Development and field validation of a reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) for the rapid detection of chikungunya virus in patient and mosquito samples

OBJECTIVES

We aimed to develop a reverse transcription loop-mediated isothermal amplification (RT-LAMP) platform for the rapid detection of chikungunya virus (CHIKV) in both patient and mosquito samples from Brazil.

METHODS

We optimized an RT-LAMP assay and then evaluated the specificity and sensitivity using visual detection. In comparison with the RT-qPCR reference method, we validated the utility of this assay as a molecular diagnostic test in a reference laboratory for arbovirus diagnostics using 100 serum samples collected from suspected CHIKV cases.

RESULTS

Our RT-LAMP assay specifically detected CHIKV without cross-reactivity against other arboviruses. The limit of detection of our RT-LAMP was estimated in -1.18 PFU (confidence interval [CI] ranging from -2.08 to 0.45), resulting in a similar analytical sensitivity when directly compared with the reference standard RT-qPCR assay. Then, we demonstrate the ability of our RT-LAMP assay to detect the virus in different human specimens (serum, urine, and saliva), and crude lysate of Aedes aegypti mosquitoes in as little as 20-30 minutes and without a separate RNA isolation step. Lastly, we showed that our RT-LAMP assay could be lyophilized and reactivated by adding water, indicating potential for room-temperature storage. Our RT-LAMP had a clinical sensitivity of 100% (95% CI, 90.97-100.00%), clinical specificity of 96.72% (95% CI, 88.65-99.60%), and overall accuracy of 98.00% (95% CI, 92.96-99.76%).

DISCUSSION

Taken together, these findings indicate that the RT-LAMP assay reported here solves important practical drawbacks to the deployment of molecular diagnostics in the field and can be used to improve testing capacity, particularly in low- and middle-income countries.

Comparison of DNA extraction methods for COVID-19 host genetics studies

The coronavirus disease 2019 (COVID-19) pandemic has resulted in global shortages in supplies for diagnostic tests, especially in the developing world. Risk factors for COVID-19 severity include pre-existing comorbidities, older age and male sex, but other variables are likely play a role in disease outcome. There is indeed increasing evidence that supports the role of host genetics in the predisposition to COVID-19 outcomes. The identification of genetic factors associated with the course of SARS-CoV-2 infections relies on DNA extraction methods. This study compared three DNA extraction methods (Chelex®100 resin, phenol-chloroform and the QIAamp DNA extraction kit) for COVID-19 host genetic studies using nasopharyngeal samples from patients. The methods were compared regarding number of required steps for execution, sample handling time, quality and quantity of the extracted material and application in genetic studies. The Chelex®100 method was found to be cheapest (33 and 13 times cheaper than the commercial kit and phenol-chloroform, respectively), give the highest DNA yield (306 and 69 times higher than the commercial kit and phenol-chloroform, respectively), with the least handling steps while providing adequate DNA quality for downstream applications. Together, our results show that the Chelex®100 resin is an inexpensive, safe, simple, fast, and suitable method for DNA extraction of nasopharyngeal samples from COVID-19 patients for genetics studies. This is particularly relevant in developing countries where cost and handling are critical steps in material processing.

Neutralizing antibodies against SARS-CoV-2 in Brazilian pregnant women vaccinated with one or two doses of BNT162b2 mRNA vaccine (Pfizer/WyethTM)

Pregnant women have an increased risk of developing severe coronavirus disease. In Brazil, the number of hospitalizations and adverse outcomes, including death caused by COVID-19, in women during the pregnancy-puerperal cycle was high in the first pandemic year. Doubts regarding vaccines' efficacy and safety for the mother and fetus delayed vaccination. This study evaluated the generation of IgG titers and neutralizing antibodies to the BNT162b2 mRNA vaccine in 209 healthy pregnant women. For this, were used the QuantiVac ELISA (IgG) and SARS-CoV-2 NeutraLISA kits (EUROIMMUN, Lübeck, SH) following the manufacturer's recommendations. One dose vaccine produced anti-SARS-CoV-2 IgG in 85% (81/95), and two produced in 95% (76/80) women. Among unvaccinated women, four of 34 (12%) showed protection. The first dose of the BNT162b2 vaccine protected 69% of the women with neutralizing antibodies (median of %IH = 97). In the second dose, protection occurred in 94% of the pregnant women (median of IH% = 97). This study showed no differences in IgG antibody titers between one- and two-dose of the BNT162b2 mRNA vaccine groups, boosting with the second dose increased the number of women who produced specific IgG and neutralizing antibodies, raising by 114-folds the chance of producing the SARS-CoV-2 neutralizing antibodies compared to the unvaccinated pregnant woman, which may contribute to reduce the chance of severe COVID-19.

Two Years into the COVID-19 Pandemic: Lessons Learned

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19), which has massively impacted global public health and caused widespread disruption to daily life. The crisis caused by COVID-19 has mobilized scientists and public health authorities across the world to rapidly improve our knowledge about this devastating disease, shedding light on its management and control, and spawned the development of new countermeasures. Here we provide an overview of the state of the art of knowledge gained in the last 2 years about the virus and COVID-19, including its origin and natural reservoir hosts, viral etiology, epidemiology, modes of transmission, clinical manifestations, pathophysiology, diagnosis, treatment, prevention, emerging variants, and vaccines, highlighting important differences from previously known highly pathogenic coronaviruses. We also discuss selected key discoveries from each topic and underline the gaps of knowledge for future investigations.

Cerebral White Matter Injury in a Newborn Infant With COVID-19: A Case Report

As the Covid pandemic evolves, reports of neurological manifestations and neuroimaging associated with SARS-CoV-2 have been reported in children and in neonates, although very few when compared to adults. Objective: To describe a 3-day-old neonate presenting afebrile seizures with a persistent positive nasopharyngeal swab for SARS-CoV-2 and neuroimaging demonstrating extensive cerebral white matter injury. Methods: Consent was obtained to report this case. SARS-CoV-2 was tested via real time reverse transcriptase-polymerase chain reaction (rRT-PCR) amplification of virus acid from a nasopharyngeal swab. Magnetic resonance imaging (MRI) of the brain was performed using axial T1, T2, FLAIR and diffusion-weighted imaging (DWI) and T1 post contrast sequences. Results: Brain MRI showed restricted diffusion in the periventricular white matter, subcortical white matter and splenium of corpus callosum. Discussion: Neurological presentation of SARS-CoV-2 in newborns appears to be rare and is not fully known. SARS-CoV-2 infection should be considered in newborns with seizures and white matter abnormalities.

Field validation of the performance of paper-based tests for the detection of the Zika and chikungunya viruses in serum samples

In low-resource settings, resilience to infectious disease outbreaks can be hindered by limited access to diagnostic tests. Here we report the results of double-blinded studies of the performance of paper-based diagnostic tests for the Zika and chikungunya viruses in a field setting in Latin America. The tests involved a cell-free expression system relying on isothermal amplification and toehold-switch reactions, a purpose-built portable reader and onboard software for computer vision-enabled image analysis. In patients suspected of infection, the accuracies and sensitivities of the tests for the Zika and chikungunya viruses were, respectively, 98.5% (95% confidence interval, 96.2–99.6%, 268 serum samples) and 98.5% (95% confidence interval, 91.7–100%, 65 serum samples) and approximately 2 aM and 5 fM (both concentrations are within clinically relevant ranges). The analytical specificities and sensitivities of the tests for cultured samples of the viruses were equivalent to those of the real-time quantitative PCR. Cell-free synthetic biology tools and companion hardware can provide de-centralized, high-capacity and low-cost diagnostics for use in low-resource settings.

Widespread Contamination of SARS-CoV-2 on Highly Touched Surfaces in Brazil During the Second Wave of the COVID-19 Pandemic

Although SARS‐CoV‐2 surface contamination has been investigated in health care settings, little is known about the SARS‐CoV‐2 surface contamination in public urban areas, particularly in tropical countries. Here, we investigated the presence of SARS‐CoV‐2 on high‐touch surfaces in a large city in Brazil, one of the most affected countries by the COVID‐19 pandemic in the world. A total of 400 surface samples were collected in February 2021 in the City of Recife, Northeastern Brazil. A total of 97 samples (24.2%) tested positive for SARS‐CoV‐2 by RT‐qPCR using the CDC‐USA protocol. All the collection sites, except one (18/19, 94.7%) had at least one environmental surface sample contaminated. SARS‐CoV‐2 positivity was higher in public transport terminals (47/84, 55.9%), followed by health care units (26/84, 30.9%), beach areas (4/21, 19.0%), public parks (14/105, 13.3%), supply centre (2/21, 9.5%), and public markets (4/85, 4.7%). Toilets, ATMs, handrails, playgrounds and outdoor gyms were identified as fomites with the highest rates of SARS‐CoV‐2 detection. Taken together, our data provide a real‐world picture of SARS‐CoV‐2 dispersion in highly populated tropical areas and identify critical control points that need to be targeted to break SARS‐CoV‐2 transmission chains.

Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil

Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led field and classroom initiatives for the monitoring of DENV in Brazil, generating 227 novel genome sequences of DENV1-2 from 85 municipalities (2015-2019). This equated to an over 50% increase in the number of DENV genomes from Brazil available in public databases. Using both phylogenetic and epidemiological models we retrospectively reconstructed the recent transmission history of DENV1-2. Phylogenetic analysis revealed complex patterns of transmission, with both lineage co-circulation and replacement. We identified two lineages within the DENV2 BR-4 clade, for which we estimated the effective reproduction number and pattern of seasonality. Overall, the surveillance outputs and training initiative described here serve as a proof-of-concept for the utility of real-time portable sequencing for research and local capacity building in the genomic surveillance of emerging viruses.

Simultaneous Circulation of DENV, CHIKV, ZIKV and SARS-CoV-2 in Brazil: an Inconvenient Truth

The emergence of SARS-CoV-2 has prompted the mobilization of a network of public health laboratories to diagnose COVID-19 patients, trace contacts and identify hot-spot areas for active community transmission at the expense of arbovirus diagnosis and control practices. In this article, we discuss the unprecedented challenges faced by the Brazilian public health system in dealing with the incursion of SARS-CoV-2 in the midst of ongoing triple arboviral epidemics caused by dengue, chikungunya, and Zika virus. Finally, we highlight the importance of the introduction of one health approach as an effective inter-disciplinary response and management to mitigate the catastrophic effect caused by these pathogens.

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SARS-CoV-2 emerged in Brazil in the midst of ongoing triple arboviral epidemics caused by DENV, CHIKV and ZIKV.

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The emergence of SARS-CoV-2 has prompted the mobilization of public health laboratories and officials at the expense of arbovirus diagnosis and control practices.

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The simultaneous circulation of SARS-CoV-2 and arboviruses in Brazil requires the integration of disease control measures and effective surveillance programs.

Survival analysis in non-congenital neurological disorders related to dengue, chikungunya and Zika virus infections in Northeast Brazil

The Northeast of Brazil has experienced a triple epidemic, with the simultaneous circulation of dengue virus (DENV), chikungunya virus (CHIKV) and Zika virus (ZIKV), which may have contributed to the observed increase across this region of atypical forms of disease and deaths. In view of this fact, non-congenital neurological disorders related to arboviruses were compared with other etiologies, mortality and survival rates of patients admitted to referral neurology hospitals in Pernambuco State, Northeast Brazil, from 2015 to 2018. Blood and cerebrospinal fluid samples were collected and tested using molecular and serological assays. The arbovirus-exposed groups were compared with respect to epidemiological, clinical and neurologic characteristics by using the Pearson’s chi-square test. For the survival analysis, the Kaplan-Meier and Hazard Ratio (HR) tests were used, with a 95% confidence interval (CI). Encephalitis and encephalomyelitis were more frequent in arboviruses, while myelitis predominated in the neurological disorders of other etiologies. Guillain-Barré Syndrome (GBS) was similarly distributed amongst the groups. Exposure to one of the arboviruses caused a six-fold increase in the risk of death (HR: 6.37; CI: 2.91 - 13.9). Amongst the arbovirus-exposed groups, infection (DENV/CHIKV) increased nine times the risk of death (HR: 9.07; CI: 3.67 - 22.4). The survival curve indicates that have been exposed to some arbovirus decreased the likelihood of survival compared to those with other etiologies (Log-Rank: p<0.001). Within this scenario, neurologic manifestations of DENV, CHIKV and ZIKV have the potential to increase mortality and decrease survival, and concomitant infection (DENV/CHIKV) is an aggravating factor in reducing the likelihood of survival when compared to monoinfections.

Epidemiological and clinical characteristics of the first 557 successive patients with COVID-19 in Pernambuco state, Northeast Brazil

Background

South America is the current epicenter of COVID-19 pandemic. Yet, the epidemiological and clinical features of the disease have not been described in Brazil, the third most affected country in the world.

Methods

In this retrospective study, we describe the demographics, epidemiology and clinical features of the first 557 consecutive patients positive for SARS-CoV-2 living in Pernambuco state, Northeast Brazil.

Results

The first COVID-19 cases occurred in the high income population. The age of infected patients ranged from 27 days to 97 years with a median of 47 years. The ratio of males to female in the SARS-CoV-2-infected group was 0.83:1. The most common symptom was cough (74.51%), followed by fever (66.79%), dyspnea (56.01%), sore throat (28.19%) and O₂ saturation <95% (24.42%). 86.44% of the lethal cases were patients older than 51 years. The median time from illness onset to diagnosis was 4.0 days (range 0–39 days) Severe patients diagnosed after 14 days of symptoms onset had higher viral load than patients with mild disease.

Conclusions

Our study provides important information about COVID-19 in the tropics and will assist physicians and health officials to face the current pandemics as SARS-CoV-2 continues to spread in the human population.

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We describe for the first time the demographics, epidemiology and clinical of COVID-19 in Brazil. .

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The first COVID-19 cases occurred in the high income population.

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86.44% of the lethal cases were patients older than 51 years.

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Severe patients diagnosed after 14 days of symptoms onset had higher viral load than patients with mild disease.