ABSTRACT
The modern response to pandemics, critical for effective public health measures, is shaped by the availability and integration of diverse epidemiological outbreak data. Genomic surveillance has come to the forefront during the coronavirus disease 2019 (COVID-19) pandemic at both local and global scales to identify variants of concern. Tracking variants of concern (VOC) is integral to understanding the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in space and time. Combining phylogenetics with epidemiological data like case incidence, spatial spread, and transmission dynamics generates actionable information. Here we discuss the genome surveillance done in Pune, India, through sequencing 10,496 samples from infected individuals and integrating them with multiple heterogeneous outbreak data. The rise and fall of VOCs along with shifting transmission dynamics in the time interval of December 2020 to March 2022 was identified. Population-based estimates of the proportion of circulating variants indicated the second and third peak of infection in Pune to be driven by VOCs Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529) respectively. Integrating single nucleotide polymorphism changes across all sequenced genomes identified C (Cytosine) > T (Thymine) and G (Guanine) > T (Thymine) substitutions to dominate with higher rates of adaptive evolution in Spike (S), RNA-dependent RNA polymerase (RdRp), and Nucleocapsid (N) genes. Spike Protein mutational profiling during and pre-Omicron VOCs indicated differential rank ordering of high-frequency mutations in specific domains that increased the charge and binding properties of the protein. Time-resolved phylogenetic analysis of Omicron sub-lineages identified specific recombinant X lineages, XZ, XQ, and XM. BA.1 from Pune was found to be highly divergent by global sequence alignment and hierarchical clustering. Our "band of five" outbreak data analytics that includes the integration of five heterogeneous data types indicates that a strong surveillance system with comprehensive high-quality metadata was critical to understand the spatiotemporal evolution of the SARS-CoV-2 genome in Pune. We anticipate the use of such integrated workflows to be critical for pandemic preparedness in the future.
ABSTRACT
To understand the spread of SARS-CoV2, in August and September 2020, the Council of Scientific and Industrial Research (India), conducted a sero-survey across its constituent laboratories and centers across India. Of 10,427 volunteers, 1058 (10.14%) tested positive for SARS CoV2 anti-nucleocapsid (anti-NC) antibodies; 95% with surrogate neutralization activity. Three-fourth recalled no symptoms. Repeat serology tests at 3 (n=346) and 6 (n=35) months confirmed stability of antibody response and neutralization potential. Local sero-positivity was higher in densely populated cities and was inversely correlated with a 30 day change in regional test positivity rates (TPR). Regional seropositivity above 10% was associated with declining TPR. Personal factors associated with higher odds of sero-positivity were high-exposure work (Odds Ratio, 95% CI, p value; 2{middle dot}23, 1{middle dot}92-2{middle dot}59, 6{middle dot}5E-26), use of public transport (1{middle dot}79, 1{middle dot}43-2{middle dot}24, 2{middle dot}8E-06), not smoking (1{middle dot}52, 1{middle dot}16-1{middle dot}99, 0{middle dot}02), non-vegetarian diet (1{middle dot}67, 1{middle dot}41-1{middle dot}99, 3{middle dot}0E-08), and B blood group (1{middle dot}36,1{middle dot}15-1{middle dot}61, 0{middle dot}001). Impact StatementWidespread asymptomatic and undetected SARS-CoV2 infection affected more than a 100 million Indians by September 2020. Declining new cases thereafter may be due to persisting humoral immunity amongst sub-communities with high exposure. FundingCouncil of Scientific and Industrial Research, India (CSIR)
ABSTRACT
OBJECTIVE: To investigate the potentiality of mosquitocidal activity of Gliricidia sepium (G. sepium) (Jacq.) (Leguminosae). METHODS: Twenty five early third instar larvae of Anopheles stephensi (An. stephensi) were exposed to various concentrations (50-250 ppm) and the 24 h LC(50) values of the G. sepium extract was determined by probit analysis. The ovicidal activity was determined against An. stephensi to various concentrations ranging from 25-100 ppm under laboratory conditions. The eggs hatchability was assessed 48 h post treatment. The pupicidal activity was determined against An. stephensi to various concentrations ranging from 25-100 ppm. Mortality of each pupa was recorded after 24 h of exposure to the extract. RESULTS: Results pertaining to the experiment clearly revealed that ethanol extract showed significant larvicidal, ovicidal and pupicidal activity against the An. stephensi. Larvicidal activity of ethanol extracts of G. sepium showed maximum mortality in 250 ppm concentration (96.0±2.4)%. Furthermore, the LC(50) was found to be 121.79 and the LC(90) value was recorded to be 231.98 ppm. Ovicidal activity of ethanol extract was assessed by assessing the egg hatchability. Highest concentration of both solvent extracts exhibited 100% ovicidal activity. Similarly, pupae exposed to different concentrations of ethanol extract were found dead with 58.10% adult emergence when it was treated with 25 ppm concentration. Similarly, 18.36 (n=30; 61.20%); 21.28(70.93) and 27.33(91.10) pupal mortality was recorded from the experimental pupae treated with 50, 75 and 100 ppm concentration of extracts. Three fractions have been tested for their larvicidal activity of which the Fraction 3 showed the LC(50) and LC(90) values of 23.23 and 40.39 ppm. With regard to the ovicidal effect fraction 3 showed highest ovicidal activities than the other two fractions. Furthermore, there were no hatchability was recorded above 50 ppm (100% egg mortality) in the experimental group. Statistically significant pupicidal activity was recorded from 75 ppm concentration. CONCLUSIONS: From the results it can be concluded the crude extract of G. sepium is an excellent potential for controlling An. stephensi mosquito. It is apparent that, fraction 3 possess a novel and active principle which could be responsible for those biological activities.
