Whole genome analysis of Human Mastadenovirus D causing Keratoconjunctivitis in India - A multicentre study.

INTRODUCTION: Human mastadenovirus (HAdV) types 8, 37, 64 have been considered the major contributors in Epidemic keratoconjunctivitis (EKC) epidemics, but recent surveillance data have shown the involvement of emerging recombinants, including HAdV-53, HAdV-54, and HAdV-56. In our initial work, positive samples for adenovirus revealed that our strains were closer to HAdV-54 than HAdV-8. Hence, the current study aimed to use whole genome technology to identify the HAdV strain correctly. METHODOLOGY: Oxford Nanopore technique was used, wherein a Targeted sequencing approach using long-range PCR amplification was performed. Primers were designed using HAdV-54 (AB448770.2) and HAdV-8 (AB897885.1) as reference sequences. Amplicons were sequenced on the GridION sequencer. Sequences were annotated using Gatu software, and similarities with standard reference sequence was calculated using Bioedit software. The phylogenetic tree was built after alignment in MEGA v7.0 using Neighbour joining method for each of the genes: Penton, Hexon, and Fiber. The effect of novel amino acid changes was evaluated using the PROVEAN tool. The Recombination Detection Program (RDP) package Beta 4.1 was used to identify recombinant sequences. RESULTS: Of the five samples sequenced, OL450401, OL540403, and OL540406 showed nucleotide similarity to HAdV-54 in the penton region. Additionally, OL450401 showed a statistically significant recombination event with HAdV-54 as minor and HAdV-8 as major parents. This was further supported by phylogenetic analysis as well. CONCLUSIONS: In the present study, we have found evidence of a shift from HAdV-8 towards HAdV-54, thus stressing the need for surveillance of HAdVs and to stay updated on the rise of new recombinants.

Epidemiology of Keratoconjunctivitis Across India from 2017 to 2019: A Multicentric Hospital-Based Study.

PURPOSE: Conjunctivitis is one of the most common ocular conditions in clinical practice. Human adenoviruses have been the common causative agents known to cause epidemic kerato-conjunctivitis (EKC) in India from 1996 to 2019 with a positivity range of 13.8%-65.2%. The current study was initiated to throw light on the distribution of keratoconjunctivitis causing agents across India covering a span of 3 years. METHODS: A total of 709 swabs were collected from patients in viral transport medium (VTM), and real-time PCR was done to identify agents including Adenovirus (HAdV), Enterovirus, HSV, and Chlamydia. RESULTS: 47.8% of the samples were positive for HAdV followed by HSV (3.4%), Enterovirus (2.7%), and Chlamydia (0.6%). Overall, 386 people (54.4%) tested positive for one of these infections, with Chandigarh (88.4%) and Port Blair (71.7%) showing higher positivity rate. Pre-auricular lymphadenopathy and follicles were significantly associated with increased risk of conjunctivitis. CONCLUSION: Epidemiology of keratoconjunctivitis in the current study revealed HAdV to be predominant causative agent. Knowledge gained in such epidemiological studies guide us in outbreak expectations, limit antibiotic over-prescription, and enhance disease prevention.

Causal identification of single-cell experimental perturbation effects with CINEMA-OT.

Recent advancements in single-cell technologies allow characterization of experimental perturbations at single-cell resolution. While methods have been developed to analyze such experiments, the application of a strict causal framework has not yet been explored for the inference of treatment effects at the single-cell level. Here we present a causal-inference-based approach to single-cell perturbation analysis, termed CINEMA-OT (causal independent effect module attribution + optimal transport). CINEMA-OT separates confounding sources of variation from perturbation effects to obtain an optimal transport matching that reflects counterfactual cell pairs. These cell pairs represent causal perturbation responses permitting a number of novel analyses, such as individual treatment-effect analysis, response clustering, attribution analysis, and synergy analysis. We benchmark CINEMA-OT on an array of treatment-effect estimation tasks for several simulated and real datasets and show that it outperforms other single-cell perturbation analysis methods. Finally, we perform CINEMA-OT analysis of two newly generated datasets: (1) rhinovirus and cigarette-smoke-exposed airway organoids, and (2) combinatorial cytokine stimulation of immune cells. In these experiments, CINEMA-OT reveals potential mechanisms by which cigarette-smoke exposure dulls the airway antiviral response, as well as the logic that governs chemokine secretion and peripheral immune cell recruitment.

Distinguishing features of long COVID identified through immune profiling.

Post-acute infection syndromes may develop after acute viral disease1. Infection with SARS-CoV-2 can result in the development of a post-acute infection syndrome known as long COVID. Individuals with long COVID frequently report unremitting fatigue, post-exertional malaise, and a variety of cognitive and autonomic dysfunctions2-4. However, the biological processes that are associated with the development and persistence of these symptoms are unclear. Here 275 individuals with or without long COVID were enrolled in a cross-sectional study that included multidimensional immune phenotyping and unbiased machine learning methods to identify biological features associated with long COVID. Marked differences were noted in circulating myeloid and lymphocyte populations relative to the matched controls, as well as evidence of exaggerated humoral responses directed against SARS-CoV-2 among participants with long COVID. Furthermore, higher antibody responses directed against non-SARS-CoV-2 viral pathogens were observed among individuals with long COVID, particularly Epstein-Barr virus. Levels of soluble immune mediators and hormones varied among groups, with cortisol levels being lower among participants with long COVID. Integration of immune phenotyping data into unbiased machine learning models identified the key features that are most strongly associated with long COVID status. Collectively, these findings may help to guide future studies into the pathobiology of long COVID and help with developing relevant biomarkers.

NK/T-cell Lymphoma With Orbital Involvement: A Case Report and Systematic Review of the Literature.

PURPOSE: To present the clinical course of a patient with recurrent NK/T-cell lymphoma (NKTL) involving the orbit and to review the literature on patients with NKTL involving the orbit. METHODS: The PubMed database was searched for all cases of NKTL involving orbital, intraocular, or adnexal ocular structures. RESULTS: Ninety-six patients were included in the final analysis. The mean age of diagnosis was 48.1 ± 16.8 years. The patients were 53/96 (55.2%) male and 43/96 (44.8%) female. Tumor location varied and included the orbit in 80/96 (83.3%), nasosinus in 56/96 (58.3%), uvea in 11/96 (11.5%), lacrimal gland in 9/96 (9.4%), lacrimal drainage system in 11/96 (11.5%), and conjunctiva in 7/96 (7.3%) cases. Management included surgical debulking in 29/96 (30.2%) cases, radiotherapy in 52/96 (54.2%) cases, and chemotherapy in 82/96 (85.4%) cases. Median survival was 6 months (95% CI: 5-9). Chemotherapy (hazard ratio = 0.80, 95% CI: 0.67-0.95, p = 0.013), radiotherapy (hazard ratio = 0.75, 95% CI: 0.64-0.87, p < 0.001), and orbital involvement being a recurrence of disease (hazard ratio = 0.79, 95% CI: 0.67-0.95, p = 0.009) were associated with improved survival. Advanced Ann Arbor stage (III-IV) at diagnosis (hazard ratio = 1.22, 95% CI: 1.08-1.38, p = 0.001), vision loss (hazard ratio = 1.18, 95% CI: 1.04-1.34, p = 0.009), proptosis (hazard ratio = 1.15, 95% CI: 1.01-1.30, p = 0.035) and periorbital swelling (hazard ratio = 1.15, 95% CI: 1.00-1.33, p = 0.048) were associated with poor survival. CONCLUSIONS: NK/T-cell lymphoma involving the orbit, globe, or ocular adnexa heralds a poor prognosis where early diagnosis and therapy are critical. The use of radiotherapy and chemotherapy is associated with improved survival.

Adenoviral Conjunctivitis in the Andaman Islands: A Clinical and Molecular Epidemiological Study.

Introduction Human adenoviruses are common causes of many acute illnesses, and keratoconjunctivitis is one of them. Acute infections, if left untreated, can progress to severity, thus causing morbidities and mortalities. It belongs to the mastadenovirus family and is characterized by seven subgenus, i.e., A-G; among those, Adenovirus D8 is the most common type associated with keratoconjunctivitis. Methodology A hospital-based study was conducted, and the samples were collected from GB Pant Hospital, Port Blair, Dr Agarwals Eye Hospital, Port Blair, from August 2017 to December 2022. Clinical data and demographic details were followed by conjunctival swab sample collection from suspected keratoconjunctivitis patients. Samples were subjected to molecular screening, and Sanger sequencing was carried out for positive samples. Results Out of 506 conjunctival samples, a prevalence of 24.9% (n=126) was observed, and the commonest type circulating among the population of Andaman was Adenovirus D8. The major symptoms associated were eye redness (87.30%, n=110), followed by watering (81.75%, n=103), eye pain (72.22%, n=91), eye itching (61.11%, n=77), and discharge (50%, n=63). Conclusion In clinical research, ocular infections are one of the underrated fields. However, the study revealed the high prevalence of adenoviral infection among the suspected patients. Thus, there is a need for proper surveillance and timely diagnosis of such infections, as their severity may lead to loss of vision.

Willingness and yield of screening for hepatitis B among outpatients of a tertiary care centre, Puducherry, South India.

India's National Viral Hepatitis Control Programme recommends screening outpatients for hepatitis B at tertiary care centres. We aimed to assess the yield of screening and reasons for refusal for testing. We included adult outpatients at a tertiary care centre, South India during September and October 2019. Participants' willingness to be tested and the reasons for refusal were noted. Fingerstick blood sample was tested for HBsAg using rapid kit. Of a total of 700 participants, 157 (22%, 95% CI: 19.4-25.7%) were unwilling to be tested. Men were more unwilling (26%) compared to women (19%) (aPR 1.90 95% CI: 1.22-2.94; p = 0.004). 'Lack of time' was the most common reason reported for refusal (10%). Of 543 participants tested, 15 (2.8%, 95% CI: 1.6-4.5%) were positive for HBsAg. Similar studies from other regions in India are required for the estimation of yield of opportunistic approach.

A survey-wide association study to identify youth-specific correlates of major depressive episodes.

BACKGROUND: Major depressive disorder is a common disease with high mortality and morbidity worldwide. Though peak onset is during late adolescence, the prevalence of major depressive disorder remains high throughout adulthood. Leveraging an association study design, this study screened a large number of variables in the 2017 National Survey on Drug Use and Health to characterize differences between adult and youth depression across a wide array of phenotypic measurements. METHODS: All dichotomous variables were manually identified from the survey for association screening. Association between each dichotomous variable and past-year major depressive episode (MDE) occurrence was calculated as an odds ratio for adults (≥18 years) and youth (12-17 years), and tested for significance with Fischer's exact test. Logarithm of the calculated odds ratios were plotted and fitted to a linear model to assess correlation between adult and youth risk factors. RESULTS: Many of the screened variables showed similar association between past-year depressive episode occurrence in youth and adults; Lin's concordance correlation coefficient between adult and youth associations was 0.91 (95% CI 0.89-0.92). Differentially associated variables were identified, tracking: female sex, alcohol use, cigarette use, marijuana use, Medicaid/CHIP coverage, cognitive changes due to a mental, physical or emotional condition, and respondents' identification of a single depressive event as the worst experienced. CONCLUSIONS: While some youth-specific correlates of major depressive episodes were identified through screening, including some novel associations, most examined variables showed similar association with youth and adult depression. Further study of results is warranted, especially concerning the finding of increased association between marijuana use and depressive episodes in youth.

Investigational approach to adenoviral conjunctivitis: comparison of three diagnostic tests using a Bayesian latent class model.

INTRODUCTION: Highly contagious adenoviral conjunctivitis represents 15-70% of all conjunctivitis worldwide. Human adenovirus (hAdV) serotypes 3,4,7,8,19 and 37 contributes to 89% of all adenoviral conjunctivitis. Accurate and rapid diagnosis of adenoviral infections at serotype level could prevent misdiagnosis, spread of disease, unnecessary antibiotic use and increased treatment costs. METHODOLOGY: Sixty-two suspected viral conjunctivitis cases were recruited from November2013-January2015. Swabs collected from inferior palpebral conjunctiva and processed for viral culture (Hep2 cell line), immunofluorescence assay (IFA) and polymerase chain reaction (PCR) (targeting hexon gene). Serotype 3,4,7,8,19 and 37 identification was carried out with an optimized multiplex-PCR (based on hypervariable region of hexon gene) and confirmed by sequence analysis. Bayesian Latent Class Model (LCM) analysis was used to compare sensitivity and specificity of three tests. RESULTS: Adenovirus was detected in 54.8% (34/62) of cases by combination of all three methods. Culture was positive in 23/34 cases (67.6%). PCR and IFA detected adenovirus in 24 (70.5%) and 21 (61.7%) cases respectively. LCM analysis revealed, sensitivity and specificity of PCR, Culture and IFA was 77.8% and 92.4%; 72.2% and 90.8%; 67.6% and 92.9% respectively. Serotyping by multiplex-PCR showed, two cases each were hAdV3 and hAdV4, 18 hAdV8 and two remained unidentified. Results of Multiplex-PCR and sequence analysis showed 100% concordance Conclusion: LCM analysis revealed, PCR is the most appropriate method for identification. Multiplex-PCR is a simple and rapid method (serotypes identification within two days); owing its short turnaround time and accuracy, it can be used as a diagnostic tool for surveillance of adenoviral keratoconjunctivitis.