Diagnostic utility and validation of a newly developed real time loop mediated isothermal amplification method for the detection of SARS CoV-2 infection

Background

Detecting SARS-CoV-2 using a simple real time molecular assay will be helpful for the mitigation efforts in low / middle income countries during the pandemic. We have developed and validated a rapid and simple real time loop mediated isothermal amplification assay (LAMP) for screening of SARS-CoV-2 infection in known infected and non-infected individuals.

Methods

Six sets of primers were designed targeting the N-gene of the SARS-CoV-2 (Accession ID MN994468). LAMP reactions were performed using Warm Start 2X Master Mix and real-time PCR machine at 65 °C for 60 cycles with 15 s for each cycle. Results were read by visualizing turbidity under ultraviolet light and real time fluorescence detection through FAM channel of the real time PCR machine. We tested a total of 320 including 240 SARS CoV-2 positive (Ct values <40) and 80 SARS CoV-2 negative samples as tested by a real time RT-PCR using the newly developed LAMP assay.

Results

A total of 206 out of 240 SARS CoV-2 positive samples were tested positive by the newly developed LAMP assay with a sensitivity of 86%. All 80 SARS CoV-2 negative samples were tested negative by the newly developed LAMP assay with a specificity of 100%.

Conclusion

The newly developed real time LAMP assay has a sensitivity of 86% and specificity of 100% compared to the real time RT-PCR for the detection of SARS CoV-2. The new assay will be useful to screen large number of samples if adopted to minimize the time and cost.

Circulating dengue virus serotypes and vertical transmission in Aedes larvae during outbreak and inter-outbreak seasons in a high dengue risk area of Sri Lanka

Background

Spatial and temporal changes in the dengue incidence are associated with multiple factors, such as climate, immunity among a population against dengue viruses (DENV), circulating DENV serotypes and vertical transmission (VT) of DENV in an area at a given time. The level of VT in a specific location has epidemiological implications in terms of viral maintenance in vectors. Identification of the circulating DENV serotypes in both patients and Aedes mosquito larvae in an area may be useful for the early detection of outbreaks. We report here the results of a prospective descriptive study that was conducted to detect the levels of VT in Aedes mosquito larvae and circulating DENV serotypes in patients and Aedes mosquito larvae from December 2015 to March 2017 in an area of Sri Lanka at high risk for dengue.

Methods

A total of 200 patients with clinically suspected dengue who had been admitted to a tertiary care hospital during a dengue outbreak (3 study periods: December 2015–January 2016, June–August 2016, December 2016–January 2017) and in the inter-outbreak periods (February–May 2016 and September–November 2016) were investigated. Blood samples were drawn from the study participants to test for DENV. The houses of the study participants were visited within 7 days of admission to the hospital, and Aedes larvae were also collected within a radius of 400 m from the houses. The larvae were separately identified to species and then pooled according to each patient’s identification number. Patients’ sera and the Aedes larvae were tested to identify the infecting DENV serotypes using a reverse transcription PCR (RT-PCR) method. Levels of VT in Aedes mosquito larvae were also identified.

Results

All four DENV serotypes (DENV-1 to -4) were identified in the study area. In the early part of the study (December 2015–February 2016), DENV-3 was predominant and from April 2016 to March 2017, DENV-2 became the most predominant type. Four cases of DENV co-infections were noted during the study period in patients. Interestingly, all four DENV serotypes were detected in Aedes albopictus larvae, which was the prominent immature vectorial form identified throughout the study period in the area, showing 9.8% VT of DENV. With the exception of DENV-4, the other three DENV serotypes were identified in Aedes aegypti larvae with a VT of 8.1%.

Conclusion

Comparatively high rates of VT of DENV was detected in Ae. albopictus and Ae. aegypti larvae. A shift in the predominant DENV serotype with simultaneous circulation of all four DENV serotypes was identified in the study area from December 2015 to March 2017.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-05114-5.

Evaluation of Aedes aegypti (Diptera: Culicidae) Life Table Attributes Upon Chikungunya Virus Replication Reveals Impact on Egg-Laying Pathways

Arthropod-borne virus disease cycles constitute interactions among three primary players-the host, the vector, and the virus-in which the virus needs to interact with the host and the vector to establish its survival. While in the host, some arboviruses replicate aggressively, resulting in host pathogenicity, and manifest as a disease condition. These viruses more often utilize the vectors as reservoirs before they are transmitted to the host and therefore do not amplify to as large titers as they do in the hosts. In spite of this, the vector undergoes stress and activates several of its defense systems, resulting in alterations in its physiology. The present study was undertaken to evaluate the physiological changes that the mosquito vector Aedes aegypti (L.) (Diptera: Culicidae) undergoes during the replication of an arbovirus, Chikungunya virus (CHIKV). After the mosquitoes were infected with CHIKV, dissemination of the virus into various tissues and physiological parameters such as fecundity, vector mortality, egg laying, survival rate, overall fitness were monitored throughout the lifespan of the mosquitoes. Our study reveals that there is a fitness cost to the mosquitoes due to the infection of CHIKV. This fitness cost is manifested as higher mortality and low survival rate of the CHIKV-infected mosquitoes. Further evaluation revealed that the egg-laying pathway was affected, resulting in lower number of eggs. Expression analysis of six transcripts in the egg-laying pathway revealed that these transcripts were downregulated during the gonotrophic cycles in CHIKV-infected mosquitoes as compared to normal blood-fed mosquitoes.

Effect of Climatic Factors and Population Density on the Distribution of Dengue in Sri Lanka: A GIS Based Evaluation for Prediction of Outbreaks

Dengue is one of the major hurdles to the public health in Sri Lanka, causing high morbidity and mortality. The present study focuses on the use of geographical information systems (GIS) to map and evaluate the spatial and temporal distribution of dengue in Sri Lanka from 2009 to 2014 and to elucidate the association of climatic factors with dengue incidence. Epidemiological, population and meteorological data were collected from the Epidemiology Unit, Department of Census and Statistics and the Department of Meteorology of Sri Lanka. Data were analyzed using SPSS (Version 20, 2011) and R studio (2012) and the maps were generated using Arc GIS 10.2. The dengue incidence showed a significant positive correlation with rainfall (p<0.0001). No positive correlation was observed between dengue incidence and temperature (p = 0.107) or humidity (p = 0.084). Rainfall prior to 2 and 5 months and a rise in the temperature prior to 9 months positively correlated with dengue incidence as based on the auto-correlation values. A rise in humidity prior to 1 month had a mild positive correlation with dengue incidence. However, a rise in humidity prior to 9 months had a significant negative correlation with dengue incidence based on the auto-correlation values. Remote sensing and GIS technologies give near real time utility of climatic data together with the past dengue incidence for the prediction of dengue outbreaks. In that regard, GIS will be applicable in outbreak predictions including prompt identification of locations with dengue incidence and forecasting future risks and thus direct control measures to minimize major outbreaks.