Vocal repertoire of Microhyla nilphamariensis from Delhi and comparison with closely related M. ornata populations from the western coast of India and Sri Lanka

Advertisement calls in frogs have evolved to be species-specific signals of recognition and are therefore considered an essential component of integrative taxonomic approaches to identify species and delineate their distribution range. The species rich genus Microhyla is a particularly challenging group for species identification, discovery and conservation management due to the small size, conserved morphology and wide distribution of its members, necessitating the need for a thorough description of their vocalization. In this study, we provide quantitative description of the vocal behaviour of Microhyla nilphamariensis, a widely distributed south Asian species, from Delhi, India, based on call recordings of 18 individuals and assessment of 21 call properties. Based on the properties measured acrossed 360 calls, we find that a typical advertisement call of M. nilphamariensis lasts for 393.5 ±  57.5 ms, has 17 pulses on average and produce pulses at rate of 39 pulses/s. The overall call dominant frequency was found to be 2.8 KHz and the call spectrum consisted of two dominant frequency peaks centered at 1.6 KHz and 3.6 KHz, ranging between 1.5-4.1 KHz. Apart from its typical advertisement call, our study also reveals the presence of three 'rare' call types, previously unreported in this species. We describe variability in call properties and discuss their relation to body size and temperature. We found that overall dominant frequency 1 (spectral property) was found to be correlated with body size, while first pulse period (temporal property) was found to be correlated with temperature. Further, we compare the vocal repertoire of M. nilphamariensis with that of the congener Microhyla ornata from the western coast of India and Sri Lanka and also compare the call properties of these two populations of M. ornata to investigate intra-specific call variation. We find statistically significant differentiation in their acoustic repertoire in both cases. Based on 18 call properties (out of 20), individuals of each locality clearly segregate on PCA factor plane forming separate groups. Discriminant function analysis (DFA) using PCA factors shows 100% classification success with individuals of each locality getting classified to a discrete group. This confirms significant acoustic differentiation between these species as well as between geographically distant conspecifics. The data generated in this study will be useful for comparative bioacoustic analysis of Microhyla species and can be utilized to monitor populations and devise conservation management plan for threatened species in this group.

Source Tracing of Leishmania donovani in Emerging Foci of Visceral Leishmaniasis, Western Nepal

We sequenced Leishmania donovani genomes in blood samples collected in emerging foci of visceral leishmaniasis in western Nepal. We detected lineages very different from the preelimination main parasite population, including a new lineage and a rare one previously reported in eastern Nepal. Our findings underscore the need for genomic surveillance.

The effect of COVID-19 on the mental health of the people in the Indian subcontinent: A scoping review

Indian subcontinent has high mental heath burden and low resources to cope the mental health challenges. Assessment of impact of COVID-19 pandemic on the mental health would help to prioritize the resource allocations. We aimed to assess the impact of COVID-19 on the mental health of people in the Indian subcontinent. Following the PRISMA 2020 guideline, a scoping review was performed by systematically searching the PubMed, Scopus, and Embase databases to identify original studies that assessed mental health conditions during the COVID-19 pandemic in the Indian subcontinent. In this review, a total of 34 studies conducted between 2020 and 2022 were analyzed. The prevalence of anxiety disorders was found to range widely, from 2.5% in North Indian urban slum to 53% in Bangladesh and 21.7% in Pakistan. Similarly, the prevalence of depression varied widely, with rates ranging from 3.5% in North India to 29.8% in Pakistan. The prevalence of stress-related problems ranged from 18.3% in Pakistan to 59.7% in Bangladesh. Factors such as female gender, married status, healthcare workers, and mental illness were identified as important predictors of anxiety and depressive disorders. The impact of COVID-19 pandemic on mental health in Indian subcontinent varies widely based on study population and methods. Therefore, a cautious interpretation is needed while generalizing the study results.

A new species of Atriplex (Amaranthaceae) from the Indian subcontinent

A new subshrubby C4-species from the lowlands and foothills of India, Pakistan and SE Afghanistan, Atriplexpseudotatarica, is described and illustrated. Previously, it was incorrectly identified as A.crassifolia auct. non C.A.Mey. belonging to a distant C3-group of the genus. A phylogenetic analysis based on nrITS and nrETS revealed its position as sister to A.schugnanica (sect. Obionopsis). Both species share aphyllous inflorescence and smooth bract-like cover, but differ in life form, leaves, seed colour, and geographical distribution. We revised native Indian Atriplex species and excluded some of them from the flora of the country. An improved checklist of the native Atriplex species in India with their corrected synonymy and nomenclature is given, and a new diagnostic key is provided.

An Overview of Angiostrongylus cantonensis (Nematoda: Angiostrongylidae), an Emerging Cause of Human Angiostrongylosis on the Indian Subcontinent

Human angiostrongylosis is an emerging zoonosis caused by the larvae of three species of metastrongyloid nematodes of the genus Angiostrongylus, with Angiostrongylus cantonensis (Chen, 1935) being dominant across the world. Its obligatory heteroxenous life cycle includes rats as definitive hosts, mollusks as intermediate hosts, and amphibians and reptiles as paratenic hosts. In humans, the infection manifests as Angiostrongylus eosinophilic meningitis (AEM) or ocular form. Since there is no comprehensive study on the disease in the Indian subcontinent, our study aims at the growing incidence of angiostrongylosis in humans, alongside its clinical course and possible causes. A systematic literature search revealed 28 reports of 45 human cases from 1966 to 2022; eosinophilic meningitis accounted for 33 cases (75.5%), 12 cases were reported as ocular, 1 case was combined, and 1 case was unspecified. The presumed source of infection was reported in 5 cases only. Importantly, 22 AEM patients reported a history of eating raw monitor lizard (Varanus spp.) tissues in the past. As apex predators, monitor lizards accumulate high numbers of L3 responsible for acute illness in humans. For ocular cases, the source was not identified. Most cases were diagnosed based on nematode findings and clinical pathology (primarily eosinophilia in the cerebrospinal fluid). Only two cases were confirmed to be A. cantonensis, one by immunoblot and the other by q-PCR. Cases of angiostrongylosis have been reported in Delhi, Karnataka, Kerala, Maharashtra, Madhya Pradesh, Puducherry, Telangana, and West Bengal. With a population of more than 1.4 billion, India is one of the least studied areas for A. cantonensis. It is likely that many cases remain undetected/unreported. Since most cases have been reported from the state of Kerala, further research may focus on this region. Gastropods, amphibians, and reptiles are commonly consumed in India; however, typical preparation methods involve cooking, which kills the nematode larvae. In addition to studying rodent and mollusk hosts, monitor lizards can be used as effective sentinels. Sequence data are urgently needed to answer the question of the identity of Angiostrongylus-like metastrongylid nematodes isolated from all types of hosts. DNA-based diagnostic methods such as q-PCR and LAMP should be included in clinical diagnosis of suspected cases and in studies of genetic diversity and species identity of nematodes tentatively identified as A. cantonensis.

Antenatal and postnatal factors associated with neonatal death in the Indian subcontinent: a multilevel analysis

OBJECTIVES

This study aimed to identify significant antenatal and postnatal factors associated with neonatal death at 2-7 days and at 2-28 days in the Indian subcontinent. Results from this study may help guide strategies to improve antenatal and postnatal care services and reduce neonatal mortality.

STUDY DESIGN

Nationally representative recent Demographic and Health Survey data sets from five countries, including Bangladesh, India, Pakistan, Maldives and Nepal, were used.

METHODS

Survey-weighted univariate distributions were used for study population characteristics and bivariate distributions, along with the chi-squared test for unadjusted associations. Finally, multilevel logistic regression models were performed to determine the association of antenatal care (ANC) and postnatal care (PNC) factors with neonatal deaths.

RESULTS

Among 200,499 live births, the highest neonatal death rate was observed in Pakistan, followed by Bangladesh, whereas the lowest rate was in Nepal. After adjusting for sociodemographic and maternal control variables, the multilevel analysis showed a significantly lower likelihood of neonatal death at 2-7 days and 2-28 days with ANC visits <12 weeks' gestation, at least four ANC visits during pregnancy, PNC visits within the first week after birth and breastfeeding. Delivery at home by a skilled birth attendant compared to unskilled birth attendant was significantly associated with lower neonatal death at 2-7 days. Multifoetal gestation was significantly associated with higher neonatal death at 2-7 days and at 2-28 days.

CONCLUSIONS

The findings suggest that strengthening ANC and PNC services will improve newborn health in the Indian subcontinent and decrease neonatal mortality.

Kukri snakes Oligodon Fitzinger, 1826 of the Western Palearctic with the resurrection of Contia transcaspica Nikolsky, 1902 (Reptilia, Squamata, Colubridae)

The kukri snakes of the genus Oligodon Fitzinger, 1826 reach the westernmost limits of their distribution in Middle and Southwest Asia (Afghanistan, Iran, and Turkmenistan), and the Palearctic portions of Pakistan. In this article, we review the systematics and distribution of the two species native to this region, Oligodon arnensis (Shaw, 1802) and Oligodon taeniolatus (Jerdon, 1853) based on an integrative approach combining morphological, molecular, and species distribution modeling (SDM) data. Phylogenetic analyses recover O. taeniolatus populations from Iran and Turkmenistan in a clade with the O. arnensis species complex, rendering the former species paraphyletic relative to O. taeniolatus sensu stricto on the Indian subcontinent. To correct this, we resurrect the name Contia transcaspica Nikolsky, 1902 from the synonymy of O. taeniolatus and assign it to populations in Middle-Southwest Asia. So far, Oligodon transcaspicus comb. et stat. nov. is known only from the Köpet-Dag Mountain Range of northeast Iran and southern Turkmenistan, but SDM mapping suggests it may have a wider range. Genetic samples of O. "arnensis" from northern Pakistan are nested in a clade sister to the recently described Oligodon churahensis Mirza, Bhardwaj & Patel, 2021, and are phylogenetically separate from O. arnensis sensu stricto in south India and Sri Lanka. Based on morphological similarity, the Afghanistan and Pakistan populations are assigned to Oligodon russelius (Daudin, 1803) and we synonymize O. churahensis with this species. Our investigation leads us to remove O. taeniolatus from the snake fauna of Afghanistan, Iran, and Turkmenistan, with the consequence that only Oligodon transcaspicus comb. et stat. nov. and O. russelius are present in these countries. Additional studies are needed to resolve the taxonomy of the O. taeniolatus and O. arnensis species complexes on the Indian subcontinent, and an updated key for both groups is provided.

Longitudinal impact of stressful life events on HIV-related risk and psychosocial problems among MSM in Chennai and Mumbai, India

BACKGROUND

Studies show that stressful life events (SLE) (e.g., discrimination, financial problems) can lead to psychosocial problems and exacerbate condomless anal sex (CAS) without protection via pre-exposure prophylaxis (PrEP) among men who have sex with men. However, few studies have examined this relationship among men who have sex with men in India, and none have examined this longitudinally.

METHODS

As a part of an HIV-prevention intervention, 608 MSM from Chennai and Mumbai, India, completed behavioral surveys at baseline, 4, 8, and 12 months. We used longitudinal generalized estimating equations (GEE) modeling to examine the relationship between SLE and its severity and subsequent psychosocial problems, CAS, and history of diagnosed sexually transmitted infection (STI). All models are adjusted for age, sexual identity, intervention arm, human immunodeficiency virus status, and recruitment city.

RESULTS

The number of SLE and their corresponding perceived impact score remained consistent at each time point. In multivariable GEE models, the number of SLE was predictive of CAS, depression, and harmful drinking. Similarly, the ratio of the impact of SLE was predictive of CAS, depression, and diagnosed STI. However, harmful drinking was not predictive in this model.

CONCLUSIONS

These findings provide evidence that can inform future interventions, which can be used to enhance self-acceptance, coping skills, and other forms of resiliency.

Extended blood group phenotyping of donors from the lower and middle Himalayan region of Uttarakhand India: A pilot study

BACKGROUND

The state of Uttarakhand, bordering countries such as Tibet and Nepal, is a multi-ethnic region. Further, erythrocyte alloimmunization may arise from the incompatibility of major and/or minor blood groups between ethnically diverse donors and recipients. We aimed to screen Uttarakhand blood donors (UBDs) for extended phenotyping of their erythrocytes serologically.

METHODS

This prospective cross-sectional analysis involved all UBD samples collected at the blood centre of our tertiary-care hospital. Samples were obtained over 9 months (Mar'22 to Nov'22). Donors who were O-typed, DAT-negative and non-reactive for TTI markers were processed further for serological testing using the column agglutination technique utilizing 21 different monoclonal antisera (Ortho diagnostics Pvt ltd, Mumbai India). The research was financially aided by UCOST, Uttarakhand, Government of India.

RESULTS

Of the 5,407 blood samples collected, the total number of O-typed samples collected was 1622. Of these 1622, 329 (20.2 %) O-typed samples were selected based on our inclusion criteria and hence further phenotyped. Amongst these 329 UBDs, the average age was 32.7 ± 9.32 (18-52) years and the male-to-female ratio was (M: F = 12:1). The prevalence of high- and low-frequency blood antigens in our study was Rh (D 96.6 %, C 84.8 %, c 63.5 %, E 27.9 % and e 92 %), Lewis (Le^a 6.3 %, Le^b 31.9 %), Kidd (Jk^a 87.8 %, Jk^b 63.2 %), Kell (K 1.8 %, k 96.3 %) and Duffy (Fy^a 63.5 %, Fy^b 10.6 %). And in the MNS system we received 21.2 % as M, 10.9 % N, 37 % S and 51.3 % as s respectively. We also identified some very rare minor antigens such as Di^a 1.8 %, In^a 1.8 %, C^w 0.6 % and, 1.2 % Mur positive donors, which are not common in our population, as per the published literature. Moreover, we also identified one Bombay blood phenotype (O_h) in one of our UBD recruits.

CONCLUSION

To sum up, practically with the outcome of this research, we were also able to identify rare phenotypes among the local people and a rare blood donor registry was created. This repository shall also come in use for our multi-transfused patients having different oncological and haematological ailments.

ArVirInd-a database of arboviral antigenic proteins from the Indian subcontinent

Background

Studies on antigenic proteins for arboviruses are important for providing diagnostics and vaccine development. India and its neighboring countries have a huge burden of arboviral diseases. Data mining for country-specific sequences from existing bioinformatics databases is cumbersome and time-consuming. This necessitated the development of a database of antigenic proteins from arboviruses isolated from the countries of the Indian subcontinent.

Methods

Arboviral antigenic protein sequences were obtained from the NCBI and other databases. In silico antigenic characterization was performed (Epitope predictions) and data was incorporated into the database. The front end was designed and developed using HTML, CSS, and PHP. For the backend of the database, we have used MySQL.

Results

A database, named ArVirInd, is created as a repository of information on curated antigenic proteins. This enlists sequences by country and year of outbreak or origin of the viral strain. For each entry, antigenic information is provided along with functional sites, etc. Researchers can search this database by virus/protein name, country, and year of collection (or in combination) as well as peptide search for epitopes. It is available publicly via the Internet at http://www.arvirind.co.in. ArVirInd will be useful in the study of immune informatics, diagnostics, and vaccinology for arboviruses.

New Genus and Two New Species of Semiterrestrial Crabs (Decapoda: Brachyura: Gecarcinucidae) from the Southern Western Ghats, India

One new genus and two new species of semiterrestrial freshwater crabs are described from the Southern Western Ghats mountain range in India: Pavizham gavi gen., sp. nov. and Rajathelphusa brunnea sp. nov. The carapace of Pavizham n. gen. is superficially similar to Baratha and Snaha described from the same region, but it can be distinguished from Baratha in having no visible postorbital cristae, complete sutures between male thoracic sternites 2 and 3, the possession of a triangular male pleon and the elongate terminal segment of the male first gonopod; and from Snaha by the presence of a long flagellum on the exopod of the third maxilliped, a complete suture separating male thoracic sternites 2 and 3, and its triangular male pleon. Rajathelphusa brunnea sp. nov. can easily be distinguished from congeners in possessing a distinctly more slender and elongate male first gonopod.

Insights into the human gut virome by sampling a population from the Indian subcontinent

Gut virome plays an important role in human physiology but remains poorly understood. This study reports an investigation of the human gut DNA-virome of a previously unexplored ethnic population through metagenomics of faecal samples collected from individuals residing in Northern India. Analysis shows that, similar to the populations investigated earlier, majority of the identified virome belongs to bacteriophages and a smaller fraction (<20 %) consists of viruses that infect animals, archaea, protists, multiple domains or plants. However, crAss-like phages, in this population, are dominated by the genera VI, VII and VIII. Interestingly, it also reveals the presence of a virus family, Sphaerolipoviridae, which has not been detected in the human gut earlier. Viral families, Siphoviridae, Myoviridae, Podoviridae, Microviridae, Herelleviridae and Phycodnaviridae are detected in all of the analysed individuals, which supports the existence of a core virome. Lysogeny-associated genes were found in less than 10 % of the assembled genomes and a negative correlation was observed in the richness of bacterial and free-viral species, suggesting that the dominant lifestyle of gut phage is not lysogenic. This is in contrast to some of the earlier studies. Further, several hundred high-quality viral genomes were recovered. Detailed characterization of these genomes would be useful for understanding the biology of these viruses and their significance in human physiology.

Reassessing riverine carbon dioxide emissions from the Indian subcontinent

Anthropogenic perturbations are increasing uncertainties in estimating CO₂ emissions via air-water CO₂ flux (F_CO2) from large rivers of the Indian subcontinent. This study aimed to provide an improved estimate of the total F_CO2 from the subcontinental rivers by combining calculations of the partial pressure of CO₂ (pCO₂) in eight major rivers with new measurements in the Ganges and Godavari. The average pCO₂ in the two newly surveyed rivers, including tributaries, wastewater drains, and impoundments, were 3-6 times greater than the previously reported values. In some highly polluted urban tributaries and middle reaches of the Ganges that drain metropolitan areas, the measured pCO₂ exceeded 20,000 μatm, ~40 times the background levels of the headwaters originating in the carbonate-rich Himalayas. The high pCO₂ above 28,000 μatm in the lower reach of the Godavari was seven times the moderate levels of pCO₂ in the headwaters of the volcanic Deccan Traps, indicating enhanced CO₂ production in soils and anthropogenic sources under favorable conditions for organic matter degradation. Across the northern rivers, pCO₂ exhibited a significant negative relationship with dissolved oxygen, but a positive relationship with inorganic N or P concentrations. The strong influence of water pollution on riverine pCO₂ suggests that CO₂ emissions from hypoxic, eutrophic reaches can greatly exceed phytoplanktonic CO₂ uptake. Spatially resolved pCO₂ data, combined with three gas transfer velocity estimates, provided a higher range of F_CO2 from the subcontinental rivers (100.9-130.2 Tg CO₂ yr^-1) than the previous estimates (7.5-61.2 Tg CO₂ yr^-1). The revised estimates representing 2-5% of the global riverine F_CO2 illustrate the importance of the Indian subcontinental rivers under increasing anthropogenic pressures in constraining global inland waters F_CO2.

Drivers of zoonotic disease risk in the Indian subcontinent: A scoping review

Literature on potential anthropogenic drivers of zoonotic disease risk in the Indian subcontinent is sparse. We conducted a scoping review to identify primary sources, published 2000-2020, to clarify what research exists and on which areas future research should focus. We summarised findings thematically by disease. Of 80 sources included, 78 (98%) were original research articles and two were conference abstracts. Study designs and methods were not always clearly described, but 74 (93%) were quantitative (including one randomised trial), five (6%) were mixed-methods, and one was qualitative. Most sources reported research from India (39%) or Bangladesh (31%), followed by Pakistan (9%), Nepal (9%), Bhutan and Sri Lanka (6% each). Topically, most focused on rabies (18; 23%), Nipah virus (16; 20%) or leptospirosis (11; 14%), while 12 (15%) did not focus on a disease but instead on knowledge in communities. People generally did not seek post-exposure prophylaxis for rabies even when vaccination programmes were available and they understood that rabies was fatal, instead often relying on traditional medicines. Similarly, people did not take precautions to protect themselves from leptospirosis infection, even when they were aware of the link with rice cultivation. Nipah was correlated with presence of bats near human habitation. Official information on diseases, modes of transmission and prevention was lacking, or shared informally between friends, relatives, and neighbours. Behaviour did not correspond to disease knowledge. This review identifies various human behaviours which may drive zoonotic disease risk in the Indian subcontinent. Increasing community knowledge and awareness alone is unlikely to be sufficient to successfully change these behaviours. Further research, using interdisciplinary and participatory methods, would improve understanding of risks and risk perceptions and thus help in co-designing context-specific, relevant interventions.

Transfer of radionuclides from soil to selected tropical plants of Indian Subcontinent: A review

Soil to plant transfer factor (TF) of radionuclides is an important input parameter in dose assessment models. The wide range of TF for each radionuclide reported in the literature for a particular plant type indicates that radionuclide concentration in soil is not the only factor influencing its uptake by the plant. Different soil properties and agricultural practices may influence the TF and these are also a function of the climate. Considering the wide variation in TF data, here we attempt to review the available literature on TF of radionuclides in tropical countries of the Indian subcontinent (India, Bangladesh, and Sri Lanka). TF under equilibrium conditions are not available for all radionuclides, in such cases TF of naturally existing stable analogs elements were compiled. With an emphasis on, transfer of radionuclides from soil to the edible compartment of the plant; the TF data for 21 elements are compiled for 12 plant groups classified as per IAEA, Technical Reports Series No. 472. The article also presents the analysis and discussion of the extent and limitations of the compiled data. The compiled TF may be useful in assessing the food chain transfer of radionuclides when site-specific information is not available.

Mesozoic origin and 'out-of-India' radiation of ricefishes (Adrianichthyidae)

The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, 'into-India' or 'out-of-India'. Phylogenies based on complete mitochondrial genomes and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these two biogeographic scenarios fits better. We found that Oryzias setnai, the only adrianichthyid distributed in and endemic to the Western Ghats, a mountain range running parallel to the western coast of the Indian subcontinent, is sister to all other adrianichthyids from eastern India and Southeast-East Asia. Divergence time estimates and ancestral area reconstructions reveal that this western Indian species diverged in the late Mesozoic during the northward drift of the Indian subcontinent. These findings indicate that adrianichthyids dispersed eastward 'out-of-India' after the collision of the Indian subcontinent with Eurasia, and subsequently diversified in Southeast-East Asia. A review of geographic distributions of 'out-of-India' taxa reveals that they may have largely fuelled or modified the biodiversity of Eurasia.

A review of soil to rice transfer of radionuclides in tropical regions of Indian subcontinent

In radioecological studies, soil to plant transfer factors (TF) is commonly used to estimate the food chain transfer of radionuclides, which is an important parameter to assess ingestion doses to humans. Rice is an important (Oryza sativa L.) staple crop in tropical countries and is the major food crop consumed all over the world. Out of the seven countries (India, Pakistan, Bangladesh, Nepal, Bhutan, and the island nations like Sri Lanka and Maldives) of the Indian subcontinent, Bangladesh, Sri Lanka, and Maldives along with a major region of India fall under tropical climate class according to Köppen climate classification. Because, the soil to rice TF under equilibrium conditions are not available for all radionuclides, TF of naturally existing stable elements, which are analogues of radionuclides were compiled. This review paper presents the collection of the TF data of soil to grain and stems & shoots of rice plant for eighteen elements. Data were generated mainly from different sub climatic regions of the tropical environment of India and Bangladesh. An overview of the compilation, analysis, and discussion of the extent and limitations of the data is presented.

Phenotypic variability of a TREX1 variant in Aicardi-Goutieres type 1 patients from the Indian subcontinent

Aicardi-Goutieres Syndrome (AGS) is a heterogeneous genetic syndrome, manifesting early as encephalopathy and is associated with abnormal neurologic findings, hepatosplenomegaly, elevated liver enzymes, thrombocytopenia and intracranial calcification. The most severe neonatal type, AGS1, is caused by biallelic disease-causing variants in TREX1. In this study, we describe four patients with TREX1-related AGS1 whose phenotype overlaps with intra-uterine infections and neonatal lupus. Exome sequencing identified a previously reported TREX1 variant, c.223dup (NM_016381.5; p. Glu75GlyfsTer82) in all the four patients belonging to the Indian subcontinent. The functional consequence of the disease-causing variant was predicted by using a new combination of bioinformatics softwares. The recurrence of this pathogenic variant indicates a possible founder effect in TREX1 for AGS1 in this population. The phenotypic variability in those with this founder mutation can mimic intrauterine infections and neonatal lupus, thereby leading to misdiagnosis warranting a targeted genetic testing approach to be a part of the diagnostic workup to obtain a definite, early and cost-effective diagnosis in patients from Indian subcontinent with early onset encephalopathy.

Heterogeneity of Cardiovascular Disease Risk Factors Among Asian Immigrants: Insights From the 2010 to 2018 National Health Interview Survey

Background The Asian population is the fastest-growing immigrant population in the United States. Prior studies have examined the Asian immigrant population as a homogenous group. We hypothesized that there will be heterogeneity in cardiovascular disease risk factors among Asian immigrant subgroups (Indian subcontinent, Southeast Asia, Asia) compared with the non-Hispanic White population. Methods and Results A cross-sectional analysis of the 2010 to 2018 National Health Interview Survey was conducted among 508 941 adults who were born in Asian regions or were non-Hispanic White and born in the United States. Generalized linear models with Poisson distribution were fitted to compare the prevalence of self-reported hypertension, overweight/obesity, diabetes mellitus, high cholesterol, physical inactivity, and current smoking among Asian immigrants compared with White adults, adjusting for known confounders. We included 33 973 Asian immigrants from Southeast Asia (45%), Asia (29%), the Indian subcontinent (26%), and 474 968 White adults. Compared with non-Hispanic White adults, Indian subcontinent immigrants had the highest prevalence of overweight/obesity (prevalence ratio, 1.22; 95% CI, 1.19-1.25); Southeast Asian immigrants had the highest prevalence of high cholesterol (prevalence ratio, 1.16; 95% CI, 1.10-1.23); Indian subcontinent (prevalence ratio, 1.69; 95% CI, 1.49-1.93) and Southeast Asian (prevalence ratio, 1.38; 95% CI, 1.26-1.52) immigrants had a higher prevalence of diabetes. All Asian immigrant subgroups were more likely to be physically inactive and less likely to smoke than White adults. Conclusions We observed significant heterogeneity in cardiovascular disease risk factors among Asian immigrants and a varied prevalence of risk factors compared with non-Hispanic White adults. Providers caring for Asian immigrants should provide tailored and culturally informed care to improve the cardiovascular health of this diverse group.

Clinical and biochemical profile of scrub typhus patients at a tertiary care hospital in Northern India

Background

Scrub typhus is a neglected rickettsial disease in India. Every year, we are facing outbreaks of Scrub typhus after Monsoon season. Patients present with a wide clinical spectrum ranging from pyrexia of unknown origin to multiple organ dysfunction. Some of these clinical features overlap with presentation of other tropical infections prevalent in Indian subcontinent, which leads to diagnostic dilemma and delay in diagnosis. Hence, we planned this study to know the demographic, clinical and biochemical profile of scrub typhus patients.

Methods

This was an observational study conducted in department of Medicine, King George's Medical University Lucknow, India a leading tertiary care hospital of Northern India. All scrub typhus patients were evaluated by detailed history, examination and laboratory tests.

Results

We enrolled 52 patients in our study. The mean age of the patients was 35.17 ± 16.90 years with majority (82.7%) of patients from rural background. All the patients had fever with an average duration of 9.6 ± 2 days. Most of the patients developed hepatitis (69.2%) followed by acute encephalitis syndrome (47%), acute kidney injury (23.1%) and acute respiratory failure (19.2%). Eschar was found in 11 patients (21.2%).

Conclusion

Scrub typhus is often misdiagnosed or diagnosed late due to its wide clinical spectrum overlapping with clinical presentation of other commonly prevalent tropical diseases. One should always consider the differential diagnosis of scrub typhus while evaluating a young febrile patient of rural background, with features of single or multiple organ dysfunction and laboratory findings of leucocytosis, thrombocytopenia and elevation of transaminases.

Visceral Leishmaniasis-HIV Coinfection as a Predictor of Increased Leishmania Transmission at the Village Level in Bihar, India

Background

Visceral leishmaniasis (VL) is on the verge of being eliminated as a public health problem in the Indian subcontinent. Although Post-kala-azar dermal leishmaniasis (PKDL) is recognized as an important reservoir of transmission, we hypothesized that VL patients co-infected with Human Immunodeficiency Virus (HIV) may also be important reservoirs of sustained leishmania transmission. We therefore investigated to what extent cases of PKDL or VL-HIV are associated with VL incidence at the village level in Bihar, India.

Methods

VL, VL-HIV, and PKDL case data from six districts within the highly VL-endemic state of Bihar, India were collected through the Kala-Azar Management Information System for the years 2014-2019. Multivariate analysis was done using negative binomial regression controlling for year as a fixed effect and block (subdistrict) as a random effect.

Findings

Presence of VL-HIV+ and PKDL cases were both associated with a more than twofold increase in VL incidence at village level, with Incidence Rate Ratios (IRR) of 2.16 (95% CI 1.81-2.58) and 2.37 (95% CI 2.01-2.81) for VL-HIV+ and PKDL cases respectively. A sensitivity analysis showed the strength of the association to be similar in each of the six included subdistricts.

Conclusions

These findings indicate the importance of VL-HIV+ patients as infectious reservoirs for Leishmania, and suggest that they represent a threat equivalent to PKDL patients towards the VL elimination initiative on the Indian subcontinent, therefore warranting a similar focus.

Spatial Epidemiologic Trends and Hotspots of Leishmaniasis, Sri Lanka, 2001-2018

Leishmaniasis, a neglected tropical disease, is on the decline in South Asia. However, cases of cutaneous leishmaniasis have risen in Sri Lanka since 2001, and the lack of in-depth research on its epidemiologic characteristics hampers control efforts. We analyzed data collected from patients with cutaneous leishmaniasis in Sri Lanka during 2001-2018 to study temporal and geographic trends and identify and monitor disease hotspots. We noted a progression in case rates, including a sharp rise in 2018, showing temporal expansion of disease-prevalent areas and 2 persistent hotspots. The northern hotspot shifted and shrank over time, but the southern hotspot progressively expanded and remained spatially static. In addition, we noted regional incidence differences for age and sex. We provide evidence of temporally progressive and spatially expanding incidence of leishmaniasis in Sri Lanka with distinct geographic patterns and disease hotspots, signaling an urgent need for effective disease control interventions.

A randomized, open-label study to evaluate the efficacy and safety of liposomal amphotericin B (AmBisome) versus miltefosine in patients with post-kala-azar dermal leishmaniasis

BACKGROUND

Treatment of post-kala-azar dermal leishmaniasis cases is of paramount importance for kala-azar elimination; however, limited treatment regimens are available as of now.

AIM

To compare the effectiveness of liposomal amphotericin B vs miltefosine in post-kala-azar dermal leishmaniasis patients.

METHODOLOGY

This was a randomized, open-label, parallel-group study. A total of 100 patients of post kala azar dermal leishmaniasis, aged between 5 and 65 years were recruited, 50 patients in each group A (liposomal amphotericin B) and B (miltefosine). Patients were randomized to receive either liposomal amphotericin B (30 mg/kg), six doses each 5 mg/kg, biweekly for 3 weeks or miltefosine 2.5 mg/kg or 100 mg/day for 12 weeks. All the patients were followed at 3rd, 6th and 12th months after the end of the treatment.

RESULTS

In the liposomal amphotericin B group, two patients were lost to follow-up, whereas four patients were lost to follow-up in the miltefosine group. The initial cure rate by "intention to treat analysis" was 98% and 100% in liposomal amphotericin B and miltefosine group, respectively. The final cure rate by "per protocol analysis" was 74.5% and 86.9% in liposomal amphotericin B and miltefosine, respectively. Twelve patients (25.5%) in the liposomal amphotericin B group and six patients (13%) in the miltefosine group relapsed. None of the patients in either group developed any serious adverse events.

LIMITATIONS

Quantitative polymerase chain reaction was not performed at all the follow-up visits and sample sizes.

CONCLUSION

Efficacy of miltefosine was found to be better than liposomal amphotericin B, hence, the use of miltefosine as first-line therapy for post-kala-azar dermal leishmaniasis needs to be continued. However, liposomal amphotericin B could be considered as one of the treatment options for the elimination of kala-azar from the Indian subcontinent.

Medium term results following heart transplantation for end stage heart failure: A single center experience of 257 patients

OBJECTIVE

End stage heart failure is a lethal disease with a dismal 5 year survival. Heart transplantation has proven to be a highly effective modality of treatment in appropriately selected group of such patients. This is a retrospective analysis of medium term outcomes of heart transplantation in the setting of a private health facility in India. The objective of this study was two fold.

METHODS

The outcome of 257 heart transplants done at a single centre from October 2012 to October 2019 was analyzed. Patients with combined Heart and lung transplants and those whose complete medical records were unavailable were excluded from the study. Survival was tracked at 60 days, 90 days, one year and beyond for a maximum of 7 years. Preoperative patient risk profiles were characterized on the basis of INTERMACS category.

RESULTS

There were 176 male and 81 female patients. The age range was from 8 months to 78 years with a mean of 32.9 years. Survival at 2 months was 87%, at 90 days was 83%, at one year was 81%, 2 years was 75%, at 3 years was 72% and at 5 years and beyond was 62% for the whole series. Strong predictors of 90 day mortality included INTERMACS category (odd's ratio 0.289, p = 0.000) and creatinine more than 1.5 mg/dl (odd's ratio 2.48, p = 0.056). Recipient pulmonary vascular resistance and donor organ ischemic times were not found to be statistically significant factors affecting outcome. Medium term survival was influenced by INTERMACS category (Hazard ratio > 3 for INTERMACS category 1 compared to INTERMACS 4 or 5, p < 0.0001) and creatinine > 1.5 mg/dl (Hazard ratio 2.15, p = 0.003). This effect of creatinine was related to the age of the recipient. Hazard ratio 1.4, p = 0.524 if age <30 and Hazard ratio 4.78, p = 0.006, if age was >50.

CONCLUSION

Satisfactory medium term outcome is possible after heart transplantation even in resource constrained environment of a developing country.

Earthquake Probability Assessment for the Indian Subcontinent Using Deep Learning

Earthquake prediction is a popular topic among earth scientists; however, this task is challenging and exhibits uncertainty therefore, probability assessment is indispensable in the current period. During the last decades, the volume of seismic data has increased exponentially, adding scalability issues to probability assessment models. Several machine learning methods, such as deep learning, have been applied to large-scale images, video, and text processing; however, they have been rarely utilized in earthquake probability assessment. Therefore, the present research leveraged advances in deep learning techniques to generate scalable earthquake probability mapping. To achieve this objective, this research used a convolutional neural network (CNN). Nine indicators, namely, proximity to faults, fault density, lithology with an amplification factor value, slope angle, elevation, magnitude density, epicenter density, distance from the epicenter, and peak ground acceleration (PGA) density, served as inputs. Meanwhile, 0 and 1 were used as outputs corresponding to non-earthquake and earthquake parameters, respectively. The proposed classification model was tested at the country level on datasets gathered to update the probability map for the Indian subcontinent using statistical measures, such as overall accuracy (OA), F1 score, recall, and precision. The OA values of the model based on the training and testing datasets were 96% and 92%, respectively. The proposed model also achieved precision, recall, and F1 score values of 0.88, 0.99, and 0.93, respectively, for the positive (earthquake) class based on the testing dataset. The model predicted two classes and observed very-high (712,375 km²) and high probability (591,240.5 km²) areas consisting of 19.8% and 16.43% of the abovementioned zones, respectively. Results indicated that the proposed model is superior to the traditional methods for earthquake probability assessment in terms of accuracy. Aside from facilitating the prediction of the pixel values for probability assessment, the proposed model can also help urban-planners and disaster managers make appropriate decisions regarding future plans and earthquake management.

Canine Toxocariosis: Its prevalence, incidence and occurrence in the Indian subcontinent

Toxocariosis is an important neglected tropical helminth disease of zoonotic significance for which canids are the definitive hosts. Dogs are also considered the sentinel host for the occurrence of T. canis infections in humans. Therefore, understanding its prevalence in canine population is imperative for any effective disease control in humans. A comprehensive review of literature on the prevalence of T. canis in canids was lacking from the Indian subcontinent which necessitated our efforts to compile available data published on this topic. Data on prevalence, incidence and occurrence of this helminths in canids were presented in this review as tabular format for easy comprehension. Moreover, the data were categorized based on the region where the studies were conducted with an aim to understand the spatial distribution of this parasite in the subcontinent. Factors influencing the regional prevalence/occurrence of T. canis such as type of canids (stray or pet), age, sex, breed, season and the choice of analytical methods were also discussed. In addition, data on the prevalence of T. canis in environmental samples and in zoo canids were also compiled and presented. We anticipate such an exhaustive review of literature available mostly in the journals published from the subcontinent would become a point source of information necessary for prioritizing future surveillance efforts in this region and for making informed policy decision to control this zoonotic helminth infection.

Modeling HIV Transmission from Sexually Active Alcohol-Consuming Men in ART Programs to Seronegative Wives

BACKGROUND

The rollout of antiviral therapy in Low and Middle Income Countries (LMICs) has reduced HIV transmission rates at the potential risk of resistant HIV transmission. We sought to predict the risk of wild type and antiviral resistance transmissions in these settings.

METHODS

A predictive model utilizing viral load, ART adherence, genital ulcer disease, condom use, and sexual event histories was developed to predict risks of HIV transmission to wives of 233 HIV+ men in 4 antiretroviral treatment centers in Maharashtra, India.

RESULTS

ARV Therapy predicted a 5.71-fold reduction in transmissions compared to a model of using condoms alone, with 79.9%, of remaining transmissions resulting in primary ART-resistance.

CONCLUSIONS

ART programs reduce transmission of HIV to susceptible partners at a substantial increased risk for transmission of resistant virus. Enhanced vigilance in monitoring adherence, use of barrier protections, and viral load may reduce risks of resistant HIV transmissions in LMIC settings.

Six years of fruit fly surveys in Bangladesh: a new species, 33 new country records and discovery of the highly invasive Bactrocera carambolae (Diptera, Tephritidae)

We engaged in six years of snap-shot surveys for fruit flies in rural environments and ten protected forest areas of Bangladesh, using traps baited with male lures (cue-lure, methyl eugenol, zingerone). Our work has increased the recorded number of species of Tephritidae in the country from seven to 37. We summarize these surveys and report eight new country occurrence records, and a new species (Zeugodacusmadhupuri Leblanc & Doorenweerd, sp. nov.) is described. The highlight among the new records is the discovery, and significant westward range extension, of Bactroceracarambolae Drew & Hancock, a major fruit pest detected in the Chattogram and Sylhet Divisions. We rectify the previously published erroneous record of Bactrocerabogorensis (Hardy), which was based on a misidentification of Zeugodacusdiaphorus (Hendel). We also report the occurrence in Bangladesh of nine other Tephritidae, the rearing of three primary fruit fly parasitoids from Zeugodacus, and records of non-target attraction to fruit fly lures.

Successful nonsurgical treatment of penile Buschke-Löwenstein tumor with 12 weeks of 5% imiquimod alone

Anogenital warts, also known as condylomata acuminata caused by human papillomavirus constitute the most common sexually transmitted infection. Rarely, the disease may evolve into a huge cauliflower-like growth called giant condyloma acuminatum or Buschke–Löwenstein tumor (BLT). In contrast with normal anogenital warts, BLT displays local invasion, lack of spontaneous resolution, posttreatment recurrence, and potential for malignant transformation. Although radical excision with split-thickness skin grafting is considered its first-line treatment, it is not always feasible. While many other treatments have shown variable success and recurrence rates, topical imiquimod 5%, a popular evidence-based therapy for warts has also been reported as an efficacious treatment for BLT. We present a case of penile BLT where the patient refused surgery but recovered completely with no recurrence at five years following 16 weeks’ therapy with topical 5% imiquimod. Excepting a single reported case, this might be another case where BLT resolved with imiquimod as a standalone therapy. We also present a succinct review of past cases of BLT treated with imiquimod.

Novel Victorivirus from a Pakistani Isolate of Alternaria alternata Lacking a Typical Translational Stop/Restart Sequence Signature

The family Totiviridae currently contains five genera Totivirus, Victorivirus, Leishmavirus, Trichomonasvirus, and Giardiavirus. Members in this family generally have a set of two-open reading frame (ORF) elements in their genome with the 5'-proximal ORF (ORF1) encoding a capsid protein (CP) and the 3'-proximal one (ORF2) for RNA-dependent RNA polymerase (RdRp). How the downstream open reading frames (ORFs) are expressed is genus-specific. All victoriviruses characterized thus far appear to use the stop/restart translation mechanism, allowing for the expression of two separate protein products from bicitronic genome-sized viral mRNA, while the totiviruses use a -1 ribosomal frame-shifting that leads to a fusion product of CP and RdRp. We report the biological and molecular characterization of a novel victorivirus termed Alternaria alternata victorivirus 1 (AalVV1) isolated from Alternaria alternata in Pakistan. The phylogenetic and molecular analyses showed AalVV1 to be distinct from previously reported victoriviruses. AalVV1 appears to have a sequence signature required for the -1 frame-shifting at the ORF1/2 junction region, rather than a stop/restart key mediator. By contrast, SDS-polyacrylamide gel electrophoresis and peptide mass fingerprinting analyses of purified virion preparations suggested the expression of two protein products, not a CP-RdRp fusion product. How these proteins are expressed is discussed in this study. Possible effects of infection by this virus were tested in two fungal species: A. alternata and RNA silencing proficient and deficient strains of Cryphonectria parasitica, a model filamentous fungus. AalVV1 showed symptomless infection in all of these fungal strains, even in the RNA silencing deficient C. parasitica strain.

A novel multilocus sequence typing scheme identifying genetic diversity amongst Leishmania donovani isolates from a genetically homogeneous population in the Indian subcontinent

In the Indian subcontinent, infection with Leishmania donovani can cause fatal visceral leishmaniasis. Genetic variation in L. donovani is believed to occur rapidly from environmental changes and through selective drug pressures, thereby allowing continued disease occurrence in this region. All previous molecular markers that are commonly in use multilocus microsatellite typing and multilocus sequence typing, were monomorphic in L. donovani originating from the Indian subcontinent (with only a few exceptions) and hence are not suitable for this region. An multilocus sequence typing scheme consisting of a new set of seven housekeeping genes was developed in this study, based on recent findings from whole genome sequencing data. This new scheme was used to assess the genetic diversity amongst 22 autochthonous L. donovani isolates from Bangladesh. Nineteen additional isolates of the L. donovani complex (including sequences of L. donovani reference strain BPK282A1) from other countries were included for comparison. By using restriction fragment length polymorphism of the internal transcribed spacer 1 region (ITS1-RFLP) and ITS1 sequencing, all Bangladeshi isolates were confirmed to be L. donovani. Population genetic analyses of 41 isolates using the seven new MLST loci clearly separated L. donovani from Leishmania infantum. With this multilocus sequence typing scheme, seven genotypes were identified amongst Bangladeshi L. donovani isolates, and these isolates were found to be phylogenetically different compared with those from India, Nepal, Iraq and Africa. This novel multilocus sequence typing approach can detect intra- and inter-species variations within the L. donovani complex, but most importantly these molecular markers can be applied to resolve the phylogenetically very homogeneous L. donovani strains from the Indian subcontinent. Four of these markers were found suitable to differentiate strains originating from Bangladesh, with marker A2P being the most discriminative one.

Into Africa via docked India: a fossil climbing perch from the Oligocene of Tibet helps solve the anabantid biogeographical puzzle

The northward drift of the Indian Plate and its collision with Eurasia have profoundly impacted the evolutionary history of the terrestrial organisms, especially the ones along the Indian Ocean rim. Climbing perches (Anabantidae) are primary freshwater fishes showing a disjunct south Asian-African distribution, but with an elusive paleobiogeographic history due to the lack of fossil evidence. Here, based on an updated time-calibrated anabantiform phylogeny integrating a number of relevant fossils, the divergence between Asian and African climbing perches is estimated to have occurred in the middle Eocene (ca. 40 Ma, Ma: million years ago), a time when India had already joined with Eurasia. The key fossil lineage is †Eoanabas, the oldest anabantid known so far, from the upper Oligocene of the Tibetan Plateau. Ancestral range reconstructions suggest a Southeast Asian origin in the early Eocene (ca. 48 Ma) and subsequent dispersals to Tibet and then India for this group. Thereby we propose their westbound dispersal to Africa via the biotic bridge between India and Africa. If so, climbing perch precursors had probably followed the paleobiogeographical route of snakehead fishes, which have a slightly older divergence between African and Asian taxa. As such, our study echoes some recent molecular analyses in rejecting the previously held "Gondwana continental drift vicariance" or late Mesozoic dispersal scenarios for the climbing perches, but provides a unique biogeographical model to highlight the role of the pre-uplift Tibet and the docked India in shaping the disjunct distribution of some air-breathing freshwater fishes around the Indian Ocean.

Rabies on the Indian subcontinent

The Indian subcontinent comprises Afghanistan, Bangladesh, Bhutan, India, Nepal, the Maldives, Myanmar, Pakistan and Sri Lanka. In all of these countries, except the Maldives, rabies is endemic. An estimated 59,000 people die from rabies each year; 45% of these deaths occur on the Indian subcontinent and approximately 33% take place in India. The majority of these deaths are attributable to dog bites, and those most affected are children and the poor. Access to post-exposure prophylaxis is limited and costly, the supply of immunoglobulins and vaccines can be irregular and public awareness of rabies is low. Moreover, the vaccination of domestic dogs is not widely implemented. There is a need for increased laboratory capacity and expertise across the continent, as well as better data, improved surveillance and more user-friendly and economical diagnostic tests. An animal birth control programme has met with mixed success in India. However, a greater focus on mass dog vaccination could eliminate the disease at its source, reducing the large burden of mortality for at-risk communities. In this paper, the authors examine the situation in each of the countries on the Indian subcontinent, discuss current needs, obstacles and progress, and examine future strategies, with the objective of eliminating dog-mediated rabies from the subcontinent by 2030.

Latitudinal Pigmentation Variation Contradicts Ultraviolet Radiation Exposure: A Case Study in Tropical Indian Drosophila melanogaster

The effects of ultraviolet radiation (UV) on the animal body have been reported in many studies, and melanin has emerged as a protective mechanism. In smaller insects such as Drosophila, replicated patterns of geographical variation in pigmentation have been observed on multiple continents. Such patterns are particularly pronounced on the Indian subcontinent where several species show a parallel cline in pigmentation traits. However, the potential role of UV exposure in generating the observed patterns of pigmentation variation has not been addressed. Here, we examine the association between UV intensity and body pigmentation in D. melanogaster natural populations collected along the latitudinal gradient of the Indian subcontinent. A strong negative relationship was observed between UV intensity and body pigmentation. This analysis clearly indicates that, in the sampled populations, pigmentation variation is independent of UV exposure and related selection pressures. Patterns of pigmentation in natural populations from the Indian subcontinent are better predicted by latitude itself and temperature-related climatic variables.

Prevalence and determinants of unprotected sex in intimate partnerships of men who inject drugs: findings from a prospective intervention study

Unprotected sex, common among people who inject drugs, puts them and their partners at risk of sexually transmitted infections including human immunodeficiency virus (HIV). This analysis assesses the changes in sexual risk behavior with regular female partners (RFPs), among married men who inject drugs, before and after implementation of a HIV prevention intervention, and identifies correlates of unprotected sex. People who inject drugs (PWID) were assessed at three points: baseline, preintervention follow-up visit (FV)1, and postintervention FV2. Descriptive analysis was used for reporting changes in sexual behavior over time. Generalized estimating equation assessed the population-averaged change in self-reported unprotected sex with an RFP, attributable to intervention uptake. Multivariable logistic regression determined correlates of self-reported unprotected sex with an RFP at FV2. Findings suggest that the proportion of men reporting any unprotected sex remained high (baseline = 46.0%, FV1 = 43.5%, FV2 = 37.0%). A reduction was observed in unprotected sex after the intervention phase, but this could not be attributed to uptake of the intervention. Higher odds of self-reported unprotected sex with an RFP in the past three months at FV2 were associated with self-reported unprotected sex at baseline, living with family, and being HIV-negative. Married male PWID should receive counseling for safe sex with RFPs, especially those who are HIV-negative and live with their families.

Genomic insights into virulence mechanisms of Leishmania donovani: evidence from an atypical strain

Background

Leishmaniasis is a neglected tropical disease with diverse clinical phenotypes, determined by parasite, host and vector interactions. Despite the advances in molecular biology and the availability of more Leishmania genome references in recent years, the association between parasite species and distinct clinical phenotypes remains poorly understood. We present a genomic comparison of an atypical variant of Leishmania donovani from a South Asian focus, where it mostly causes cutaneous form of leishmaniasis.

Results

Clinical isolates from six cutaneous leishmaniasis patients (CL-SL); 2 of whom were poor responders to antimony (CL-PR), and two visceral leishmaniasis patients (VL-SL) were sequenced on an Illumina MiSeq platform. Chromosome aneuploidy was observed in both groups but was more frequent in CL-SL. 248 genes differed by 2 fold or more in copy number among the two groups. Genes involved in amino acid use (LdBPK_271940) and energy metabolism (LdBPK_271950), predominated the VL-SL group with the same distribution pattern reflected in gene tandem arrays. Genes encoding amastins were present in higher copy numbers in VL-SL and CL-PR as well as being among predicted pseudogenes in CL-SL. Both chromosome and SNP profiles showed CL-SL and VL-SL to form two distinct groups. While expected heterozygosity was much higher in VL-SL, SNP allele frequency patterns did not suggest potential recent recombination breakpoints. The SNP/indel profile obtained using the more recently generated PacBio sequence did not vary markedly from that based on the standard LdBPK282A1 reference. Several genes previously associated with resistance to antimonials were observed in higher copy numbers in the analysis of CL-PR. H-locus amplification was seen in one cutaneous isolate which however did not belong to the CL-PR group.

Conclusions

The data presented suggests that intra species variations at chromosome and gene level are more likely to influence differences in tropism as well as response to treatment, and contributes to greater understanding of parasite molecular mechanisms underpinning these differences. These findings should be substantiated with a larger sample number and expression/functional studies.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5271-z) contains supplementary material, which is available to authorized users.

Late diagnosis of human immunodeficiency virus infections in high-risk groups in Karachi, Pakistan

Human immunodeficiency virus (HIV) infection prevalence in Pakistan has been increasing in high-risk groups, including people who inject drugs (PWID) and transgender hijra sex workers (TG-HSWs) nationwide. Effective control of HIV requires early diagnosis of the infection. We investigated recency of HIV infections in newly-diagnosed cases in PWID and TG-HSWs. This was an observational study with convenience sampling. Overall, 210 HIV-positive subjects comprising an equal number of PWID and TG-HSWs were included. Antibody avidity was tested using the Maxim HIV-1 Limiting Antigen Avidity (LAg) EIA (Maxim Biomedical, Inc. Rockville, Maryland, USA). The mean age of study subjects was 29.5 years: PWID, 28.5 years and TG-HSWs, 30.4 years. Study subjects were married, 27%, or unmarried. Eighteen percent of individuals had recently-acquired HIV infections: 19% of PWID and 17% of TG-HSWs. Eighty-two percent of individuals had long-term HIV infections: 81% of PWID and 83% of TG-HSWs. This is the first study identification of recent HIV-1 infections in Pakistan. We show that most newly-diagnosed HIV patients in the high-risk groups studied had long-term infections. There is an urgent need for intervention in these groups to facilitate early diagnosis and treatment of HIV infection to reduce transmission in Pakistan.

Mutation Spectrum of GNE Myopathy in the Indian Sub-Continent

BACKGROUND

GNE myopathy is an adult onset recessive genetic disorder that affects distal muscles sparing the quadriceps. GNE gene mutations have been identified in GNE myopathy patients all over the world. Homozygosity is a common feature in GNE myopathy patients worldwide.

OBJECTIVES

The major objective of this study was to investigate the mutation spectrum of GNE myopathy in India in relation to the population diversity in the country.

MATERIALS AND METHODS

We have collated GNE mutation data of Indian GNE myopathy patients from published literature and from recently identified patients. We also used data of people of Indian subcontinent from 1000 genomes database, South Asian Genome database and Strand Life Science database to determine frequency of GNE mutations in the general population.

RESULTS

A total of 67 GNE myopathy patients were studied, of whom 21% were homozygous for GNE variants, while the rest were compound heterozygous. Thirty-five different mutations in the GNE gene were recorded, of which 5 have not been reported earlier. The most frequent mutation was p.Val727Met (65%) found mainly in the heterozygous form. Another mutation, p.Ile618Thr was also common (16%) but was found mainly in patients from Rajasthan, while p.Val727Met was more widely distributed. The latter was also seen at a high frequency in general population of Indian subcontinent in all the databases. It was also present in Thailand but was absent in general population elsewhere in the world.

CONCLUSION

p.Val727Met is likely to be a founder mutation of Indian subcontinent.

Foot-and-Mouth Disease in the Middle East Caused by an A/ASIA/G-VII Virus Lineage, 2015-2016

Phylogenetic analyses of foot-and-mouth disease type A viruses in the Middle East during 2015-2016 identified viruses belonging to the A/ASIA/G-VII lineage, which originated in the Indian subcontinent. Changes in a critical antigenic site within capsid viral protein 1 suggest possible evolutionary pressure caused by an intensive vaccination program.

Unsafe injecting practices, sexual risk behaviours and determinants of HIV among men who inject drugs: Results from Integrated Biological and Behavioural Surveillance in India

In India, while an overall reduction in HIV is achieved among most key populations, the continued higher prevalence among people who inject drugs (PWIDs) is an area of concern. This paper analyses unsafe injecting and sexual risk behaviours in male PWIDs according to HIV status and also examines the determinants of HIV infection in this high-risk group. Data from India's Integrated Biological and Behavioural Surveillance, conducted across 29 Indian states and Union Territories among 19,902 male PWIDs, were used. Informed consent was obtained and men aged 15 years or more, who used psychotropic substances or drugs in the past three months for non-medical reasons were recruited for the survey. Results from the multivariable analysis suggest that drug use debut at age 25 years or above (adjusted odds ratio [AOR]: 1.41, confidence interval [CI]: 1.05-1.88), engagement in drug use for a longer duration (AOR: 1.81, CI: 1.32-2.48), injecting three times or more per day (AOR: 1.53, CI: 1.1-2.12), sharing of needle/syringes (AOR: 1.34, CI: 1.02-1.76), self-reported sexually transmitted infections (AOR: 1.55, CI: 1.12-2.14) and higher self-risk perception for exposure to HIV (AOR: 2.08, CI: 1.58-2.75) increase the likelihood of HIV infection. Sustained higher prevalence, unsafe injecting and risky sexual practices are major challenges which may prevent India from reaching the 'end of AIDS' by 2030. This underscores the need for adoption of a tailored, evidence-driven HIV prevention approach that adequately addresses local needs to limit the spread of HIV within this population, and thereby prevents the onward transmission of HIV to the general population.

Leishmaniasis: current challenges and prospects for elimination with special focus on the South Asian region

Leishmania donovani, the most virulent species of Leishmania, is found in the South Asian region that harbours the majority of visceral leishmaniasis (VL) cases in the world. The traditionally accepted relationships between the causative species of Leishmania and the resultant disease phenotype have been challenged during recent years and have underscored the importance of revisiting the previously established taxonomy with revisions to its classification. The weak voice of the afflicted with decades of neglect by scientists and policy makers have led to the miserably inadequate and slow advancements in product development in the fields of diagnostics, chemotherapeutics and vector control that continue to hinder the effective management and control of this infection. Limitations notwithstanding, the regional drive for the elimination of VL initiated over a decade ago that focused on India, Nepal and Bangladesh, the three main afflicted countries in the Indian subcontinent is therefore, commendable, with the subsequent status reviews and restructuring of strategies possibly even more so. However, the renewed efforts would need to be combined with plans to combat new challenges in the South-Asian region that includes the emergence of atypical parasite variants, in order to realistically achieve the set goal of regional elimination of VL.

The Geographic Origins of Ethnic Groups in the Indian Subcontinent: Exploring Ancient Footprints with Y-DNA Haplogroups

Several studies have evaluated the movements of large populations to the Indian subcontinent; however, the ancient geographic origins of smaller ethnic communities are not clear. Although historians have attempted to identify the origins of some ethnic groups, the evidence is typically anecdotal and based upon what others have written before. In this study, recent developments in DNA science were assessed to provide a contemporary perspective by analyzing the Y chromosome haplogroups of some key ethnic groups and tracing their ancient geographical origins from genetic markers on the Y-DNA haplogroup tree. A total of 2,504 Y-DNA haplotypes, representing 50 different ethnic groups in the Indian subcontinent, were analyzed. The results identified 14 different haplogroups with 14 geographic origins for these people. Moreover, every ethnic group had representation in more than one haplogroup, indicating multiple geographic origins for these communities. The results also showed that despite their varied languages and cultural differences, most ethnic groups shared some common ancestors because of admixture in the past. These findings provide new insights into the ancient geographic origins of ethnic groups in the Indian subcontinent. With about 2,000 other ethnic groups and tribes in the region, it is expected that more scientific discoveries will follow, providing insights into how, from where, and when the ancestors of these people arrived in the subcontinent to create so many different communities.

Cryptosporidiosis in children in the Indian subcontinent

Cryptosporidiosis is a leading cause of diarrheal disease among children under two in developing countries. Previous estimates have shown a high burden of cryptosporidial diarrhea in children from Sub-Saharan Africa and South Asia. Asymptomatic cryptosporidial infections which go undetected and untreated have been shown to result in significant malnutrition. In this review, we carried out a literature search of studies published on cryptosporidiosis in children in the Indian subcontinent from 1983 to 2016. Of the 154 publications identified, 54 were included for final analysis with both hospital-based and community-based studies. There were wide variations in reported prevalence rates from hospital studies and highlight the need to be carry out these studies with uniform sampling and molecular tools for detection, especially in countries with a dearth of information. Community-based studies, however, showed similarities in spite of differences in when (the late 1990s up until recently) and where (South India or Bangladesh) they were conducted. When more sensitive detection methods were used, cryptosporidial diarrhea accounted for 7%–9% of all diarrhea episodes and 20%–30% of children in these cohorts experienced at least one cryptosporidial diarrheal episode. High rates of asymptomatic infections with increased detection by serology and multiple infections (symptomatic and asymptomatic) were also documented in all cohorts. This overview brings to light the high burden of disease associated with cryptosporidiosis in children in the subcontinent and the gaps in knowledge to be addressed.

Elimination of visceral leishmaniasis in the Indian subcontinent: a comparison of predictions from three transmission models

We present three transmission models of visceral leishmaniasis (VL) in the Indian subcontinent (ISC) with structural differences regarding the disease stage that provides the main contribution to transmission, including models with a prominent role of asymptomatic infection, and fit them to recent case data from 8 endemic districts in Bihar, India. Following a geographical cross-validation of the models, we compare their predictions for achieving the WHO VL elimination targets with ongoing treatment and vector control strategies. All the transmission models suggest that the WHO elimination target (<1 new VL case per 10,000 capita per year at sub-district level) is likely to be met in Bihar, India, before or close to 2020 in sub-districts with a pre-control incidence of 10 VL cases per 10,000 people per year or less, when current intervention levels (60% coverage of indoor residual spraying (IRS) of insecticide and a delay of 40days from onset of symptoms to treatment (OT)) are maintained, given the accuracy and generalizability of the existing data regarding incidence and IRS coverage. In settings with a pre-control endemicity level of 5/10,000, increasing the effective IRS coverage from 60 to 80% is predicted to lead to elimination of VL 1-3 years earlier (depending on the particular model), and decreasing OT from 40 to 20days to bring elimination forward by approximately 1year. However, in all instances the models suggest that L. donovani transmission will continue after 2020 and thus that surveillance and control measures need to remain in place until the longer-term aim of breaking transmission is achieved.

Highly Pathogenic Reassortant Avian Influenza A(H5N1) Virus Clade 2.3.2.1a in Poultry, Bhutan

Highly pathogenic avian influenza A(H5N1), clade 2.3.2.1a, with an H9-like polymerase basic protein 1 gene, isolated in Bhutan in 2012, replicated faster in vitro than its H5N1 parental genotype and was transmitted more efficiently in a chicken model. These properties likely help limit/eradicate outbreaks, combined with strict control measures.

Insecticide resistance in phlebotomine sandflies in Southeast Asia with emphasis on the Indian subcontinent

BACKGROUND

Visceral leishmaniasis, commonly known as kala-azar in India, is a global public health problem. In Southeast Asia, Bangladesh, Bhutan, India, Nepal, Sri Lanka and Thailand are endemic for visceral leishmaniasis. The role of sandflies as the vector of kala-azar was first confirmed in 1942 in India. Insecticide resistance in Phlebotomus argentipes Annandale and Brunetti, the vector of kala-azar in the Indian subcontinent, was first reported in 1987 in Bihar, India. This article provides a scoping review of the studies undertaken from 1959 to 2015 on insecticide resistance in P. argentipes and P. papatasi (Scopoli), the vectors of visceral and cutaneous leishmaniasis respectively, in Southeast Asia, mainly in Bangladesh, India, Nepal and Sri Lanka.

RESULTS

Studies undertaken in areas of Bihar and West Bengal in India where kala-azar is endemic have reported resistance of P. argentipes to DDT, while in non-endemic areas it has been reported to be susceptible. In areas of Nepal bordering India, there are indications of resistance to DDT; biochemical resistance has been reported in Sri Lanka. No laboratory studies have been undertaken in Bangladesh; however, the sandfly vector is reported to be still susceptible to pyrethroids in all kala-azar endemic areas in the aforementioned countries.

CONCLUSIONS

Studies are needed to determine the resistance of sandfly vectors to all available classes of potential insecticides in kala-azar endemic areas. There is a need to assess the impact of indoor residual spraying with DDT and pyrethroids on the incidence of kala-azar in India where 54 districts remain endemic for the disease, strengthen entomological surveillance capacity, and develop and implement an insecticide management plan. Alpha-cypermethrin indoor residual spraying has been introduced in 33 kala-azar endemic districts in Bihar State of India in a pilot trial; the outcomes should be used to inform decisions on expanding coverage with alpha-cypermethrin in all remaining endemic districts to achieve the revised goal of elimination of visceral leishmaniasis by 2020.

Use of a Macintosh blade in extrahepatic portal vein obstruction with difficult intubation: two case reports

Background

We report the management of two patents from the Indian subcontinent with extrahepatic portal vein obstruction presenting with anticipated difficult airway. A Macintosh blade was used to secure the airway after using various instruments designed for difficult airway. To the best of our knowledge, no case has previously been reported in which a Macintosh blade was used successfully in patients with extrahepatic portal vein obstruction with a difficult airway.

Case presentation

Two women (case 1 and case 2) of South Asian ethnicity with extrahepatic portal vein obstruction presented for an elective splenorenal shunt. They both had micrognathia and restricted mouth openings. They had similar airway profiles with mouth openings of just 2 cm, Mallampati class IV, a thyromental distance <4 cm, a hyomental distance <2.5 cm, and a sternomental distance of 10 cm. Awake intubation was attempted in both patients after standard airway preparation in the form of preoperative 4 % lignocaine nebulization and 2 % viscous lignocaine gargle along with an on-table supralaryngeal nerve block using 2 % lignocaine and transtracheal infiltration with 4 % lignocaine.

The patient in case 1 tolerated the procedure well whereas the patient in case 2 had to be given propofol 60 mg. Endotracheal intubation with a 6.5 mm polyvinyl chloride endotracheal tube was attempted using a Truview EVO2, an Airtraq, and a Miller blade no. 3 but was unsuccessful. Finally, a trial intubation was performed successfully with a Macintosh blade with a stubby handle assisted by a Frova Intubating Introducer in case 1 and a gum elastic bougie in case 2.

Conclusions

Although many instruments have been introduced to manage difficult airways, our experience in these cases suggests that the Macintosh blade can be used first when attempting endotracheal intubation before using other instruments. Patients from the Indian subcontinent with extrahepatic portal vein obstruction are often found to have associated temporomandibular joint ankyloses (hence difficult airways). We hypothesize that a difficult intubation should be anticipated in these patients. Such an association has not been made before.

Nerve abscess in Hansen's disease as part of immune reconstitution inflammatory syndrome: a case report

Immune reconstitution inflammatory syndrome is an inflammatory reaction in HIV-infected patients after initiation of antiretroviral therapy resulting from restored immunity to specific infectious or non-infectious antigens. A 36-year-old male patient on highly active antiretroviral therapy of six months duration, presented with reddish, tender lesions over medial aspect of arm and a single, anaesthetic patch. Tender fluctuant swellings were seen on the medial aspect of left forearm. A few of them had ruptured spontaneously discharging pus. A skin biopsy from the anaesthetic patch showed caseating epitheloid granulomas. A diagnosis of Hansen's disease borderline tuberculoid in type 1 reversal reaction, with formation of nerve abscess due to Immune Reconstitution Inflammatory Syndrome was made. The patient was started on multibacillary multidrug therapy as per WHO guidelines and highly active antiretroviral therapy was continued.