Genetic population structure of the malaria vector Anopheles baimaii in north-east India using mitochondrial DNA

<p>Abstract</p> <p>Background</p> <p><it>Anopheles baimaii </it>is a primary vector of human malaria in the forest settings of Southeast Asia including the north-eastern region of India. Here, the genetic population structure and the basic population genetic parameters of <it>An. baimaii </it>in north-east India were estimated using DNA sequences of the mitochondrial cytochrome oxidase sub unit II (COII) gene.</p> <p>Methods</p> <p><it>Anopheles baimaii </it>were collected from 26 geo-referenced locations across the seven north-east Indian states and the COII gene was sequenced from 176 individuals across these sites. Fifty-seven COII sequences of <it>An. baimaii </it>from six locations in Bangladesh, Myanmar and Thailand from a previous study were added to this dataset. Altogether, 233 sequences were grouped into eight population groups, to facilitate analyses of genetic diversity, population structure and population history.</p> <p>Results</p> <p>A star-shaped median joining haplotype network, unimodal mismatch distribution and significantly negative neutrality tests indicated population expansion in <it>An. baimaii </it>with the start of expansion estimated to be ~0.243 million years before present (MYBP) in north-east India. The populations of <it>An. baimaii </it>from north-east India had the highest haplotype and nucleotide diversity with all other populations having a subset of this diversity, likely as the result of range expansion from north-east India. The north-east Indian populations were genetically distinct from those in Bangladesh, Myanmar and Thailand, indicating that mountains, such as the Arakan mountain range between north-east India and Myanmar, are a significant barrier to gene flow. Within north-east India, there was no genetic differentiation among populations with the exception of the Central 2 population in the Barail hills area that was significantly differentiated from other populations.</p> <p>Conclusions</p> <p>The high genetic distinctiveness of the Central 2 population in the Barail hills area of the north-east India should be confirmed and its epidemiological significance further investigated. The lack of genetic population structure in the other north-east Indian populations likely reflects large population sizes of <it>An. baimaii </it>that, historically, were able to disperse through continuous forest habitats in the north-east India. Additional markers and analytical approaches are required to determine if recent deforestation is now preventing ongoing gene flow. Until such information is acquired, <it>An. baimaii </it>in north-east India should be treated as a single unit for the implementation of vector control measures.</p

Molecular characterization and identification of members of the Anopheles subpictus complex in Sri Lanka

BACKGROUND: Anopheles subpictus sensu lato is a major malaria vector in South and Southeast Asia. Based initially on polytene chromosome inversion polymorphism, and subsequently on morphological characterization, four sibling species A-D were reported from India. The present study uses molecular methods to further characterize and identify sibling species in Sri Lanka. METHODS: Mosquitoes from Sri Lanka were morphologically identified to species and sequenced for the ribosomal internal transcribed spacer-2 (ITS2) and the mitochondrial cytochrome c oxidase subunit-I (COI) genes. These sequences, together with others from GenBank, were used to construct phylogenetic trees and parsimony haplotype networks and to test for genetic population structure. RESULTS: Both ITS2 and COI sequences revealed two divergent clades indicating that the Subpictus complex in Sri Lanka is composed of two genetically distinct species that correspond to species A and species B from India. Phylogenetic analysis showed that species A and species B do not form a monophyletic clade but instead share genetic similarity with Anopheles vagus and Anopheles sundaicus s.l., respectively. An allele specific identification method based on ITS2 variation was developed for the reliable identification of species A and B in Sri Lanka. CONCLUSION: Further multidisciplinary studies are needed to establish the species status of all chromosomal forms in the Subpictus complex. This study emphasizes the difficulties in using morphological characters for species identification in An. subpictus s.l. in Sri Lanka and demonstrates the utility of an allele specific identification method that can be used to characterize the differential bio-ecological traits of species A and B in Sri Lanka

Molecular surveillance of dengue virus in field-collected Aedes mosquitoes from Bhopal, central India: evidence of circulation of a new lineage of serotype 2

IntroductionDengue fever is hyperendemic in several Southeast and South Asian countries, including India, with all four serotypes (DENV 1–4) circulating at different periods and in different locations. Sustainable and improved virological and entomological surveillance is the only tool to prevent dengue and other vector-borne diseases.ObjectivesThe present study has been carried out to detect and characterize the circulating dengue virus (DENV) in field-collected Aedes mosquitoes in Bhopal, Central India.MethodsAedes mosquitoes were collected from 29 localities within Bhopal city during October 2020 to September 2022. DENV infection was assessed in the individual head and thorax regions of Aedes mosquitoes using reverse transcriptase PCR. Positive samples were sequenced, and the circulating serotypes and genotypes were determined using phylogenetic analysis.ResultsDENV RNA was detected in 7 Aedes aegypti and 1 Aedes albopictus, with infection rates of 0.59 and 0.14%, respectively. Phylogenetic analysis revealed all the isolates belonged to DENV serotype 2 and distinctly clustered with the non-Indian lineage (cosmopolitan genotype 4a), which was not recorded from the study area earlier. The time to most common recent ancestor (TMRCA) of these sequences was 7.4 years old, with the highest posterior density (HPD) of 3.5–12.2 years, indicating that this new lineage emerged during the year 2014. This is the first report on the DENV incrimination in both Ae. aegypti and Ae. albopictus mosquitoes collected from Bhopal, Central India.ConclusionThe observed emergence of the non-Indian lineage of DENV-2 in Bhopal, which again is a first report from the area, coincides with the gradual increase in DENV cases in Bhopal since 2014. This study emphasizes the importance of DENV surveillance and risk assessment in this strategically important part of the country to decipher its outbreak and severe disease-causing potential

Spatial epidemiology of acute respiratory infections in children under 5 years and associated risk factors in India: District-level analysis of health, household, and environmental datasets

BackgroundIn India, acute respiratory infections (ARIs) are a leading cause of mortality in children under 5 years. Mapping the hotspots of ARIs and the associated risk factors can help understand their association at the district level across India.MethodsData on ARIs in children under 5 years and household variables (unclean fuel, improved sanitation, mean maternal BMI, mean household size, mean number of children, median months of breastfeeding the children, percentage of poor households, diarrhea in children, low birth weight, tobacco use, and immunization status of children) were obtained from the National Family Health Survey-4. Surface and ground-monitored PM2.5 and PM10 datasets were collected from the Global Estimates and National Ambient Air Quality Monitoring Programme. Population density and illiteracy data were extracted from the Census of India. The geographic information system was used for mapping, and ARI hotspots were identified using the Getis-Ord Gi* spatial statistic. The quasi-Poisson regression model was used to estimate the association between ARI and household, children, maternal, environmental, and demographic factors.ResultsAcute respiratory infections hotspots were predominantly seen in the north Indian states/UTs of Uttar Pradesh, Bihar, Delhi, Haryana, Punjab, and Chandigarh, and also in the border districts of Uttarakhand, Himachal Pradesh, and Jammu and Kashmir. There is a substantial overlap among PM2.5, PM10, population density, tobacco smoking, and unclean fuel use with hotspots of ARI. The quasi-Poisson regression analysis showed that PM2.5, illiteracy levels, diarrhea in children, and maternal body mass index were associated with ARI.ConclusionTo decrease ARI in children, urgent interventions are required to reduce the levels of PM2.5 and PM10 (major environmental pollutants) in the hotspot districts. Furthermore, improving sanitation, literacy levels, using clean cooking fuel, and curbing indoor smoking may minimize the risk of ARI in children

Malaria in North-East India: Importance and Implications in the Era of Elimination

Worldwide and in India, malaria elimination efforts are being ramped up to eradicate the disease by 2030. Malaria elimination efforts in North-East (NE) India will have a great bearing on the overall efforts to eradicate malaria in the rest of India. The first cases of chloroquine and sulfadoxine-pyrimethamine resistance were reported in NE India, and the source of these drug resistant parasites are most likely from South East Asia (SEA). NE India is the only land route through which the parasites from SEA can enter the Indian mainland. India&rsquo;s malaria drug policy had to be constantly updated due to the emergence of drug resistant parasites in NE India. Malaria is highly endemic in many parts of NE India, and Plasmodium falciparum is responsible for the majority of the cases. Highly efficient primary vectors and emerging secondary vectors complicate malaria elimination efforts in NE India. Many of the high transmission zones in NE India are tribal belts, and are difficult to access. The review details the malaria epidemiology in seven NE Indian states from 2008 to 2018. In addition, the origin and evolution of resistance to major anti-malarials are discussed. Furthermore, the bionomics of primary vectors and emergence of secondary malaria vectors, and possible strategies to prevent and control malaria in NE are outlined

Novel approach to analysis of AMR: looking at the composite resistance phenotype

Submission of detail report with codes for the Vivli AMR Surveillance Open Data Re-use Data Challenge 2023 Team ID: 9049 [Lead: Shraddha Karve] Objectives: The escalating challenge of antimicrobial resistance (AMR) poses a significant global concern for public healthcare systems1,2. Current AMR surveillance and molecular mechanism studies traditionally focus on specific drug-bug combinations, like carbapenem-resistant Klebsiella pneumoniae, designated as a priority pathogen by the WHO3. While wastewater and environmental surveillance aim to detect Klebsiella species and genes conferring carbapenem resistance4, it is known that resistance genes for one antibiotic often coexist with genes for resistance to others5. To address these complexities, we propose a novel analysis approach using Klebsiella pneumoniae as a model. We consider the resistance profile of an isolate for a set of common antibiotics across two datasets, ATLAS and GEARS. We term this composite phenotype, encompassing resistance/sensitivity to a group of antibiotics, a 'subtype' of the pathogen. Our primary objective is to track and study the prevalence of different subtypes across time and space, enabling a more comprehensive understanding of AMR dynamics. We then explore the impact of climatic parameters on the prevalence of different Klebsiella pneumoniae subtypes, aiming to uncover additional insights into antibiotic resistance patterns. Rising temperatures and climate change have been associated with recent antibiotic resistance developments, as bacterial growth and genetic material dissemination are closely tied to temperature conditions6. Heavy rainfall has been linked to bacterial mutagenesis and antibiotic resistance gene expression7. Rising local temperatures in the United States and Europe have shown correlations with increased antibiotic resistance at the population level in various pathogens8,9. GitHub repository: https://github.com/KutumLab/amr-vivli-ashoka-submissio

Assessment of Acrocentric Chromosome Association/Satellite Associations in the Human Health Conditions and Exposure to Genotoxic Agents: A Comprehensive Review

This review aims to provide a comprehensive overview of both conventional and molecular studies focusing on acrocentric chromosome association/satellite association (ACA/SA) research for assessing human health conditions including cancer as well as in evaluating exposure to genotoxic agents. It is well documented that the ACA/SA frequency in lymphocytes of patients with oral squamous cell carcinoma and gastrointestinal and breast cancer has been evaluated by many workers. Literature was searched using various combinations of keywords in different databases. The articles that appeared till March 2023 were considered depending on their relevance, and relevant information was extracted by two independent reviewers. A total of 97 studies were selected based on our criteria describing the relevant keywords, 46 studies described SAs/acrocentric association with different diseases, 35 studies demonstrated effects of genotoxic agents, 8 studies were on characteristics and general aspects of ACA/SA phenomenon, and 8 studies described the molecular mechanisms of acrocentric chromosomes. Thus, ACA/SA was crucial in assessing human health conditions, including genetic disorders and cancer, as well as in evaluating exposure to genotoxic agents. The information collected would help to promote a deeper understanding of the impact of ACA/SA on human health including cancer and emphasize the importance of integrating molecular approaches into genotoxic exposure studies. Continued research in this field will undoubtedly contribute to the advancements in medical genetics and improved patient care

Effect of climate change and deforestation on vector borne diseases in the North-Eastern Indian State of Mizoram bordering Myanmar

Malaria and dengue are the two major vector-borne diseases in Mizoram. Malaria is endemic in Mizoram, and dengue was first reported only in 2012. The study was designed to study the impact of climate variables, and deforestation on the incidence of dengue and malaria in Mizoram. Temperature, rainfall, and humidity data of Mizoram in the monsoon period (May-September) from 1979 to 2013 were obtained from the National Centers for Environmental Prediction Climate Forecast System Reanalysis. Forest cover data were extracted from the Forests Survey of India Reports and satellite products of Advanced Very High Resolution Radiometer and Moderate Resolution Imaging Spectroradiometer missions. Vector-borne diseases data were obtained from the State Vector Borne Disease Control Program. Non-parametric tests (Mann-Kendall test and Sen's slope method) were used to estimate the long-term trends in the climate and forest cover variables. The Mann-Kendall test indicates that the minimum temperature during the monsoon period is increasing (p<0.001). The Sen's slope estimate shows an average annual 0.02 °C (0.01–0.03 at 95% CI) increase in minimum temperature, and there is an annual ~0.1 °C increase after 2007. There is a 20.45 mm increase in annual monsoon rainfall (5.90–34.37 at 95% CI), and a 0.08% (0.02–0.18 at 95% CI) increase in relative annual humidity. Forest cover data shows that there is an annual average decrease of 162 sq.km (272.81–37.53 at 95% CI, p<0.001) in the dense forest cover. Malaria transmission continues to be stable in Mizoram; compared to 2007, cases have increased in 2019. Over the study period, in the monsoon season, there was an ~0.8 °C rise in the minimum temperature, which could have facilitated the establishment of Aedes aegypti in Mizoram. Furthermore, the increase in rainfall and humidity may have also helped the biology of Ae. aegypti. Deforestation could be an important factor responsible for the consistently high number of malaria cases in Mizoram