Molecular characterization of rotavirus indicates predominance of G9P[4] genotype among children with acute gastroenteritis: First report after vaccine introduction in Pakistan.

Globally, Group A rotavirus (RVA) is the leading cause of acute gastroenteritis in children under 5 years old, with Pakistan having the highest rates of RVA-related morbidity and mortality. The current study aims to determine the genetic diversity of rotavirus and evaluate the impact of Rotarix-vaccine introduction on disease epidemiology in Pakistan. A total of 4749 children, hospitalized with acute gastroenteritis between 2018 and 2020, were tested at four hospitals in Lahore and Karachi. Of the total, 19.3% (918/4749) cases were tested positive for RVA antigen, with the positivity rate varying annually (2018 = 22.7%, 2019 = 14.4%, 2020 = 20.9%). Among RVA-positive children, 66.3% were under 1 year of age. Genotyping of 662 enzyme-linked immuno sorbent assay-positive samples revealed the predominant genotype as G9P[4] (21.4%), followed by G1P[8] (18.9%), G3P[8] (11.4%), G12P[6] (8.7%), G2P[4] (5.7%), G2P[6] (4.8%), and 10.8% had mixed genotypes. Among vaccinated children, genotypes G9P[4] and G12P[6] were more frequently detected, whereas a decline in G2P[4] was observed. Phylogenetic analysis confirmed the continued circulation of indigenous genotypes detected earlier in the country except G9 and P[6] strains. Our findings highlight the predominance of G9P[4] genotype after the vaccine introduction thus emphasizing continual surveillance to monitor the disease burden, viral diversity, and their impact on control of rotavirus gastroenteritis in children.

Automated detection and classification of polioviruses from nanopore sequencing reads using piranha.

Widespread surveillance, rapid detection, and appropriate intervention will be critical for successful eradication of poliovirus. Using deployable next-generation sequencing (NGS) approaches, such as Oxford Nanopore Technologies' MinION, the time from sample to result can be significantly reduced compared to cell culture and Sanger sequencing. We developed piranha (poliovirus investigation resource automating nanopore haplotype analysis), a 'sequencing reads-to-report' solution to aid routine poliovirus testing of both stool and environmental samples and alleviate the bioinformatic bottleneck that often exists for laboratories adopting novel NGS approaches. Piranha can be used for efficient intratypic differentiation of poliovirus serotypes, for classification of Sabin-like polioviruses, and for detection of wild-type and vaccine-derived polioviruses. It produces interactive, distributable reports, as well as summary comma-separated values files and consensus poliovirus FASTA sequences. Piranha optionally provides phylogenetic analysis, with the ability to incorporate a local database, processing from raw sequencing reads to an interactive, annotated phylogeny in a single step. The reports describe each nanopore sequencing run with interpretable plots, enabling researchers to easily detect the presence of poliovirus in samples and quickly disseminate their results. Poliovirus eradication efforts are hindered by the lack of real-time detection and reporting, and piranha can be used to complement direct detection sequencing approaches.

Is geopolitics a new risk to environmental policy in the European union?

Geopolitical risks and environmental policy have become increasingly important in the European Union (EU), which is committed to tackling climate change and protecting the environment. However, geopolitical risks can undermine its environmental policy objectives. Thus, the study evaluates the relationship between geopolitical risks and environmental policy in nineteen EU countries from 1994 to 2020 through panel bootstrap Granger causality. The results show that geopolitical risks significantly influence environmental policy in Denmark, Estonia, Finland, France, Germany, Luxembourg, and Romania. On the other hand, the findings reveal that environmental policy causes geopolitical risks only in Latvia, while there is no relationship in the remaining countries. Therefore, policymakers must develop resilience to geopolitical risks, promote renewable energy, strengthen environmental regulations, and address social and economic implications to reduce environmental policy vulnerability to geopolitical risks.

Comparison of Eleven RNA Extraction Methods for Poliovirus Direct Molecular Detection in Stool Samples.

Direct detection by PCR of poliovirus RNA in stool samples provides a rapid diagnostic and surveillance tool that can replace virus isolation by cell culture in global polio surveillance. The sensitivity of direct detection methods is likely to depend on the choice of RNA extraction method and sample volume. We report a comparative analysis of 11 nucleic acid extraction methods (7 manual and 4 semiautomated) for poliovirus molecular detection using stool samples (n = 59) that had been previously identified as poliovirus positive by cell culture. To assess the effect of RNA recovery methods, extracted RNA using each of the 11 methods was tested with a poliovirus-specific reverse transcription-quantitative PCR (RT-qPCR), a pan-poliovirus RT-PCR (near-whole-genome amplification), a pan-enterovirus RT-PCR (entire capsid region), and a nested VP1 PCR that is the basis of a direct detection method based on nanopore sequencing. We also assessed extracted RNA integrity and quantity. The overall effect of extraction method on poliovirus PCR amplification assays tested in this study was found to be statistically significant (P < 0.001), thus indicating that the choice of RNA extraction method is an important component that needs to be carefully considered for any diagnostic based on nucleic acid amplification. Performance of the methods was generally consistent across the different assays used. Of the 11 extraction methods tested, the MagMAX viral RNA isolation kit used manually or automatically was found to be the preferable method for poliovirus molecular direct detection considering performance, cost, and processing time. IMPORTANCE Poliovirus, the causative agent of poliomyelitis, is a target of global eradication led by the World Health Organization since 1988. Direct molecular detection and genomic sequencing without virus propagation in cell culture is arguably a critical tool in the final stages of polio eradication. Efficient recovery of good-quality viral RNA from stool samples is a prerequisite for direct detection by nucleic acid amplification. We tested 11 nucleic acid extraction methods to identify those facilitating sensitive, fast, simple, and cost-effective extraction, with flexibility for manual and automated protocols considered. Several different PCR assays were used to compare the recovered viral RNA to test suitability for poliovirus direct molecular detection. Our findings highlight the importance of choosing a suitable RNA extraction protocol and provide useful information to diagnostic laboratories and researchers facing the choice of RNA extraction method for direct molecular virus detection from stool.

The Empirical Analysis of Environmental Regulation's Spatial Spillover Effects on Green Technology Innovation in China.

Green technology innovation is one of the driving forces of industrial structure upgrading. This innovation is thought to be related to environmental regulation. The study uses panel data for 30 Chinese provinces and cities from 2009 to 2020 and presents a comprehensive research-based explanation of how environmental regulations impact green innovation. This study employs the spatial Durbin model to analyze the spillover effect of the region. The results show that the total impact of environmental regulations is 0.223%, of which the direct effect is 0.099%. This impact includes the effects of both formal and informal environmental regulation. It indicates that ecological regulations significantly enhance green technology innovation. Furthermore, the spatial spillover effect is significantly positive at the 1% level with a coefficient of 0.124. Such spillover effects represent a learning effect of regional environmental regulation. Based on the results, the study suggests a few policy measures based on the detailed outcomes.

COVID-19 impact on multifractality of energy prices: Asymmetric multifractality analysis.

This article assesses the asymmetric multifractality of the energy prices in the different periods during the coronavirus pandemic (COVID-19) through asymmetric multifractality detrended fluctuation analysis. The higher (lower) multifractality shows a rapid rise (fall), which has different consequences for the energy prices. The findings explore strong multifractality in the downward movements for crude oil, heating oil, diesel, gasoline, propane and kerosene oil returns. The upside multifractality for coal and natural gas returns are bigger than the downside in both periods. Furthermore, the access asymmetry is more pronounced during the COVID-19, implying increased market inefficiency. The outcomes explore if energy prices are inefficient during the pandemic. A special attention is required in order to observe such unexpected fluctuations in the price dynamic and guidelines are vital. The level of efficiency can be improved by a greater transference in information while the government must play its role in regulations. Such aspects can increase stability and decrease the expected risks and price movements.

Migratory birds as the vehicle of transmission of multi drug resistant extended spectrum ß lactamase producing Escherichia fergusonii, an emerging zoonotic pathogen.

The acquisition of multi-drug resistance (MDR) genes by pathogenic bacterial bugs and their dispersal to different food webs has become a silent pandemic. The multiplied use of different antibacterial therapeutics during COVID-19 pandemic has accelerated the process among emerging pathogens. Wild migratory birds play an important role in the spread of MDR pathogens and MDR gene flow due to the consumption of contaminated food and water. Escherichia fergusonii is an emerging pathogen of family Enterobacteriaceae and commonly causes disease in human and animals. The present study focused on the isolation of E. fergusonii from blood, saliva, and intestine of selected migratory birds of the Hazara Division. The sensitivity of isolated strains was assessed against ten different antibiotics. The isolation frequency of E. fergusonii was 69%. In blood samples, a high rate of resistance was observed against ceftriaxone (80%) followed by ampicillin (76%) whereas, in oral and intestinal samples, ceftriaxone resistant strains were 56% and 57% while ampicillin resistance was 49% and 52% respectively. The overall ceftriaxone and ampicillin-resistant cases in all three sample sources were 71% and 65% respectively. In comparison to oral and intestinal samples, high numbers of ceftriaxone-resistant strains were isolated from the blood of mallard while ampicillin-resistant strains were observed in blood samples of cattle egrets. 16S rRNA-based confirmed strains of E. fergusonii were processed for detection of CTX-M and TEM-1 gene through Polymerase chain reaction (PCR) after DNA extraction. Hundred percent ceftriaxone resistant isolates possessed CTX-M and all ampicillin-resistant strains harbored TEM-1 genes. Amplified products were sequenced by using the Sanger sequencing method and the resulted sequences were checked for similarity in the nucleotide Database through the BLAST program. TEM-1 gene showed 99% and the CTX-M gene showed 98% similar sequences in the Database. The 16S rRNA sequence and nucleotide sequences for TEM-1 and CTX-M genes were submitted to Gene Bank with accession numbers LC521304, LC521306, LC521307 respectively. We posit to combat MDR gene flow among the bacterial pathogens across different geographical locations, regular surveillance of new zoonotic pathogens must be conducted.

Optimized Super-Wideband MIMO Antenna with High Isolation for IoT Applications.

A compact, low profile, multiple-input-multiple-output (MIMO) diversity antenna with super-wideband (SWB) characteristics has been proposed. The proposed antenna comprises four symmetric monopole-radiating elements printed on low-cost FR4 substrate with the slotted ground plane. The single antenna of a monopole structure and a quad-port MIMO antenna, with the dimensions of 30 × 20 mm2 and 60 × 55 mm2, respectively, are ideal for IoT and high-speed data applications. The proposed MIMO antenna has a high diversity gain and low envelope correlation coefficient (ECC) within the frequency range. Simulated results demonstrate the performance of the MIMO-SWB antenna, which operates from 2.3 to 23 GHz, with a high isolation level over 20 dB in the achieved frequency band. Moreover, the proposed MIMO antenna has been investigated with mirror fashion and orthogonal structure. Both structures provide similar results except for mutual coupling performance. The orthogonal adjustment for high isolation achieves better results with the proposed model. Further, the prototype of the proposed antenna is fabricated and measured effectively. Simulated and measured results show good agreement for super-wideband applications.

Are there bubbles in the vanilla price?

This paper investigates the presence of the bubbles that are experienced in the global vanilla (VNL) price, using the GSADF approach. The results show that there are five bubbles in the VNL price that are driven by specific reasons. Also, in this regard, the opening and ending points of each bubble coincide with specific events that contribute toward the formation, as well as the rupture of the bubbles. It has also been noted that the cyclone Hudah and the monopoly of the cartels trigger the first bubble, while the regulation and export taxation policy drive the second bubble. However, market-oriented policies, the abolition of cartels, and the exchange rate adjustments are the leading factors that form the third bubble. Furthermore, political instability, hurricanes and bad weather are the key factors driving the fourth bubble. And finally, the rising global demand and decreasing supply, price speculation, poor quality, and cyclone Enawo create the last bubble. It needs the VNL market to be more stable in order to continue supply, which can then control the price fluctuations. The minimum role of the cartels and middlemen is vital for VNL price stability. Therefore, the governments should ideally facilitate the big companies to directly negotiate with farmers which may be beneficial for both companies and the farmers alike.

Molecular detection and genetic characterization of human metapneumovirus strains circulating in Islamabad, Pakistan.

Lower respiratory illness is one of the leading causes of death among children in low- and high-income countries. Human metapneumovirus (hMPV) is a key contributor to respiratory illnesses commonly reported among children and causes serious clinical complications ranging from mild respiratory infections to severe lower respiratory tract anomalies mainly in the form of bronchiolitis and pneumonia. However, due to the lack of a national surveillance system, the clinical significance of hMPV remains obscure in the Pakistani population. This study was conducted to screen throat swabs samples collected from 127 children reported with respiratory symptoms at a tertiary care hospital in Islamabad. Out of 127, 21 (16.5%) samples were positive for hMPV with its genotype distribution as A2a (10%), A2b (20%), B1 (10%), and B2 (60%). Phylogenetic analysis showed that the hMPV viruses were closely related to those reported from neighboring countries including India and China. This work will contribute to a better understanding of this virus, its diagnosis, and the handling of patients in clinical setups. Further studies at a large-scale are warranted for a better understanding of the disease burden and epidemiology of hMPV in Pakistan.

The role of pricing strategies, clean technologies, and ecological regulation on the objectives of the UN 2030 Agenda.

The dynamics of global emissions and the increasing focus on market-based policy instruments have prompted this research to examine the extent to which such instruments are successful in emission control. The study explores the influence of carbon taxes, eco-friendly innovations, and ecological policy in attaining sustainable development goals and fulfilling the mitigation targets of climate change for 2030. The article selected 15 EU countries from southern and western regions and tested the empirical relationship between 2000 and 2018. This work used second-generation testing approaches and error correction-based modeling approaches to analyze the relationship between the variables. The results show that eco-friendly innovations and environmental policies help reduce emissions in the long and short run. On the other hand, carbon taxes have a more prominent effect on mitigation efforts, specifically in the short run. Factors such as urbanization, economic growth, and energy consumption are the most prominent polluting elements, the results being consistent in all models. The results further show a unidirectional and bidirectional causality relationship between the variables, and outcomes are more country-specific. Given these arguments, carbon taxes are a short-term instrument in combating carbon emissions. However, the sustainable development vision 2030 relies on eco-innovations linked with research and development and the transition from gray to green energy.

The role of green innovations, environmental policies and carbon taxes in achieving the sustainable development goals of carbon neutrality.

The green innovations, environmental policies, and carbon taxes are the tools to achieve sustainable development goals (SDGs) in the mitigation process. This study is intended to examine the impact of innovation, carbon pricing (CTAX), environmental policies (EP), and energy consumption (ECON) on PM2.5 and greenhouse gas (GHG) emission for Central-Eastern European countries. The panel effect during 2000-2018 is tested using a dynamic panel data model while the Granger causality approach obtains country-related outcomes. The outcomes reveal that eco-friendly innovations have a more profound effect on carbon mitigation. Environmental policies reduce emissions by 2.7% in the short run and 17.4% in the long run. Similarly, CTAX mitigates GHG emissions by 8.6% in the short-run and PM2.5 by 0.9% and 5.7% in the short and long run. However, urbanization, energy consumption and trade openness are the leading polluters in the region. The main findings remain dominant in the country-specific results and find unidirectional and bidirectional causality evidence among variables. The research concludes that green innovations and strict environmental policy can lead towards achieving sustainable development goals using carbon taxes as a tool on the way.

Spatial analysis of genetic clusters and epidemiologic factors related to wild poliovirus type 1 persistence in Afghanistan and Pakistan.

Following the certification of the World Health Organization Region of Africa as free of serotype 1 wild poliovirus (WPV1) in 2020, Afghanistan and Pakistan represent the last remaining WPV1 reservoirs. As efforts continue in these countries to progress to eradication, there is an opportunity for a deeper understanding of the spatiotemporal characteristics and epidemiological risk factors associated with continual WPV1 circulation in the region. Using poliovirus surveillance data from 2017-2019, we used pairwise comparisons of VP1 nucleotide sequences to illustrate the spatiotemporal WPV1 dispersal to identify key sources and destinations of potentially infected, highly mobile populations. We then predicted the odds of WPV1 detection at the district level using a generalized linear model with structural indicators of health, security, environment, and population demographics. We identified evidence of widespread population mobility based on WPV1 dispersal within and between the countries, and evidence indicating five districts in Afghanistan (Arghandab, Batikot, Bermel, Muhamandara and Nawzad) and four districts in Pakistan (Charsada, Dera Ismail Khan, Killa Abdullah and Khyber) act as cross-border WPV1 circulation reservoirs. We found that the probability of detecting WPV1 in a district increases with each armed conflict event (OR = 1·024, +- 0·008), level of food insecurity (OR = 1·531, +-0·179), and mean degrees Celsius during the months of greatest precipitation (OR = 1·079, +- 0·019). Our results highlight the multidisciplinary complexities contributing to the continued transmission of WPV1 in Afghanistan and Pakistan. We discuss the implications of our results, stressing the value of coordination during this final chapter of the wild polio virus eradication initiative.

Conserved Antigenic Structure of Contemporary Wild Poliovirus Type 1 Strains Endemic in Pakistan.

BACKGROUND: Elimination of poliovirus in Pakistan and Afghanistan is challenged by notions against the role of oral poliovirus vaccine (OPV) in eradicating contemporary wild poliovirus (WPV) strains. METHODS: A total of 1055 WPV type 1 (WPV1) strains isolated between 2013 and 2018 were categorized into 68 antigenic groups and tested for neutralization by OPV-derived antibodies. Molecular docking was conducted to determine neutralization efficiency of antibodies against WPV. The clinical significance of WPV1 variants was assessed to ascertain their role in patient outcomes. RESULTS: We found that 88% of WPV1 strains isolated from paralytic children belonged to a single antigenic lineage identical to the WPV1 strain detected in 1993. WPV1 antigenic variants were effectively neutralized by OPV-derived antibodies, with geometric mean titers comparable to the neutralization titers found for 3 strains in OPV (OPV1-3, 7.96-9.149 [95% confidence interval, 6.864-10.171]; WPV1 strains, 7.542-8.786 [6.493-9.869]). Docking examination underscored a strong antigen-antibody interaction despite variations within the viral protein 1 epitopes. There was no significant association (P = .78) with clinical prognosis among patients infected with antigenically diverse WPV1 strains and patient outcomes, including death. CONCLUSIONS: Our findings substantiate the robustness of OPV for neutralizing the contemporary WPV1 strains endemic in Pakistan and Afghanistan. Vaccination coverage must be augmented to achieve early eradication.

The dynamic interaction between COVID-19 and shipping freight rates: a quantile on quantile analysis.

This study determines the impact of the coronavirus disease (COVID-19) that has been prevalent since the year 2019, on the shipping freights. This task has been undertaken by using the wavelet quantile on the quantile approach. The results of the study affirm that the pandemic has in fact affected the shipping freight costs, primarily due to the lower demand for energy and raw materials, and the unavailability of the vessels. In addition to this, the spread of COVID-19 has had a positive impact on the Baltic Dry Index in the high quantiles and is deemed to be more responsive in the long run. Also, the COVID-19 infection has had a negative effect on the Baltic Dry Tanker Index and the Baltic Clean Tanker Index in the medium to high quantiles, particularly in the short and the medium run. The positive impact of COVID-19 on the Baltic Clean Tanker Index has been recognized in the long term in the high quantiles. These findings support the theoretical model which states that the spread of COVID-19 and the shipping freights are closely related. The results suggest that the degree of the effect is more causal in the short. Therefore, the shipping industry must ideally pay special attention to the detection of abrupt changes in the freight rate dynamics, and the specific regulations regarding these intricacies are critical.

Genetic and evolutionary analysis of SARS-CoV-2 circulating in the region surrounding Islamabad, Pakistan.

Genomic epidemiology of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has provided global epidemiological insight into the COVID-19 pandemic since it began. Sequencing of the virus has been performed at scale, with many countries depositing data into open access repositories to enable in-depth global phylogenetic analysis. To contribute to these efforts, we established an Oxford Nanopore Technologies (ONT) sequencing capability at the National Institutes of Health (NIH), Pakistan. This study highlights multiple SARS-CoV-2 lineages co-circulating during the peak of a second COVID-19 wave in Pakistan (Nov 2020-Feb 2021), with virus origins traced to the United States of America and Saudi Arabia. Ten SARS-CoV-2 positive samples were used for ONT library preparation. Sequence and phylogenetic analysis determined that the patients were infected with lineage B.1.1.250, originally identified in the United Kingdom and Bangladesh during March and April of 2020, and in circulation until the time of this study in Europe, USA and Australia. Lineage B.1.261 was originally identified in Saudi Arabia with widespread local dissemination in Pakistan. One sample clustered with the parental B.1 lineage and the other with lineage B.6 originally from Singapore. In the future, monitoring the evolutionary dynamics of circulating lineages in Pakistan will enable improved tracing of the viral spread, changing trends of their expansion trajectories, persistence, changes in their demographic dynamics, and provide guidance for better implementation of control measures.

Detection of SARs-CoV-2 in wastewater using the existing environmental surveillance network: A potential supplementary system for monitoring COVID-19 transmission.

The ongoing COVID-19 pandemic is caused by SARs-CoV-2. The virus is transmitted from person to person through droplet infections i.e. when infected person is in close contact with another person. In January 2020, first report of detection of SARS-CoV-2 in faeces, has made it clear that human wastewater might contain this virus. This may illustrate the probability of environmentally facilitated transmission, mainly the sewage, however, environmental conditions that could facilitate faecal oral transmission is not yet clear. We used existing Pakistan polio environment surveillance network to investigate presence of SARs-CoV-2 using three commercially available kits and E-Gene detection published assay for surety and confirmatory of positivity. A Two-phase separation method is used for sample clarification and concentration. An additional high-speed centrifugation (14000Xg for 30 min) step was introduced, prior RNA extraction, to increase viral RNA yield resulting a decrease in Cq value. A total of 78 wastewater samples collected from 38 districts across Pakistan, 74 wastewater samples from existing polio environment surveillance sites, 3 from drains of COVID-19 infected areas and 1 from COVID 19 quarantine center drainage, were tested for presence of SARs-CoV-2. 21 wastewater samples (27%) from 13 districts turned to be positive on RT-qPCR. SARs-COV-2 RNA positive samples from areas with COVID 19 patients and quarantine center strengthen the findings and use of wastewater surveillance in future. Furthermore, sequence data of partial ORF 1a generated from COVID 19 patient quarantine center drainage sample also reinforce our findings that SARs-CoV-2 can be detected in wastewater. This study finding indicates that SARs-CoV-2 detection through wastewater surveillance has an epidemiologic potential that can be used as supplementary system to monitor viral tracking and circulation in cities with lower COVID-19 testing capacity or heavily populated areas where door-to-door tracing may not be possible. However, attention is needed on virus concentration and detection assay to increase the sensitivity. Development of highly sensitive assay will be an indicator for virus monitoring and to provide early warning signs.

Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan.

Since its emergence in China, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide including Pakistan. During the pandemic, whole genome sequencing has played an important role in understanding the evolution and genomic diversity of SARS-CoV-2. Although an unprecedented number of SARS-CoV-2 full genomes have been submitted in GISAID and NCBI, data from Pakistan is scarce. We report the sequencing, genomic characterization, and phylogenetic analysis of five SARS-CoV-2 strains isolated from patients in Pakistan. The oropharyngeal swabs of patients that were confirmed positive for SARS-CoV-2 through real-time RT-PCR at National Institute of Health, Pakistan, were selected for whole-genome sequencing. Sequencing was performed using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEW ENGLAND BioLabs Inc., MA, US) and Illumina iSeq 100 instrument (Illumina, San Diego, US). Based on whole-genome analysis, three Pakistani SARS-CoV-2 strains clustered into the 20A (GH) clade along with the strains from Oman, Slovakia, United States, and Pakistani strain EPI_ISL_513925. The two 19B (S)-clade strains were closely related to viruses from India and Oman. Overall, twenty-nine amino acid mutations were detected in the current study genome sequences, including fifteen missense and four novel mutations. Notably, we have found a D614G (aspartic acid to glycine) mutation in spike protein of the sequences from the GH clade. The G614 variant carrying the characteristic D614G mutation has been shown to be more infectious that lead to its rapid spread worldwide. This report highlights the detection of GH and S clade strains and G614 variant from Pakistan warranting large-scale whole-genome sequencing of strains prevalent in different regions to understand virus evolution and to explore their genetic diversity.

Reverse transcriptase loop-mediated isothermal amplification (RT-LAMP)-based diagnosis: A potential alternative to quantitative real-time PCR based detection of the novel SARS-COV-2 virus.

The sudden outbreak of the novel Coronavirus infectious disease (COVID-19) resulted in significant challenges to global health systems. One of the primary challenges is rapid, reliable, and accurate detection of the severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) virus among the suspected COVID-19-infected individuals. At present, quantitative real-time PCR (qRT-PCR) is a widely used diagnostic method. However, it requires expensive instruments and expertise in the interpretation of results. These constraints reflect the significant need for the development of alternative diagnostic options. This study will validate the use and efficiency of the reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay as a potential alternative for the detection of COVID-19. For this purpose, a cohort of 297 suspected COVID-19 patients was tested using both the RT-LAMP assay and the conventional RT-PCR method. For the RT-LAMP assay, three genes (orf-1ab, N, and S) were identified as the target sites for the detection of COVID-19. Based on a comparative assessment, 117 out of 124 positive COVID-19 cases were observed using the RT-LAMP technique with an overall 91.45% sensitivity. Interestingly, where a consensus on 163 individuals free of SARS-Cov-2 was observed, RT-LAMP specificity was 90%. Based on these findings, the robustness of the technique, and the reduced dependency on expensive instrumentation, RT-LAMP-based COVID-19 detection is strongly recommended as a potential alternative assay.