samples with low viral loads. It is also significantly faster than conventional RT-qPCR and does not require special equipment or a standard PCR laboratory. The combination of the isothermal amplification technology developed in this study with point-of-care molecular testing offers the potential for rapid, on-site, low-cost molecular diagnosis of CHIKV.

Molecular detection of dengue and chikungunya viruses in surveillance of wild-caught Aedes mosquitoes in Punjab, North India

BACKGROUND

Dengue (DENV), Zika (ZIKV) and chikungunya (CHIKV) viruses are transmitted mainly by Aedes mosquitoes and are responsible for a significant global healthcare burden. The current study aimed to detect arboviruses in the Aedes mosquitoes in close proximity of patients during the transmission season.

METHODS

Both immature and adult mosquitoes were collected from in and around the patients' houses. Mosquito pools were homogenized and extracted RNA was subjected to reverse transcription polymerase chain reaction for arboviral detection. Transovarian transmission (TOT) was assessed by screening F0 adults. Mosquito positivity was correlated with the aetiological agents identified in patients.

RESULTS

Of 46 pools, 19 consisted of wild Aedes, with arboviral positivity in 53% (10/19) of pools. Among wild A. aegypti pools, positivity of DENV mono-infection, CHIKV mono-infection and DENV+CHIKV co-infection was noted in four, two and three pools, respectively. One wild pool of Aedes albopictus was positive for DENV-1. Similarly, A. aegypti F0 (adult Aedes developed from immatures) pools showed 59.2% (16/27) positivity for arboviruses. F0 Aedes showed positivity in three, six and seven pools for DENV-2, CHIKV and DENV+CHIKV, respectively, suggestive of TOT. DENV serotypes and CHIKV from 24 patients' serum samples were matched with strains isolated from Aedes and correlation was observed in four instances.

CONCLUSIONS

The study detected DENV and CHIKV from wild-caught Aedes and found evidence of DENV and CHIKV TOT in F0 adults.

Understanding the Biology and Immune Pathogenesis of Chikungunya Virus Infection for Diagnostic and Vaccine Development

Chikungunya virus, the causative agent of chikungunya fever, is generally characterized by the sudden onset of symptoms, including fever, rash, myalgia, and headache. In some patients, acute chikungunya virus infection progresses to severe and chronic arthralgia that persists for years. Chikungunya infection is more commonly identified in tropical and subtropical regions. However, recent expansions and epidemics in the temperate regions have raised concerns about the future public health impact of chikungunya diseases. Several underlying factors have likely contributed to the recent re-emergence of chikungunya infection, including urbanization, human travel, viral adaptation to mosquito vectors, lack of effective control measures, and the spread of mosquito vectors to new regions. However, the true burden of chikungunya disease is most likely to be underestimated, particularly in developing countries, due to the lack of standard diagnostic assays and clinical manifestations overlapping with those of other endemic viral infections in the regions. Additionally, there have been no chikungunya vaccines available to prevent the infection. Thus, it is important to update our understanding of the immunopathogenesis of chikungunya infection, its clinical manifestations, the diagnosis, and the development of chikungunya vaccines.

Electrochemical investigations for COVID-19 detection-A comparison with other viral detection methods

Virus-induced infection such as SARS-CoV-2 is a serious threat to human health and the economic setback of the world. Continued advances in the development of technologies are required before the viruses undergo mutation. The low concentration of viruses in environmental samples makes the detection extremely challenging; simple, accurate and rapid detection methods are in urgent need. Of all the analytical techniques, electrochemical methods have the established capabilities to address the issues. Particularly, the integration of nanotechnology would allow miniature devices to be made available at the point-of-care. This review outlines the capabilities of electrochemical methods in conjunction with nanotechnology for the detection of SARS-CoV-2. Future directions and challenges of the electrochemical biosensors for pathogen detection are covered including wearable and conformal biosensors, detection of plant pathogens, multiplexed detection, and reusable biosensors for on-site monitoring, thereby providing low-cost and disposable biosensors.

Non-Invasive versus Invasive Samples for Zika Virus Surveillance: A Comparative Study in New Caledonia and French Guiana in 2015-2016

Zika virus, an arbovirus responsible for major outbreaks, can cause serious health issues, such as neurological diseases. In the present study, different types of samples (serum, saliva, and urine), collected in 2015–2016 in New Caledonia and French Guiana from 53 patients presenting symptoms and clinical signs triggered by arbovirus infections, were analyzed using a recently developed, and in-house validated, 4-plex RT-qPCR TaqMan method for simultaneous detection and discrimination of the Zika and Chikungunya viruses. Subsequently, statistical analyses were performed in order to potentially establish recommendations regarding the choice of samples type to use for an efficient and early stage Zika infection diagnosis. On this basis, the use of only urine samples presented the highest probability to detect viral RNA from Zika virus. Moreover, such a probability was improved using both urine and saliva samples. Consequently, the added value of non-invasive samples, associated with a higher acceptance level for collection among patients, instead of serum samples, for the detection of Zika infections was illustrated.

Internet of medical things (IoMT)-integrated biosensors for point-of-care testing of infectious diseases

On global scale, the current situation of pandemic is symptomatic of increased incidences of contagious diseases caused by pathogens. The faster spread of these diseases, in a moderately short timeframe, is threatening the overall population wellbeing and conceivably the economy. The inadequacy of conventional diagnostic tools in terms of time consuming and complex laboratory-based diagnosis process is a major challenge to medical care. In present era, the development of point-of-care testing (POCT) is in demand for fast detection of infectious diseases along with “on-site” results that are helpful in timely and early action for better treatment. In addition, POCT devices also play a crucial role in preventing the transmission of infectious diseases by offering real-time testing and lab quality microbial diagnosis within minutes. Timely diagnosis and further treatment optimization facilitate the containment of outbreaks of infectious diseases. Presently, efforts are being made to support such POCT by the technological development in the field of internet of medical things (IoMT). The IoMT offers wireless-based operation and connectivity of POCT devices with health expert and medical centre. In this review, the recently developed POC diagnostics integrated or future possibilities of integration with IoMT are discussed with focus on emerging and re-emerging infectious diseases like malaria, dengue fever, influenza A (H1N1), human papilloma virus (HPV), Ebola virus disease (EVD), Zika virus (ZIKV), and coronavirus (COVID-19). The IoMT-assisted POCT systems are capable enough to fill the gap between bioinformatics generation, big rapid analytics, and clinical validation. An optimized IoMT-assisted POCT will be useful in understanding the diseases progression, treatment decision, and evaluation of efficacy of prescribed therapy.

Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection

The current COronaVIrus Disease 2019 (COVID-19) pandemic started in December 2019. COVID-19 cases are confirmed by the detection of SARS-CoV-2 RNA in biological samples by RT-qPCR. However, limited numbers of SARS-CoV-2 genomes were available when the first RT-qPCR methods were developed in January 2020 for initial in silico specificity evaluation and to verify whether the targeted loci are highly conserved. Now that more whole genome data have become available, we used the bioinformatics tool SCREENED and a total of 4755 publicly available SARS-CoV-2 genomes, downloaded at two different time points, to evaluate the specificity of 12 RT-qPCR tests (consisting of a total of 30 primers and probe sets) used for SARS-CoV-2 detection and the impact of the virus' genetic evolution on four of them. The exclusivity of these methods was also assessed using the human reference genome and 2624 closely related other respiratory viral genomes. The specificity of the assays was generally good and stable over time. An exception is the first method developed by the China Center for Disease Control and prevention (CDC), which exhibits three primer mismatches present in 358 SARS-CoV-2 genomes sequenced mainly in Europe from February 2020 onwards. The best results were obtained for the assay of Chan et al. (2020) targeting the gene coding for the spiking protein (S). This demonstrates that our user-friendly strategy can be used for a first in silico specificity evaluation of future RT-qPCR tests, as well as verifying that the former methods are still capable of detecting circulating SARS-CoV-2 variants.