Molecular characterization of DENV-3 circulating during the post-monsoon period of 2013-14 in Delhi, India.
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ABSTRACT:
SUBMITTER: Sharma P
PROVIDER: S-EPMC8200893 | biostudies-literature | 2015 Dec
REPOSITORIES: biostudies-literature
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Molecular characterization of DENV-3 circulating during the post-monsoon period of 2013-14 in Delhi, India.
Sharma Pankaj P Mittal Veena V Chhabra Mala M Kumari Roop R Singh Priyanka P Bhattacharya Dipesh D Venkatesh Srinivas S Rai Arvind A
Virologica Sinica 20151201 6
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Project description:The National Capital Region (NCR) of India, Delhi, has experienced high post-monsoon pollution along with several peak pollution episodes in recent years. Diwali, the festival of lights, which is among the biggest festivals of India celebrated during the post-monsoon season, is also considered a pollution event associated as it is with the lighting of a large number of firecrackers. 2016 Diwali pollution episode continued for a week creating severe discomfort to residents of Delhi, prompting the judiciary to ban the sale and use of firecrackers in Delhi from 2017 onwards. The current study analyzes different sectoral and temporal emissions contribution to the 2016 post monsoonal pollution episode over Delhi using a fully coupled chemical transport model. The findings of the study indicate that aerosols produced from crop residue open burning at the northwestern states contributed more than 60% of the total simulated surface concentration during the period under study. Model experimental simulations show that despite emissions from within the city, what explains the severity of pollution over Delhi during the period under consideration is an additional pollution load emanating from these intense crop open burning sessions from nearby areas. Further, model simulations show that while Diwali emissions can elevate the pollution load over Delhi, the effects do not last beyond 48 h. It is found that the stagnation of the pollutants several days beyond the 2016 Diwali day was due to favorable meteorological conditions like low surface temperature, lower boundary layer height, and weak northwesterly winds. The study shows that in order to improve air quality in Delhi during the post-monsoon period, mitigation efforts should target the adjacent rural areas, especially when there is massive burning of crop residue in those areas.
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Project description:Dengue fever is a self-limiting, acute febrile disease which may aggravate to haemorrhage, plasma leakage and organ impairment in small number of cases. An outbreak of dengue fever occurred in Delhi, India after rainy season in the year 2013. Dengue virus specific RT-PCR was carried out on 378 suspected blood samples that were collected during the outbreak. Dengue virus was detected in 71% samples with highest number of patients infected by DENV-2 (86%) followed by DENV-1 (19 %) and DENV-3 (8%). Co-infection with more than one DENV serotype was detected in 14% samples. Twenty nine DENV strains (10 DENV-1, 12 DENV-2 and 7 DENV-3) were sequenced for partial envelope protein gene. Phylogenetic analysis grouped DENV-1 strains in the American African genotype, DENV-2 strains in the Cosmopolitan genotype and DENV-3 in Genotype III. We report the serotype distribution, circulating genotypes and partial envelope protein gene sequence of 29 DENV strains detected during 2013 outbreak in Delhi, India.
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Project description:Between 1986 and 1993, 72% of rotavirus strains isolated from newborns at five hospitals in New Delhi, India, had long electropherotypes, subgroup II VP6 antigens, and G and P genotypes (G9P11) identical to those of prototype strain 116E. A novel strain with a G9P6 genotype, representing 13% of the isolates, was identified. These results demonstrate that G9P11 and G9P6 rotavirus strains are common in nurseries in New Delhi.
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Project description:BackgroundChikungunya virus is an alpha virus with high similarity to Dengue and Zika viruses, both in transmission cycle and in clinical presentation. Chikungunya is a re-emerging mosquito-borne infection known to cause small to very large outbreaks/epidemics at frequent intervals. In 2016, India witnessed a large outbreak of Chikungunya infection affecting more than 58,000 people. This study was undertaken to look at the genotypic phylogeny to know the relatedness with previously reported strains.MethodsDuring the 2016 outbreak, samples from all patients clinically suspected to have Chikungunya were collected and subjected to testing for IgM antibody by ELISA and viral RNA detection by RT-PCR. Sequencing of the E1 gene segment was done to create a phylogenetic tree comparison with other strains.ResultsSerum samples were collected from 142 patients of clinically suspected Chikungunya infection. Majority of the patients were in the age group of 31-50 years accounting for more than 35% of the total cases. Twenty eight samples were positive for IgM antibody. Thirty seven samples were positive for viral RNA by RT-PCR. Only 06 cases were positive by both tests. Mutations in the amino acids K211E, M269V and D284E in the E1 gene segment of the Chikungunya virus were observed in the seven strains that were sequenced. On phylogeny tree, all the strains were found to belong to the ECSA genotype.ConclusionActively searching for the potential epidemic causing mutations and reporting of novel mutations may help in better understanding and probably forecasting of future CHIKV outbreaks and its nature.
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Project description:Dengue virus type 2 (DENV-2) has been associated with severe dengue outbreaks in many countries including India. Its predominance was recorded nearly after a decade in the capital city, Delhi in 2013. The present study characterizes DENV-2 circulated during 2013-2014. Analysis based on envelope (E) gene showed the presence of two clades (I and II) of DENV-2, within the Cosmopolitan genotype. Analysis of time of most recent common ancestor revealed the existence of clade I for more than a decade (95 % HPD 13-16 years) however, clade II showed comparatively recent emergence (95 % HPD 5-13 years). Presence of different clades is of high significance as this may result in increased virus transmission and major outbreaks. Further, the presence of a unique amino acid substitution, Q325H was also observed in an isolate; 14/D2/Del/2013 (KT717981). This substitution falls in immune epitope (epitope id: 150268) and may have important role in host immune response.
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Project description:Two hundred and six strains of avian infectious bronchitis virus (IBV) were isolated from chickens showing signs of disease in southern China during the period from 2013-2015. The nucleotide and amino acid sequences from the isolated field strains were compared to 42 published references. Nucleotide homologies ranged from 63.1-99.9% and amino acid homologies ranging from 60.2-100%. At least seven IBV genotypes were co-circulating in commercial chicken farms in southern China. The IBV isolates were genetically diverse and underwent continuing evolution. The QX-type, TW I-type, and 4/91-type were the most common genotypes during the three-year observation period and accounted for 88.8% of the isolated strains. Notably, the prevalence of the TW I-type strains has been increasing in recent years and has become the most common genotype in China. The emergence of variant IBV strains can be attributed to recombination. Serologic analysis and antigenic 3D cartography of 4 reference and 14 field isolated strains indicated the surveyed IBVs had diverse serology types and that the serotype of the isolated QX-type and TW I-type strains was distinct from the vaccines strains. Therefore, long-term continuing surveillance is necessary for IBV prevention and control.
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Project description:Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.
| S-EPMC7612010 | biostudies-literature
Project description:In the present investigation we molecularly characterized nontypeable rotavirus strains previously identified during surveillance in New Delhi, India. The majority of strains were demonstrated to belong to genotype G1 (54.5%) or P[8] (77.8%) on the basis of nucleotide sequencing of fragments from their VP7 and VP4 genes. The other genotypes detected included G2, G8, G9, G12, and P[4]. A G8P[6] strain, strain DS108, was detected for the first time in northern India. The VP7 gene of DS108 was most homologous with the VP7 gene of a bovine G8 strain, strain A5 (98.9%), indicating its bovine parentage. In contrast, the VP4 gene had a high degree of nucleotide sequence homology (92.9% to 99.1%) with the VP4 genes of human P[6] strains. The VP6 gene and nonstructural genes (NSP1 to NSP3 and NSP5) were most homologous with the VP6 gene and nonstructural genes of human rotaviruses belonging to the DS1 genogroup. Interestingly, the NSP4 gene of DS108 clustered within genotype E6 that until now had only two representative strains, both with G12P[6] specificity (strains RV176-00 and N26-02). Together, these results indicate that G8 strain DS108 belongs to the DS1 genogroup and could be the result of the acquisition of the VP7, VP4, and NSP4 genes by a human G2P[4] strain from more than one donor, similar to the evolution of G12P[6] strain RV176-00. The present study highlights the importance of characterizing multiple genes of nontypeable rotavirus strains to detect novel strains and get a more complete picture of rotavirus evolution.
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Project description:BACKGROUND:India is expected to experience an increase in the frequency and intensity of extreme weather events in the coming decades, which poses serious risks to human health and wellbeing in the country. OBJECTIVE:This paper aims to shed light on the possible detrimental effects of monsoon weather shocks on childhood undernutrition in India using the Demographic and Health Survey 2015-16, in combination with geo-referenced climate data. METHODS:Undernutrition is captured through measures of height-for-age, weight-for-height, stunting and wasting among children aged 0-59 months. The standardised precipitation and evapotranspiration index (SPEI) is used to measure climatic conditions during critical periods of child development. RESULTS:The results of a multivariate logistic regression model show that climate anomalies experienced in utero and during infancy are associated with an increased risk of child undernutrition; exposure to excessive monsoon precipitation during these early periods of life elevates the risk of stunting, particularly for children in the tropical wet and humid sub-tropical regions. In contrast, the risk of stunting is reduced for children residing in the mountainous areas who have experienced excessive monsoon precipitation during infancy. The evidence on the short-term effects of climate shocks on wasting is inconclusive. We additionally show that excessive precipitation, particularly during the monsoon season, is associated with an increased risk of contracting diarrhoea among children under five. Diseases transmitted through water, such as diarrhoea, could be one important channel through which excessive rainfall increases the risk of stunting. CONCLUSIONS:We find a positive association between childhood undernutrition and exposure to excessive monsoon precipitation in India. Pronounced differences across climate zones are found. The findings of the present analysis warn of the urgent need to provide health assistance to children in flood-prone areas.
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