COVID-19 in children in Odisha state, India: a retrospective review
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ABSTRACT:
SUBMITTER: Dash G
PROVIDER: S-EPMC8568531 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:High throughput sequencing is performed on mRNA isolated from whole blood of adult Covid-19 patients, bacterial coinfection with Covid-19 and healthy controls in a South Indian cohort. Samples were collected from individuals at the time of hospitalization or visit to clinic. The Covid-19 samples are categorized by severeity.
2022-02-22 | GSE196822 | GEO
Project description:Purpose: This study aims to characterize the early innate and adaptive responses induced by SARS-CoV-2 infection in children and adults over time up to 8 weeks post symptoms onset (POS). We report the gene signature of COVID-19 over the course of the disease in both age groups. The kinetic of infection was divided in 5-time intervals according to the calculated days POS: interval 1 (0-5), interval 2 (6-14), interval 3 (15-22), interval 4 (23-35), and interval 5 (36-81). Methods: RNA extraction was performed automatically via the PAXgene Blood miRNA Kit and the QIAcube instrument (Qiagen) following the manufacturer’s protocol. RNA concentration and quality were assessed by using the Qubit instrument (Invitrogen) and the Agilent 2100 Bioanalyzer, respectively. The Stranded Total RNA Ribo-Zero Plus kit from Illumina was used for the library preparation with 100 ng of total RNA as input. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM for clustering and sequenced on an Illumina HiSeq 4000 sequencer for a minimum of 30 million single-end 100 reads per sample. Main results: (I) we observed an antiviral-IFN-signature and innate-cell-activation within the first 5 days post symptoms onset (POS), while genes associated with CD4 T-cell responses, plasma cells and immunoglobulin were upregulated in both age groups during the first two weeks POS, indicative of SARS-CoV-2-specific adaptive immune responses; (II) in adults, genes associated with IFN antiviral responses and activated dendritic cells were maintained during the second week of disease, and subsided only after 14 days. By contrast, those transcriptome changes subsided already after 5 days in children.
2021-09-22 | GSE166190 | GEO
Project description:Early diagnosis and prompt treatment is a cornerstone of malaria control. In India, artemisinin combination therapy (ACT) became the first-line treatment for falciparum malaria and rapid diagnostic test (RDTs) kits were recommended for use at the grass-root level in the new malaria treatment policy (2010). Odisha State contributes about one-fourth of the total Indian malaria burden and 40% of falciparum infection. The present study assessed the health system readiness to deploy RDTs and ACT for malaria control across the State.Data collection was carried out from February to July 2012. Five of Odisha's 30 districts were selected through stratified random sampling, with stratification based on the phased roll-out of ACT and RDT. Two administrative 'blocks' were selected randomly in each district and data collected through health facility, auxiliary nurse midwives (ANMs) and accredited social health activist (ASHAs) assessments. Key informant interviews were conducted with individuals involved in the implementation of the malaria control programme.Of the 220 ANMs interviewed, 51.4% had been trained in malaria case management, including the use of ACT and RDT. A high proportion of ANM (80%) and AHSA (77%) had the necessary level of knowledge to be able to use RDT for malaria diagnosis. The proportion of ASHAs trained on malaria case management was 88.9% (209/235). However, 71% of ANM and 55% of ASHAs usually referred falciparum-positive patients to the health facility for treatment, the major reason for referral being the non-availability of drugs at the ANM and ASHA level.The relatively high level of knowledge about how to diagnose and treat malaria at the grass-root level was undermined by the poor availability of RDTs, ACT and primaquine tablets. This was associated with an unnecessarily high referral rate and potential delays in the treatment of this potentially life-threatening infection. Improvements in the supply chain for RDTs and ACT could dramatically enhance the effectiveness of malaria control in Odisha.
| S-EPMC3850888 | biostudies-other
Project description:We conducted 131 semi-structured phone interviews with householders in rural Odisha, India to explore participants' COVID-19 related knowledge, perceptions, and preventative actions, as well as how the pandemic affected their daily life, economic and food security, and the village-level response. Interviews were conducted with 73 heads of household, 37 primary caregivers, and 21 members of village water and sanitation committees from 43 rural villages in Ganjam and Gajapati districts in Odisha state. The study took place between May-July 2020 throughout various lockdown restrictions and at a time when many migrant workers were returning to their villages and cases were rising. Most respondents could name at least one correct symptom of COVID-19 (75%), but there was lower knowledge about causes of the disease and high-risk groups, and overall COVID-19 knowledge was lowest among caregivers. Respondents reported high compliance with important preventative measures, including staying home as much as possible (94%), social distancing (91%), washing hands frequently (96%), and wearing a facial mask (95%). Additionally, many respondents reported job loss (31%), financial challenges (93%), challenges related to staying home whether as a preventative measure or due to lockdowns (57%), changes in types and/or amount of food consumed (61%), and adverse emotional effects as a result of the pandemic and lockdown. We also provide detailed summaries of qualitative responses to allow for deeper insights into the lived experience of villagers during this pandemic. Although the research revealed high compliance with preventative measures, the pandemic and associated lockdowns also led to many challenges and hardships faced in daily life particularly around job loss, economic security, food security, and emotional wellbeing. The results underscore the vulnerability of marginalized populations to the pandemic and the need for measures that increase resilience to large-scale shocks.
| S-EPMC7998707 | biostudies-literature
Project description:BACKGROUND. Coronavirus disease 2019 (COVID-19) is more benign in children compared with adults for unknown reasons. This contrasts with other respiratory viruses where disease manifestations are often more severe in children. We hypothesize that a more robust early innate immune response to SARS coronavirus 2 (SARS-CoV-2) protects against severe disease. METHODS. Clinical outcomes, SARS-CoV-2 viral copies, and cellular gene expression were compared in nasopharyngeal swabs obtained at the time of presentation to the emergency department from 12 children and 27 adults using bulk RNA sequencing and quantitative reverse-transcription PCR. Total protein, cytokines, and anti–SARS-CoV-2 IgG and IgA were quantified in nasal fluid. We used a subset of 21 samples for RNAseq analysis. RESULTS. SARS-CoV-2 copies, angiotensin-converting enzyme 2 (ACE2), and TMPRSS2 gene expression were similar in children and adults, but children displayed higher expression of genes associated with IFN signaling, NLRP3 inflammasome, and other innate pathways. Higher levels of IFN-α2, IFN-γ, IP-10, IL-8, and IL-1β protein were detected in nasal fluid in children versus adults. Children also expressed higher levels of genes associated with immune cells, whereas expression of those associated with epithelial cells did not differ in children versus adults. Anti–SARS-CoV-2 IgA and IgG were detected at similar levels in nasal fluid from both groups. None of the children required supplemental oxygen, whereas 7 adults did (P = 0.03); 4 adults died. CONCLUSION. These findings provide direct evidence of a more vigorous early mucosal immune response in children compared with adults and suggest that this contributes to favorable clinical outcomes.
2021-05-11 | GSE172274 | GEO
Project description:IntroductionGovernments around the world suspended immunization outreach to control COVID-19 spread. Many have since resumed services with an emphasis on catch-up vaccinations. This paper evaluated immunization disruptions during India's March-May 2020 lockdown and the extent to which subsequent catch-up efforts reversed them in Rajasthan, India.MethodsIn this retrospective observational study, we conducted phone surveys to collect immunization details for 2,144 children that turned one year old between January and October 2020. We used logistic regressions to compare differences in immunization timeliness and completed first-year immunization status among children that were due immunizations just before (unexposed), during (heavily exposed), and after (post-exposure) the lockdown.ResultsRelative to unexposed children, heavily exposed children were significantly less likely to be immunized at or before 9 months (OR 0.550; 95% CI 0.367-0.824; p = 0.004), but more likely to be immunized at 10-12 months (OR 1.761; 95% CI 1.196-2.591; p = 0.004). They were also less likely to have completed their key first-year immunizations (OR 0.624; 95% CI 0.478-0.816; p = 0.001) by the time of survey. In contrast, post-exposure children showed no difference in timeliness or completed first-year immunizations relative to unexposed children, despite their younger age. First-year immunization coverage among heavily exposed children decreased by 6.9 pp to 10.4 pp (9.7% to 14.0%). Declines in immunization coverage were larger among children in households that were poorer, less educated, lower caste, and residing in COVID red zones, although subgroup comparisons were not statistically significant.ConclusionDisruptions to immunization services resulted in children missing immunization during the lockdown, but catch-up efforts after it was eased ensured many children were reached at later ages. Nevertheless, catch-up was incomplete and children due their immunizations during the lockdown remained less likely to be fully immunized 4-5 months after it lifted, even as younger cohorts due immunizations in June or later returned to pre-lockdown schedules.
| S-EPMC8196298 | biostudies-literature
Project description:To analyse gene expression pattern in different disease state of COVID-19 patients. Experimental workflow: 1) rRNA was removed by using RNase H method, 2) QAIseq FastSelect RNA Removal Kit was used to remove the Globin RNA, 3) The purified fragmented cDNA was combined with End Repair Mix, then add A-Tailing Mix, mix well by pipetting, incubation, 4) PCR amplification, 5) Library quality control and pooling cyclization, 6) The RNA library was sequenced by MGI2000 PE100 platform with 100bp paired-end reads. Analysis steps: 1) RNA-seq raw sequencing reads were filtered by SOAPnuke (Li et al., 2008) to remove reads with sequencing adapter, with low-quality base ratio (base quality < 5) > 20%, and with unknown base (’N’ base) ratio > 5%. 2) Reads aligned to rRNA by Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) were removed. 3) The clean reads were mapped to the reference genome using HISAT2 (Kim et al., 2015). Bowtie2 (v2.2.5) was applied to align the clean reads to the transcriptome. 4)Then the gene expression level (FPKM) was determined by RSEM (Li and Dewey, 2011). Genes with FPKM > 0.1 in at least one sample were retained.
2021-03-24 | E-MTAB-10298 | biostudies-arrayexpress
Project description:To analyse gene expression pattern in different disease state of COVID-19 patients. Experimental workflow: 1) Small RNA enrichment and purification, 2) Adaptor ligation and Unique molecular identifiers (UMI) labeled Primer addition, 3) RT-PCR, Library quantitation and pooling cyclization, 4) Library quality control, 5) Small RNAs were sequenced by BGI500 platform with 50bp single-end reads resulting in at least 20M reads for each sample. Analysis steps: 1) Small RNA raw sequencing reads with low quality tags (which have more than four bases whose quality is less than ten, or have more than six bases with a quality less than thirteen.), the reads with poly A tags, and the tags without 3’ primer or tags shorter than 18nt were removed. 2) After data filtering, the clean reads were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA using Bowtie2 (Langmead and Salzberg, 2012). Particularly, cmsearch (Nawrocki and Eddy, 2013) was performed for Rfam mapping. 3) The small RNA expression level was calculated by counting absolute numbers of molecules using unique molecular identifiers (UMI, 8-10nt). MiRNA with UMI count lager than 1 in at least one sample were considered as expressed.
2021-03-24 | E-MTAB-10299 | biostudies-arrayexpress
Project description:BackgroundCoronavirus disease 2019 (COVID-19) has been declared a global public-health crisis due to its impact on health, economy, and mental well-being. Here, we evaluated the clinical and epidemiological parameters associated with COVID-19 in South India.MethodsA retrospective, quaternary care hospital-based study that included COVID-19 positive patients admitted to MIOT International Hospital, Chennai between 8 April-7 August 2020. Cases were identified by reverse transcriptase-polymerase chain reaction. Epidemiological, demographic, clinical, and radiological findings were recorded and analyzed. The primary endpoint was stable discharge from hospital/patient recovery or death. Associations between risk factors and comorbidities were analyzed using Chi-Square/Fisher's exact test.ResultsOf the 5264 cases reviewed, 3345 cases were included. The mean (standard deviation, SD) age of the patients was 47.58 (16.69) years with a median and range hospital stay of 5 (2-41) days. 69.20% of patients were male. The most frequent comorbidities were diabetes (37.10%) and hypertension (29.10%). Contact history was available for 58% of patients. The most common symptoms were cough (36.60%), fever (28.30%), and myalgia (15.40%). Abnormal chest radiography was reported in 16.9% of patients. Phase of admission, age ≥50 years, hypertension, diabetes, coronary artery disease, chronic kidney disease was significantly associated with mortality (p < 0.05). There were 142 (4.2%) deaths in this study.ConclusionIn this single centre hospital-based study, late presentation and more severe form of COVID pneumonia lead to higher mortality although it had lower mortality rate for COVID-19 in comparison. Late phase of the pandemic showed better outcomes vs. the early group.
| S-EPMC8074520 | biostudies-literature
Project description:This study is aimed to estimate the epidemiological burden of dengue in Odisha, India using the disability adjusted life year (DALY) methods and to explore the associated factors in the year 2010-2016. During the period of 2010-2016, 27 772 cases (68.4% male) were reported in the state. Mean age (years) of male and female was 31.63 and 33.82, respectively. Mean district wise disability adjusted life years (DALY) per 100 000 people was higher in the year 2016 (0.45) and mean DALY lost per person was highest in the year 2015 (34.90?years). Adjusted regression model indicates, every unit increase in humidity and population density increases DALY by 1.05 and 1.02?units respectively. Whereas, unit change in sex ratio (females per 1000 males) and forest coverage increases the DALY by 0.98?units. Our results indicate geographical variation of DALY in Odisha, which is associated with population density, humidity and forest cover. Discrepancies identified between standard incidence and DALY maps suggests, latter can be used to present disease burden more effectively. More prevalence among young males suggests the need of strengthening the targeted prevention and control measures.
| S-EPMC6501402 | biostudies-literature