The Sela macaque (Macaca selai) is a distinct phylogenetic species that evolved from the Arunachal macaque following allopatric speciation.

Arunachal macaque (M. munzala) is an endangered and recently discovered cercopithecine primate from Western Arunachal Pradesh, India. On genetic analyses of Arunachal macaques, we observed spatially distributed substantial inter-species genetic divergence among the samples collected from Arunachal Pradesh. The results suggested that Arunachal macaque evolved into two phylogenetic species about 1.96 mya following allopatric speciation by means of Sela mountain pass in Arunachal Pradesh, India. We describe - Sela macaque (M. selai) as a new macaque species that interestingly exhibited high intra-specific genetic variation and also harbors at least two conservation units. Further, we report the past demographic trajectories and quantify genetic variation required for taxonomic clarification. The present study also identifies gap areas for undertaking surveys to document the relic and unknown trans-boundary populations of macaques through multinational, multi-lateral cross border collaboration.

National sero-surveillance to monitor the trend of SARS-CoV-2 infection transmission in India: Protocol for community-based surveillance.

Conducting population-based serosurveillance for severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) will estimate and monitor the trend of infection in the adult general population, determine the socio-demographic risk factors and delineate the geographical spread of the infection. For this purpose, a serial cross-sectional survey would be conducted with a sample size of 24,000 distributed equally across four strata of districts categorized on the basis of the incidence of reported cases of COVID-19. Sixty districts will be included in the survey. Simultaneously, the survey will be done in 10 high-burden hotspot cities. ELISA-based antibody tests would be used. Data collection will be done using a mobile-based application. Prevalence from the group of districts in each of the four strata will be pooled to estimate the population prevalence of COVID-19 infection, and similarly for the hotspot cities, after adjusting for demographic characteristics and antibody test performance. The total number of reported cases in the districts and hotspot cities will be adjusted using this seroprevalence to estimate the expected number of infected individuals in the area. Such serosurveys repeated at regular intervals can also guide containment measures in respective areas. State-specific context of disease burden, priorities and resources should guide the use of multifarious surveillance options for the current COVID-19 epidemic.

Outbreak Investigation of Nipah Virus Disease in Kerala, India, 2018.

BACKGROUND: Nipah Virus (NiV) is a highly fatal emerging zoonotic virus and a potential threat to global health security. Here we describe the characteristics of the NiV outbreak that occurred in Kerala, India, during May-June 2018. METHODS: We used real-time reverse transcription polymerase chain reaction analysis of throat swab, blood, urine, and cerebrospinal fluid specimens to detect NiV. Further, the viral genome was sequenced and subjected to phylogenetic analysis. We conducted an epidemiologic investigation to describe the outbreak and elucidate the dynamics of NiV transmission. RESULTS: During 2-29 May 2018, 23 cases were identified, including the index case; 18 were laboratory confirmed. The lineage of the NiV responsible for this outbreak was closer to the Bangladesh lineage. The median age of cases was 45 years; the sex of 15 (65%) was male. The median incubation period was 9.5 days (range, 6-14 days). Of the 23 cases, 20 (87%) had respiratory symptoms. The case-fatality rate was 91%; 2 cases survived. Risk factors for infection included close proximity (ie, touching, feeding, or nursing a NiV-infected person), enabling exposure to droplet infection. The public health response included isolation of cases, contact tracing, and enforcement of hospital infection control practices. CONCLUSION: This is the first recorded NiV outbreak in South India. Early laboratory confirmation and an immediate public health response contained the outbreak.

Emerging/re-emerging viral diseases & new viruses on the Indian horizon.

Infectious diseases remain as the major causes of human and animal morbidity and mortality leading to significant healthcare expenditure in India. The country has experienced the outbreaks and epidemics of many infectious diseases. However, enormous successes have been obtained against the control of major epidemic diseases, such as malaria, plague, leprosy and cholera, in the past. The country's vast terrains of extreme geo-climatic differences and uneven population distribution present unique patterns of distribution of viral diseases. Dynamic interplays of biological, socio-cultural and ecological factors, together with novel aspects of human-animal interphase, pose additional challenges with respect to the emergence of infectious diseases. The important challenges faced in the control and prevention of emerging and re-emerging infectious diseases range from understanding the impact of factors that are necessary for the emergence, to development of strengthened surveillance systems that can mitigate human suffering and death. In this article, the major emerging and re-emerging viral infections of public health importance have been reviewed that have already been included in the Integrated Disease Surveillance Programme.

Identifying the tick Amblyomma javanense (Acari: Ixodidae) from Chinese pangolin: generating species barcode, phylogenetic status and its implication in wildlife forensics.

Zoonotic diseases transmitted through ticks and other ectoparasites often travel across the globe with illegally traded wildlife parts and products. In this study, we analyzed a confiscated case of pangolin scales and observed a few dead ticks attached. On genetic analysis, the pangolin scales were identified to be originated from Chinese pangolin (Manis pentadactyla), an IUCN listed Critically Endangered species, and ticks were identified as Amblyomma javanense. Here, we provide the first authentic physical record of A. javanense from India as a parasite of Chinese pangolin and also generated its species DNA barcode that may be useful for biologists working on ticks in species validation and constructing phylogenies across the globe.

WHO-Point Prevalence Survey of Antibiotic Use Among Inpatients at a Core National Antimicrobial Consumption Network Site in North India: Findings and Implications.

Data on Point Prevalence Surveys (PPSs) in India are limited yet. We report findings of a PPS conducted in a core "National Antimicrobial Consumption Network site" under National Centre for Disease Control - WHO project "Point prevalence survey of antimicrobial consumption at healthcare facilities." A cross-sectional survey was conducted as per the "WHO methodology for PPS on antibiotic use in hospitals" in a tertiary care hospital in India in December 2021. Data were collected using predesigned and pretested questionnaire in separate hospital, ward, and patient forms. Eight hundred two inpatients (excluding ICUs) were covered out of whom 299 (37.3%) were on antibiotics with 11.7% receiving 3 or more antibiotics. Surgical prophylaxis (SP) (42.5%) and community acquired infections (32.8%) were the most common indications for antibiotic use. Of the patients, 92.5% received SP for more than 24 hrs. Most commonly prescribed antibiotics were penicillins with beta-lactamase inhibitors (22.3%). Of the total antibiotic prescriptions, 81.5% were from WHO essential medicines list and 12% from "not recommended" WHO AWaRe classification. Of the antibiotic prescriptions, 84.6% were parenteral. Few prescriptions complied with standard treatment guidelines (1.9%), documented indication for antibiotic use (11.6%), and stop/review date (4.4%) in notes. Double anaerobic cover accounted for 6.8% of the total prescriptions. Some identified areas for improvement were: formulation of hospital antibiotic guidelines, promoting culture of sending cultures, improvement in surgical antibiotic prophylaxis, decreasing use of antibiotic combinations and double anaerobic cover, fostering IV to oral switch of antibiotics, and ensuring effective communication among health care workers by documenting adequate information in medical notes.

Utility of smear examination, culture, and serological tests in the diagnosis of visceral leishmaniasis/post-kala-azar dermal leishmaniasis at National Centre for Disease Control, Delhi.

Introduction: A range of assays have been developed to detect specific antileishmanial antibody, such as rK 39 immunochromatographic test (ICT), KE 16 ICT, ELISA test, and indirect immunofluorescent antibody test (IFAT), which play a crucial role in serological diagnosis of visceral leishmaniasis (VL). However, limited published reports are available on the utility of serological test (IFAT test/rk 39), smear examination, and culture in the diagnosis of VL and post-kala-azar dermal leishmaniasis (PKDL) in our country. Materials and Methods: We present utility of serological test (IFAT test/rK 39), smear examination for Leishmania donovani (LD) bodies, and culture in 2589 samples from 2294 VL/PKDL suspected patients (January 2009-December 2019) tested in Centre for Arboviral and Zoonotic diseases, National Centre for Disease Control, New Delhi, India, for laboratory diagnosis of VL/PKDL. Results: A total of 80/553 (14.4%) cases were confirmed of VL (74/522 cases by demonstration of LD bodies in bone marrow smear examination, 5/12 in splenic smear examination 1/19 by culture) and 4/21 (19.0%) cases were confirmed of PKDL (demonstration of LD bodies in slit skin smear examination. In our study 197/1368 (14.4%) cases were diagnosed positive by IFAT, 34/646 (5.2%) cases by rk 39 ICT for VL/PKDL by demonstration of specific antileishmanial antibodies. Conclusion: As the goal of elimination of VL as a public health problem is approaching, apart from serological tests such as rk 39 and IFAT, direct methods of detection such as (parasitic demonstration in BM smear, culture, and molecular tests) for Leishmania may play a crucial role for achieving a correct diagnosis and treatment. We also concluded that IFAT though not field-friendly, its optimal use as an adjunct test with BM smear in all stages of infections may be required. Further rk39 is a simple, reliable, noninvasive, and field-friendly test for diagnosis VL, especially in endemic areas.

Rabies can be a disease of puppyhood.

This brief report documents an interesting and a rare case of 10 week old male puppy who suddenly showed a change in his behavior (irritable, agitated, anorexic, and refusing feeds), bitten six humans, and was laboratory-confirmed as died due to rabies (Rapid antigen test and reverse transcriptase polymerase chain reaction positive for rabies at the National Rabies Reference Laboratory, WHO collaborating Centre for Rabies Epidemiology, Centre for Arboviral and Zoonotic Diseases, National Centre for Disease Control, Delhi). All animal bite victims were timely provided postexposure prophylaxis for rabies who had shown sufficient seroconversion by IgG antirabies antibody using enzyme linked immunoassay (ELISA) and have been reported healthy. This case report reinforces the role of veterinarians/primary care physicians for strong suspicion of rabies encephalitis in puppies with behavioral or neurologic abnormalities and timely/appropriate rabies immunization of the animal bite victims. Shreds of evidence also focus that rabies in puppies younger than 3 months of age is grave and the risk of human beings contracting rabies from young puppies is of public health importance because of fatal consequences. Continuing medical education for primary care physicians and veterinarians, and outreach community public awareness campaigns should be regularly done to promote knowledge of pre-exposure/post-exposure prophylaxis, preventive measures, and animal bite management.

Intravitam Diagnosis of Rabies in Patients with Acute Encephalitis: A Study of Two Cases.

Rabies is one of the oldest known zoonotic diseases. Rhabdovirus, an RNA virus belonging to the genus Lyssavirus and family Rhabdoviridae, causes rabies. Rabies diagnosis is challenging as the rabies virus remains confined to neurons after the initial animal bite. It largely remains immune-evasive until the infection reaches the central nervous system. The bottleneck in rabies diagnosis remains the non-availability of technical expertise and failure to collect an appropriate sample. The laboratory confirmation of rabies in both antemortem and postmortem samples is important. The samples were tested for anti-rabies antibodies using quantitative ELISA. In this report, two case studies are presented to demonstrate the suitability of ELISA for the intra vitam diagnosis of rabies using cerebrospinal fluid (CSF) as a diagnostic sample. The interpretation of serology results for both vaccinated and unvaccinated individuals has been discussed in detail, which has helped to confirm the antemortem diagnosis of rabies. In this report, we observed that ELISA can be a viable alternative for anti-rabies antibody detection in CSF and can be used as a viable alternative to more technically challenging tests, such as Rapid Fluorescent Focus Inhibition Test (RFFFIT) and Immunofluorescence Assays (IFA).

Rabies Outbreak in the Urban Area of Delhi: An Investigation Report and One Health Perspective for Outbreak Management.

Rabies is a global problem and is endemic in India. Rabies cases occur throughout the year, and the majority of cases are associated with dog bites. We report a rabies outbreak investigation in an urban area of Delhi conducted by our multidisciplinary team, and its role in proactively controlling a rabies outbreak by concerted efforts and timely advice to various stakeholders using a "One Health Approach." A veterinary care NGO from Delhi picked up a suspected rabid stray dog and submitted a brain sample for diagnosis of rabies, as they had received information from a resident of the locality about an unprovoked animal bite incident involving a girl (category III bite) and close contact of two more stray dogs living in the vicinity of the suspected rabid dog. The laboratory diagnosis of rabies in the suspected dog brain sample was confirmed by using Fluorescence Antibody Test (FAT). A multi-expert investigation team with expertise in medicine, microbiology, veterinary sciences, laboratory diagnosis, and public health was constituted to investigate the outbreak. The timely, adequate, and appropriate anti-rabies management initiated for the animal bite victims in this incident could prevent rabies. Proactive involvement of multiple stakeholders and knowledge attributes and practice of local residents could prevent human rabies. As there were no further reports of dog bites from the area, the chain of rabies transmission in that area could be controlled. The presented work is a classical case scenario where concerted efforts of all stakeholders achieved effective control and prevention of rabies by adopting the "One Health approach".

Chronicle down memory lane: India's sixty years of plague experience.

BACKGROUND: This perspective documents the historical aspects of outbreaks of plague of last six decades, establishment of plague surveillance network in India with detailed insights about its activities and recent developments requiring focus on plague surveillance. Human plague was reported in Mulbagal area of Karnataka in 1966-67 only to re-emerge in the country in 1994 in Beed district (Maharashtra) and subsequently in Surat (Gujarat). Later Plague outbreak has been reported in the year 2002 with index case from Village Hatkoti, Shimla District in Himachal Pradesh. The last outbreak reported from India was in 2004 from Village Dangaud, Uttarkashi District in Uttarakhand followed by a period of quiescent since last 17 years. OBJECTIVES: During the last few decades, at least three geographical areas experienced outbreaks of plague after silent period of 28 years. We recapitulate the response mechanism for containing outbreaks during the last three outbreaks of plague held in Maharashtra & Gujarat (1994), Himachal Pradesh (2002) and Uttarakhand (2004). We also document the Plague surveillance network of India and its activities which is a comprehensive surveillance system comprising of rodent, flea, canine and human surveillance whose foundation was started in 1964. The recent developments of last decade in terms of revised Human plague surveillance case definitions, Plague surveillance sites, vector control, novel diagnostics and vaccines in our country are also mentioned. CONCLUSION: The thrust areas in control of plague outbreak are early detection and isolation of cases, timely effective antibiotic treatment, chemoprophylaxis to contacts, strengthening of surveillance system and massive IEC campaign in infected areas. Yersinia pestis (causative agent of Plague) also being an important bioterrorism agent, clinicians need to pay special attention to diagnose and microbiologists must be provided skilled training for laboratory confirmation to this pestilential disease for effective and timely management.

Seroprevalence of anti-SARS-CoV-2 antibodies in Indore, Madhya Pradesh: A community-based cross-sectional study, August 2020.

BACKGROUND: In India, laboratory diagnosis of SARS - CoV-2 infection has been mostly based on real-time reverse transcriptase-polymerase chain reaction (RT-PCR). Studies have shown that Viral titres peak within the first week of symptoms but may decline later hampering RT-PCR-based diagnostic strategies. Exact estimate is difficult under high-risk screening strategy with evidences of having large number of asymptomatic cases. This has prompted a call for adoption of antibody testing as potential source of data. MATERIALS AND METHODS: A cross-sectional study with a sample size of 7000 was conducted for 15 days including all the 85 wards under Indore Municipal Corporation. Stratified Random Sampling was used to collect the samples. Trained teams collected basic sociodemographic information and serum samples which were tested for the presence of specific antibodies to COVID-19 using ICMR-Kavach IgG ELISA kits. The data collected was compiled and analysed using appropriate statistical software. RESULTS: Overall weighted seroprevalence of the study population was found to be 7.75%. The prevalence in males and females was comparable (7.91% vs 7.57%). Highest seropositivity (10.04%) was seen among individuals aged more than 60 years. Total number of infections in the population were estimated to be 2,03,160. Overall Case Infection Ratio was found to be 27.43. CONCLUSION: The current seroprevalence study provides information on proportion of the population exposed, but the correlation between presence and absence of antibodies is not a marker of total or partial immunity. It must also be noted that more than 90 percent of the population is still susceptible for COVID-19 infection. Hence, non-pharmaceutical interventions like respiratory hygiene, physical distancing, hand sanitization, usage of personal protective equipment such as masks and implementation of public health measures need to be continued.

Outbreak of ceftriaxone-resistant Salmonella enterica serotype Typhi-Tiruchirappalli, Tamil Nadu, India, June 2018.

Objectives: In May 2018, a laboratory network for antimicrobial resistance (AMR) surveillance in Tamil Nadu, India, detected a cluster of Salmonella enterica serotype Typhi (S. Typhi) isolates resistant to ceftriaxone. We investigated to describe the epidemiology and identify risk factors for the outbreak. Methods: We conducted unmatched case-control studies. We defined a case as illness (fever with abdominal pain, diarrhea or vomiting) in a person with blood culture-confirmed ceftriaxone-resistant S. Typhi isolated between January 1 and July 4, 2018 in Tiruchirappalli, Tamil Nadu. We interviewed cases using a semi-structured questionnaire to identify common exposures to food, water and places visited. Results: We identified 7 cases (5 men) during March 25-June 8, 2018, median age 23 years (range: 12-42); all were hospitalized, none died. Eating at Restaurant A (odds ratio [OR]=22) and chicken gravy (OR=16) was associated with illness. Of the 10 workers at Restaurant A, stool culture from 8 did not detect S. Typhi; 2 did not consent to provide samples. Five water samples around the restaurant showed low or no residual chlorine content. Conclusions: The investigation highlights the value of AMR surveillance in detecting emerging pathogens and the need for timely investigations, along with strengthening food safety.

Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India.

Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.

A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry.

In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel coronavirus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation are key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to detect the virus using a targeted mass spectrometric approach, which can directly detect the presence of virus from naso-oropharyngeal swabs. Using a multiple reaction monitoring we can detect the presence of two peptides specific to SARS-CoV-2 in a 2.3 min gradient run with 100% specificity and 90.5% sensitivity when compared to RT-PCR. Importantly, we further show that these peptides could be detected even in the patients who have recovered from the symptoms and have tested negative for the virus by RT-PCR highlighting the sensitivity of the technique. This method has the translational potential of in terms of the rapid diagnostics of symptomatic and asymptomatic COVID-19 and can augment current methods available for diagnosis of SARS-CoV-2.

Resolving the trans-boundary dispute of elephant poaching between India and Nepal.

In Kangchenjunga Landscape (KL), which is shared by three countries - Bhutan, India, and Nepal, the wild elephants migrate from east of Jhapa (Nepal), through West Bengal (India) and Sibsoo (Bhutan) to further east in Assam (India). The route Jhapa-WB-Sibsoo-Assam is a known route for elephant movements where maximum causalities have been reported in the past. The present study was undertaken to ascertain the individual identity of a poached elephant in Jhapa, Nepal and ivory which was suspected to be from the same individual elephant confiscated in Siliguri, India. We undertook STR profiling of the confiscated specimens with nine polymorphic STRs. The forensic parameters has established the fact that the two analyzed samples of elephant were not identical and belong to two different individuals. The present study highlights the necessity of transboundary research for elephant conservation and monitoring their movements in Kangchenjunga Landscape and emphasizes the use of forensic genetics in curbing illegal wildlife trade.

Cross-species validation of human specific STR system, SureID® 21G and SureID® 23comp (Health Gene Technologies) in Chimpanzee (Pan Troglodytes).

OBJECTIVES: The human specific commercially available STRs system are often not tested in non human primates for their cross applicability. The aim of this study is to test Cross-species validation of two commercially available human specific STR kits i.e. SureID® 21G and SureID® 23comp (Health Gene Technologies) for their positive application in Chimpanzee (Pan troglodytes). RESULT: In SureID® 21G, 19 loci amplified and while 20 loci amplified in SureID® 23comp. All the amplified loci in both STR kits were found polymorphic and the locus Amelogenin showed differential banding patterns between male and female revealing their known gender. The present study validates the applicability of these human specific STR kits in Chimpanzee that can be used in forensics analysis, paternity testing and population genetic studies.

Understanding the cryptic introgression and mixed ancestry of Red Junglefowl in India.

Red Junglefowls (RJFs), the wild progenitor of modern day chickens (DCs), are believed to be in genetic endangerment due to introgression of domestic genes through opportunistic matings with domestic or feral chickens. Previous studies from India reported rare hybridization of RJFs in the wild. However, RJF population genetic structure, pattern of gene flow and their admixture with DC populations are poorly understood at the landscape level. We conducted this study with a large sample size, covering the predicted natural distribution range of RJFs in India. We documented strong evidence of directional gene flow from DCs to free-ranging wild RJFs, with the Northeastern RJF population exhibiting the most genetic variants in their nuclear and mitochondrial genomes, indicating it to be the ancestral population from which early radiation may have occurred. The results provide evidence that landscape features do not act as a barrier to gene flow and the distribution pattern could not be explored due to physical sharing or exchange of wild birds in the past when forests were continuous across RJF range in India.