B cell repertoire sequencing of HIV-1 pediatric elite-neutralizers identifies multiple broadly neutralizing antibody clonotypes.

Introduction: A limited subset of HIV-1 infected adult individuals typically after at least 2-3 years of chronic infection, develop broadly neutralizing antibodies (bnAbs), suggesting that highly conserved neutralizing epitopes on the HIV-1 envelope glycoprotein are difficult for B cell receptors to effectively target, during natural infection. Recent studies have shown the evolution of bnAbs in HIV-1 infected infants. Methods: We used bulk BCR sequencing (BCR-seq) to profile the B cell receptors from longitudinal samples (3 time points) collected from a rare pair of antiretroviralnaïve, HIV-1 infected pediatric monozygotic twins (AIIMS_329 and AIIMS_330) who displayed elite plasma neutralizing activity against HIV-1. Results: BCR-seq of both twins revealed convergent antibody characteristics including V-gene use, CDRH3 lengths and somatic hypermutation (SHM). Further, antibody clonotypes with genetic features similar to highly potent bnAbs isolated from adults showed ongoing development in donor AIIMS_330 but not in AIIMS_329, corroborating our earlier findings based on plasma bnAbs responses. An increase in SHM was observed in sequences of the IgA isotype from AIIMS_330. Discussion: This study suggests that children living with chronic HIV-1 can develop clonotypes of HIV-1 bnAbs against multiple envelope epitopes similar to those isolated from adults, highlighting that such B cells could be steered to elicit bnAbs responses through vaccines aimed to induce bnAbs against HIV-1 in a broad range of people including children.

Statistical estimation of noise induced hearing loss among the drivers in one of the most polluted cities of India.

In the present study, an attempt has been made to assess the impact of vehicular noise upon the 3-wheeler tempo drivers and to know whether there is any relationship between hearing loss and cumulative noise exposure. For this purpose, 3-wheeler tempo drivers (Exposed group) and non-commercial light motor vehicle car drivers (Unexposed group) were chosen as study subjects. Three traffic routes were selected to assess the noise level during waiting and running time in the exposed and unexposed groups. Among all three routes, the highest mean noise level (Leq) was observed on the Chowk to Dubagga route for waiting and en-route noise measurement. It was measured as 84.13 dB(A) and 86.36 dB(A) for waiting and en-route periods of 7.68 ± 3.46 and 31.05 ± 6.6 min, respectively. Cumulative noise exposure was found to be significantly different (p < 0.001) in all age groups of exposed and unexposed drivers. Audiometric tests have been performed over both exposed and unexposed groups. The regression analysis has been done keeping hearing loss among tempo drivers as the dependent variable and age (years) and Energy (Pa2 Hrs) as the independent variable using three different criteria of hearing loss definitions, i.e., World Health Organization, National Institute for Occupational Safety and Health (NIOSH), Occupational Safety and Health Administration criteria. Among these three criteria, the NIOSH criterion of hearing loss best explained the independent variables. It could explain the total variation in dependent variable by independent variable quite well, i.e., 68.1%. The finding showed a linear relationship between cumulative noise exposures (Pa2 Hrs) and the exposed group's hearing loss (dB), i.e., hearing loss increases with increasing noise dose. Based on the findings, two model equations were developed to identify the safe and unsafe noise levels with exposure time.

Severe disease during both primary and secondary dengue virus infections in pediatric populations.

Dengue is a global epidemic causing over 100 million cases annually. The clinical symptoms range from mild fever to severe hemorrhage and shock, including some fatalities. The current paradigm is that these severe dengue cases occur mostly during secondary infections due to antibody-dependent enhancement after infection with a different dengue virus serotype. India has the highest dengue burden worldwide, but little is known about disease severity and its association with primary and secondary dengue infections. To address this issue, we examined 619 children with febrile dengue-confirmed infection from three hospitals in different regions of India. We classified primary and secondary infections based on IgM:IgG ratios using a dengue-specific enzyme-linked immunosorbent assay according to the World Health Organization guidelines. We found that primary dengue infections accounted for more than half of total clinical cases (344 of 619), severe dengue cases (112 of 202) and fatalities (5 of 7). Consistent with the classification based on binding antibody data, dengue neutralizing antibody titers were also significantly lower in primary infections compared to secondary infections (P ≤ 0.0001). Our findings question the currently widely held belief that severe dengue is associated predominantly with secondary infections and emphasizes the importance of developing vaccines or treatments to protect dengue-naive populations.

Estimation of Access to Safe Drinking Water to Households in Etawah District: A Cross-Sectional Study.

CONTEXT: Unsafe drinking water causes diarrheal disease and environmental enteropathy. The quality of water is determined by its physical, chemical, and biological characteristics. Water sources have a significant impact on household members' health, particularly children. To combat this, India is committed to providing household tap connections to ensure the delivery of safe drinking water with the "Jal Jeevan Mission." AIMS: This study aims to estimate the access to safe drinking water and the physical and chemical qualities of water (qualitatively) in the urban and rural areas of Etawah district, India. SETTINGS AND DESIGN: A cross-sectional study was conducted in Etawah district from January 2020 to December 2021. The study subjects were the eldest female of the family. A total of 312 females were included. The data collected were analyzed using IBM SPSS Statistics for Windows, version 25 (released 2017; IBM Corp., Armonk, New York, United States) for descriptive analysis. RESULTS: In the present study, 76.3% (238/312) of households in the urban and rural areas had access to safe drinking water (here, the meaning of the word "safe" is based on its operational definition). A total of 130 (83.3%) households in rural areas and only 21 (13.5%) in urban areas had private supply as the primary water source. The physical and chemical qualities of water were within the requirement (acceptable limit) and permissible limit in all the study areas, so the water is considered safe for drinking. CONCLUSIONS: This study reported that 76.3% (238) households had access to safe drinking water according to the operational definition. The major public source of drinking water was public-supplied tap water, and in private sources, submersible or boreholes were the most common.

Barriers of household toilet utilization among toilet owners in a rural area of Northern India: An analytical cross-sectional study.

Background: Open defecation continues to prevail among toilet owners despite effective implementation of the Swachh Bharat Mission (Gramin). We conducted this study to determine toilet utilization rates and learn about the barriers to toilet use in the rural areas. By understanding the barriers, physicians can provide targeted education and become better equipped to manage their patients' conditions and advocate for their demands. Materials and Methods: We conducted a cross-sectional study on the households of the rural field practice areas of the department in central Uttar Pradesh by the census method. House listing was procured from the departmental records. The questionnaire was directed at both the household level and individual level. Results: The proportion of households with access to a toilet was found to be 91.1% of which 504 households were included in the study. Among the toilet owners, 115 (22.8%) households were not using toilets exclusively by all the members. At the individual level, age groups (of 20-59 years, and ≥60 years) and female gender were found to be significantly associated with open defecation. At the household level, government assistance for toilet construction and livestock keeping was found to be associated with open defecation. Major barriers to toilet use were childhood habits, dearth of toilets in the farming grounds/workplace, women during menstruation and having a non-functional toilet. Conclusion: This study indicates that merely installing a household toilet does not ensure exclusive utilization of toilet and the practice of open defecation might continue to be prevalent if corrective measures are not undertaken.

Functional and transcriptional heterogeneity within the massively expanding HLADR+CD38+ CD8 T cell population in acute febrile dengue patients.

IMPORTANCE: CD8 T cells play a crucial role in protecting against intracellular pathogens such as viruses by eliminating infected cells and releasing anti-viral cytokines such as interferon gamma (IFNγ). Consequently, there is significant interest in comprehensively characterizing CD8 T cell responses in acute dengue febrile patients. Previous studies, including our own, have demonstrated that a discrete population of CD8 T cells with HLADR+ CD38+ phenotype undergoes massive expansion during the acute febrile phase of natural dengue virus infection. Although about a third of these massively expanding HLADR+ CD38+ CD8 T cells were also CD69high when examined ex vivo, only a small fraction of them produced IFNγ upon in vitro peptide stimulation. Therefore, to better understand such functional diversity of CD8 T cells responding to dengue virus infection, it is important to know the cytokines/chemokines expressed by these peptide-stimulated HLADR+CD38+ CD8 T cells and the transcriptional profiles that distinguish the CD69+IFNγ+, CD69+IFNγ-, and CD69-IFNγ- subsets.

Erratum: Recognition determinants of improved HIV-1 neutralization by a heavy chain matured pediatric antibody.

[This corrects the article DOI: 10.1016/j.isci.2023.107579.].

Recognition determinants of improved HIV-1 neutralization by a heavy chain matured pediatric antibody.

The structural and characteristic features of HIV-1 broadly neutralizing antibodies (bnAbs) from chronically infected pediatric donors are currently unknown. Herein, we characterized a heavy chain matured HIV-1 bnAb 44m, identified from a pediatric elite-neutralizer. Interestingly, in comparison to its wild-type AIIMS-P01 bnAb, 44m exhibited moderately higher level of somatic hypermutations of 15.2%. The 44m neutralized 79% of HIV-1 heterologous viruses (n = 58) tested, with a geometric mean IC50 titer of 0.36 µg/mL. The cryo-EM structure of 44m Fab in complex with fully cleaved glycosylated native-like BG505.SOSIP.664.T332N gp140 envelope trimer at 4.4 Å resolution revealed that 44m targets the V3-glycan N332-supersite and GDIR motif to neutralize HIV-1 with improved potency and breadth, plausibly attributed by a matured heavy chain as compared to that of wild-type AIIMS-P01. This study further improves our understanding on pediatric HIV-1 bnAbs and structural basis of broad HIV-1 neutralization by 44m may be useful blueprint for vaccine design in future.

Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response.

Understanding the molecular features of neutralizing epitopes is important for developing vaccines/therapeutics against emerging SARS-CoV-2 variants. We describe three monoclonal antibodies (mAbs) generated from COVID-19 recovered individuals during the first wave of the pandemic in India. These mAbs had publicly shared near germline gene usage and potently neutralized Alpha and Delta, poorly neutralized Beta, and failed to neutralize Omicron BA.1 SARS-CoV-2 variants. Structural analysis of these mAbs in complex with trimeric spike protein showed that all three mAbs bivalently bind spike with two mAbs targeting class 1 and one targeting a class 4 receptor binding domain epitope. The immunogenetic makeup, structure, and function of these mAbs revealed specific molecular interactions associated with the potent multi-variant binding/neutralization efficacy. This knowledge shows how mutational combinations can affect the binding or neutralization of an antibody, which in turn relates to the efficacy of immune responses to emerging SARS-CoV-2 escape variants.

Prediction of human protein interactome of dengue virus non-structural protein 5 (NS5) and its downstream immunological implications.

The non-structural protein 5 (NS5) is the most conserved protein among flaviviruses, a family that includes the dengue virus. It functions both as an RNA-dependent RNA polymerase and an RNA-methyltransferase and is therefore essential for the replication of viral RNA. The discovery that dengue virus NS5 protein (DENV-NS5) can also localize to the nucleus has resulted in renewed interest in its potential roles at the host-virus interface. In this study, we have used two complementary computational approaches in parallel - one based on linear motifs (ELM) and another based on tertiary structure of the protein (DALI) - to predict the host proteins that DENV-NS5 might interact with. Of the 42 human proteins predicted by both these methods, 34 are novel. Pathway analysis of these 42 human proteins shows that they are involved in key host cellular processes related to cell cycle regulation, proliferation, protein degradation, apoptosis, and immune responses. A focused analysis of transcription factors that directly interact with the predicted DENV-NS5 interacting proteins was performed, followed by the identification of downstream genes that are differentially expressed after dengue infection using previously published RNA-seq data. Our study provides unique insights into the DENV-NS5 interaction network and delineates mechanisms whereby DENV-NS5 could impact the host-virus interface. The novel interactors identified in this study could be potentially targeted by NS5 to modulate the host cellular environment in general, and the immune response in particular, thereby extending the role of DENV-NS5 beyond its known enzymatic functions. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03569-0.

Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response.

A detailed understanding of the molecular features of the neutralizing epitopes developed by viral escape mutants is important for predicting and developing vaccines or therapeutic antibodies against continuously emerging SARS-CoV-2 variants. Here, we report three human monoclonal antibodies (mAbs) generated from COVID-19 recovered individuals during first wave of pandemic in India. These mAbs had publicly shared near germline gene usage and potently neutralized Alpha and Delta, but poorly neutralized Beta and completely failed to neutralize Omicron BA.1 SARS-CoV-2 variants. Structural analysis of these three mAbs in complex with trimeric spike protein showed that all three mAbs are involved in bivalent spike binding with two mAbs targeting class-1 and one targeting class-4 Receptor Binding Domain (RBD) epitope. Comparison of immunogenetic makeup, structure, and function of these three mAbs with our recently reported class-3 RBD binding mAb that potently neutralized all SARS-CoV-2 variants revealed precise antibody footprint, specific molecular interactions associated with the most potent multi-variant binding / neutralization efficacy. This knowledge has timely significance for understanding how a combination of certain mutations affect the binding or neutralization of an antibody and thus have implications for predicting structural features of emerging SARS-CoV-2 escape variants and to develop vaccines or therapeutic antibodies against these.

Structural insights for neutralization of Omicron variants BA.1, BA.2, BA.4, and BA.5 by a broadly neutralizing SARS-CoV-2 antibody.

In this study, by characterizing several human monoclonal antibodies (mAbs) isolated from single B cells of the COVID-19-recovered individuals in India who experienced ancestral Wuhan strain (WA.1) of SARS-CoV-2 during early stages of the pandemic, we found a receptor binding domain (RBD)-specific mAb 002-S21F2 that has rare gene usage and potently neutralized live viral isolates of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron sublineages (BA.1, BA.2, BA.2.12.1, BA.4, and BA.5) with IC50 ranging from 0.02 to 0.13 µg/ml. Structural studies of 002-S21F2 in complex with spike trimers of Omicron and WA.1 showed that it targets a conformationally conserved epitope on the outer face of RBD (class 3 surface) outside the ACE2-binding motif, thereby providing a mechanistic insights for its broad neutralization activity. The discovery of 002-S21F2 and the broadly neutralizing epitope it targets have timely implications for developing a broad range of therapeutic and vaccine interventions against SARS-CoV-2 variants including Omicron sublineages.

Contrasting behavior between the three human monocyte subsets in dengue pathophysiology.

Monocytes are known to play a critical role in dengue pathophysiology. However, which monocyte subset expresses what inflammatory mediator(s) and what transcriptional features distinguish each of the monocyte subset in vivo remain poorly understood. In this study we provide a detailed transcriptional analysis of the three human monocyte subsets in healthy children and in children with dengue febrile illness. Notably, we found that the CD14+ CD16high intermediate monocyte subset from dengue patients highly upregulated key genes involved in mediating inflammation, endothelial dysfunction, vascular permeability, tissue extravasation, and clot prevention compared to healthy children. The CD14+CD16low classical monocytes shared some of these features. These two subsets increased massively in patients with severe dengue. By contrast, the CD14-CD16high nonclassical monocyte subset upregulated key genes involved in vasoconstriction, endothelial barrier stability, and are involved in endothelial patrolling while showing a significant decline from circulation. These findings improve our understanding of monocyte responses in dengue.

An epidemiological study and trend analysis of laboratory confirmed COVID-19 cases among children in North India.

Background: The role of children in transmitting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is difficult to ascertain and the consequences remain unclear. This is necessary for public health or infection control purposes. The objective of this study was to describe the epidemiological, month-wise trends and clinical characteristics of coronavirus disease 2019 (COVID-19) infection among children in a tertiary care hospital. Materials and Methods: A cross-sectional study was performed on all pediatric samples of suspected cases of SARS-CoV-2 infection. The samples were received from the adjoining districts and our Institution in the Department of Microbiology from June to November 2020. Cases were then confirmed by real-time reverse transcriptase-polymerase chain reaction. Results: Of the total 62,030 pediatric samples tested, 847 (1.3%) were SARS-CoV-2 positive. The majority of positive cases were between the ages of 11-15 years. The median age of confirmed patients was 14 years. The male to female ratio was 1.5:1. Infants represented 1.6% of the positive cases. About 62.1% of all positive cases were asymptomatic. Childhood cases increased from June 2020 and peaked in September 2020 before declining. Conclusion: Children of all ages appeared susceptible to COVID-19 and accounted for a very small proportion of confirmed cases. Mostly, children were found to be asymptomatic. Young children can be important transmitters of SARS-CoV-2 infection in the general population. This population can be important for targeting immunization efforts throughout a rapidly evolving situation. Our findings provide further evidence of the distribution of infection in children and the transmission of SARS-CoV-2.

Assessment of knowledge and their practices regarding malaria among members of Village Health Sanitation Committee in rural Uttar Pradesh: A cross-sectional study.

Background: In 2019, the global number of malaria cases was estimated at 229 million. An estimated 409,000 deaths were attributed to malaria in 2019. Under-five children are the most susceptible to malaria, accounting for 67% (274,000) of all malaria deaths worldwide in 2019. This study aimed to assess knowledge and practices regarding malaria among Village Health Sanitation Committee (VHSC) members in rural Uttar Pradesh. Methodology: This cross-sectional study was conducted in the villages of four districts of Uttar Pradesh with high malaria burden. In the present study, 484 participants were interviewed from four districts of Uttar Pradesh. Results: Nearly all the participants (97.1%) have heard about malaria. Majority of the participants (97.1) were aware that mosquito bites spread malaria. However, many participants were also having a false awareness that malaria is spread by other modes like drinking contaminated water, touching each other, eating contaminated food, and so on. More than half of the participants told that mosquitoes are responsible for malaria breeds in stagnant clean water (25.6%) and stagnant dirty water (28.5%). Nearly half of them were aware that mosquitoes' biting time was sunset (42.1%) and sunrise (7.8%). Conclusion: In the present study, many participants were having a false awareness that malaria is spread by other modes like drinking contaminated water, touching each other, eating contaminated food, and so on. Even the knowledge regarding any government program for the prevention and control of malaria of the mosquitoes was very weak. There is an urgent requirement of increasing knowledge among the VHSC members to reduce the malaria burden in the country.

ACE2 protein expression in lung tissues of severe COVID-19 infection.

Angiotensin-converting enzyme 2 (ACE2) is a key host protein by which severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) enters and multiplies within cells. The level of ACE2 expression in the lung is hypothesised to correlate with an increased risk of severe infection and complications in COrona VIrus Disease 2019 (COVID-19). To test this hypothesis, we compared the protein expression status of ACE2 by immunohistochemistry (IHC) in post-mortem lung samples of patients who died of severe COVID-19 and lung samples obtained from non-COVID-19 patients for other indications. IHC for CD61 and CD163 was performed for the assessment of platelet-rich microthrombi and macrophages, respectively. IHC for SARS-CoV-2 viral antigen was also performed. In a total of 55, 44 COVID-19 post-mortem lung samples were tested for ACE2, 36 for CD163, and 26 for CD61, compared to 15 non-covid 19 control lung sections. Quantification of immunostaining, random sampling, and correlation analysis were used to substantiate the morphologic findings. Our results show that ACE2 protein expression was significantly higher in COVID-19 post-mortem lung tissues than in controls, regardless of sample size. Histomorphology in COVID-19 lungs showed diffuse alveolar damage (DAD), acute bronchopneumonia, and acute lung injury with SARS-CoV-2 viral protein detected in a subset of cases. ACE2 expression levels were positively correlated with increased expression levels of CD61 and CD163. In conclusion, our results show significantly higher ACE2 protein expression in severe COVID-19 disease, correlating with increased macrophage infiltration and microthrombi, suggesting a pathobiological role in disease severity.

Are the labour rooms of primary healthcare facilities capable of providing basic delivery and newborn services? A cross-sectional study.

OBJECTIVES: The study aimed to assess the functionality of labour rooms by evaluating the labour room infrastructure with reference to the standard guidelines, the status of the availability of human resources, the availability of essential equipment and consumables in the labour room and by documenting the knowledge of the healthcare provider in terms of labour room practices. The study also explored the facility parameters associated with its delivery load taking the facility as a unit of analysis. DESIGN: A cross-sectional analytical study. SETTING: India has realised the importance of improving the quality of care in public health facilities, and steps are being taken to make healthcare more responsive to women's needs. With an increase in the proportion of institutional deliveries in India, the outcome of the delivery process can be improved by optimising the health facility components. PARTICIPANTS: The study was conducted in 52 health facilities and healthcare providers involved in the delivery process in the selected facilities. RESULTS: The infrastructure of the facilities was found to be the best for medical college followed by district hospitals, Community Health Centres (CHCs), Primary Health Centres (PHCs) and subcentres. Similar findings were observed in terms of the availability of equipment and consumables. Lack of healthcare providers was observed as only 20% of the posts for health personnel were fulfilled in CHCs followed by PHCs, subcentres and district hospitals where 43, 50 and 79% of the available vacancies were fulfilled. The level of knowledge of healthcare providers in terms of partograph, active management of the third stage of labour and post-partum haemorrhage ranged as per their designation. The specialists were the most knowledgeable while the Auxiliary Nurse Midwife (AMNs) were the least. All the components of structural capacity, i.e. infrastructure (r 2 = 0.377, P value < 0.001), equipment and consumable (r 2 = 0.606, P value < 0.001) and knowledge of healthcare providers (r 2 = 0.456, P value < 0.001) along with the overall facility score were positively correlated with the average delivery load of the health facility. The results from multivariate linear regression depict significant relation between the delivery load and availability of equipment and consumables (t = 4.015, P < 0.01) and with the knowledge of healthcare providers (t = 2.129, P = 0.039). CONCLUSIONS: The higher facilities were better equipped to provide delivery and newborn care. A higher delivery load was found at high-level facilities which can be attributed to better infrastructure, adequate supply of equipment and consumables and availability of trained human resources.

Pregnancy outcomes and vertical transmission capability of SARS-CoV-2 infection among asymptomatic females: A cross-sectional study in a tertiary care rural hospital.

BACKGROUND: The COVID-19 pandemic is still spreading throughout the world along with its strange and frightening mutations, and the World Health Organization (WHO) has declared it as a global pandemic. OBJECTIVE: The present investigation aims to evaluate the effect of SARS-CoV-2 infection on mother and newborn outcomes and the vertical transmission potential of this virus. STUDY DESIGN: This was a cross-sectional study conducted at a tertiary care dedicated COVID-19 hospital. A total of 40 pregnant females (RT-PCR positive for SARS-CoV-2) and their 41 neonates (including stillbirths and a twin delivery) were included in the present study. RESULTS: All the mothers in the study were SARS-CoV-2 positive on the RT-PCR test, but none had any COVID-19 symptoms (pneumonia-like fever, cough, fatigue, sore throat, shortness of breath, and diarrhea). Out of 41 newborns, 38 (92.7%) were healthy, one (2.4%) was a stillbirth, and two newborns (4.9%) could not be revived. All the 41 (100.0%) neonates, including stillborn and preterm were negative for the SARS-CoV-2 RT-PCR test. Twenty-Six neonates (63.4%) were delivered by caesarean section, whereas 15 cases (36.6%) had a normal vaginal delivery. CONCLUSION: The present study showed no suggestion of vertical transmission of SARS-CoV-2 in pregnant females. Therefore, the placenta might function as a barrier to the SARS-CoV-2 virus. Also, there were no complications come upon during the delivery of any neonate in the present study.