Survey of the present health & nutritional status of Shompen tribe of Great Nicobar Island.

BACKGROUND OBJECTIVES: Shompens are one of the two mongoloid tribes of Nicobar district. There is little information about their recent health status since the last survey which was conducted in 1998. Hence, a comprehensive health and nutritional survey was conducted in March 2017 to assess the changes. The survey was carried out by a joint team of various organizations including the ICMR-Regional Medical Research Centre and Tribal Welfare and Health Department both located in Port Blair. METHODS: A detailed health and nutrition survey of the Shompen community was planned by deputing a field research team. The survey included demographic data, anthropometric data, clinical examination, screening for the markers of infectious diseases, respiratory pathogens, tuberculosis and haemoglobinopathies. RESULTS: About half of the Shompen adults (both males and females) had a body mass index (BMI) of ≥23. However, Shompen children had a good nutritional status with no child suffering from undernutrition. As per BMI for age, none of the children <5 yr were under-nourished, while in the 5-17 yr group, 12 per cent of children were undernourished. Anaemia prevalence was about 48.3 per cent, with 54 per cent prevalence in females and 43.8 per cent in males. Fungal infection of the skin, acute respiratory infection and abdominal pain were the common morbidities observed. None had active pulmonary tuberculosis. Of 38 Shompens screened for IgG (immunoglobulin G) antibodies, 42.1 and 18.4 per cent were positive for measles and rubella, respectively. Seroprevalence of Leptospira was 35.5 per cent. The prevalence of hypertension was 13.2 per cent, whereas another 28.9 per cent were pre-hypertensive. INTERPRETATION CONCLUSIONS: The population structure of the Shompen is not skewed and under nutrition was not widely prevalent among the children of <5 yr. The other positive observations were the absence of malaria, filariasis and dengue. However, there was natural infection of measles and rubella. Fungal skin infection and intestinal parasitic infestations were widely prevalent. Although cardiovascular risk profile was low, there were signs of emerging risk of over-weight, hypertension and dyslipidaemia. These together with the high prevalence of smokeless tobacco use may have a serious effect on the cardiovascular disease susceptibility of the Shompen population in the future.

Expansion of the measles and rubella laboratory network, India.

Objective: To expand the measles and rubella laboratory network of India by integrating new laboratories. Methods: In collaboration with the World Health Organization (WHO), the Indian government developed a 10-step scheme to systematically expand the number of laboratories performing serological and molecular testing for measles and rubella. The Indian Council of Medical Research and WHO identified suitable laboratories based on their geographical location, willingness, preparedness, past performance and adherence to national quality control and quality assurance mechanisms. The 10-step scheme was initiated with training on measles and rubella diagnostic assays followed by testing of both measles and rubella serology and molecular unknown panels, cross-verification with reference laboratories and ended with WHO on-site accreditation. Findings: After extensive training, technical support, funding and monitoring, all six selected laboratories attained passing scores of 90.0% or more in serological and molecular proficiency testing of measles and rubella. Since 2018, the laboratories are a part of the measles and rubella network of India. Within 12 months of initiation of independent reporting, the six laboratories have tested 2287 serum samples and 701 throat or nasopharyngeal swabs or urine samples. Conclusion: The process led to strengthening and expansion of the network. This proficient laboratory network has helped India in scaling up serological and molecular testing of measles and rubella while ensuring high quality testing. The collaborative model developed by the Indian government with WHO can be implemented by other countries for expanding laboratory networks for surveillance of measles and rubella as well as other infectious diseases.

Nipah Virus Outbreak in Kerala State, India Amidst of COVID-19 Pandemic.

We report here a Nipah virus (NiV) outbreak in Kozhikode district of Kerala state, India, which had caused fatal encephalitis in a 12-year-old boy and the outbreak response, which led to the successful containment of the disease and the related investigations. Quantitative real-time reverse transcription (RT)-PCR, ELISA-based antibody detection, and whole genome sequencing (WGS) were performed to confirm the NiV infection. Contacts of the index case were traced and isolated based on risk categorization. Bats from the areas near the epicenter of the outbreak were sampled for throat swabs, rectal swabs, and blood samples for NiV screening by real-time RT-PCR and anti-NiV bat immunoglobulin G (IgG) ELISA. A plaque reduction neutralization test was performed for the detection of neutralizing antibodies. Nipah viral RNA could be detected from blood, bronchial wash, endotracheal (ET) secretion, and cerebrospinal fluid (CSF) and anti-NiV immunoglobulin M (IgM) antibodies from the serum sample of the index case. Rapid establishment of an onsite NiV diagnostic facility and contact tracing helped in quick containment of the outbreak. NiV sequences retrieved from the clinical specimen of the index case formed a sub-cluster with the earlier reported Nipah I genotype sequences from India with more than 95% similarity. Anti-NiV IgG positivity could be detected in 21% of Pteropus medius (P. medius) and 37.73% of Rousettus leschenaultia (R. leschenaultia). Neutralizing antibodies against NiV could be detected in P. medius. Stringent surveillance and awareness campaigns need to be implemented in the area to reduce human-bat interactions and minimize spillover events, which can lead to sporadic outbreaks of NiV.

Characterization of the anopheline vector breeding habitats: Implications for elimination of malaria in tribal inhabited Car Nicobar Island.

Background & objectives: Malaria is an important public health problem in Andaman & Nicobar archipelago. Among the three districts, Nicobar is the most endemic district where API is >2. In this district, the malaria incidence in Car Nicobar Tehsil has declined steadily over the past 10 years. A renewed initiative to consolidate this gain is being made with the ultimate objective of achieving zero indigenous transmission of malaria in Car Nicobar. So, the present study undertook a close environmental monitoring of water bodies for assessing changes in the risk potential of mosquito vector breeding habitats which can augment the elimination programme. Methods: The breeding habitats of anopheline mosquitoes were sampled in 16 areas of Car Nicobar Island for eight time periods during 2017-2020. Along with anophelines, various associated water parameters (n=60) were estimated, viz. physicochemical (n=13), and biological, which included culicine mosquito immatures, insect predators (n=5), phytoplanktons (n=31) and zooplanktons (n=10). Results: In the 16 study sites, overall 1126 surface water stagnating bodies constituting 21 different habitat types were surveyed. Of these, 17 were positive for anopheline breeding. Water bodies from three villages were consistently found to be positive for anopheline breeding. However, early instars of anopheline larvae were more abundant compared to the late instars. Four anopheline species were recorded, including Anopheles sundaicus, A. barbirostris, A. insulaeflorum and A. subpictus, in which 48 per cent were A. sundaicus. Multivariable analysis indicated that anopheline density was significantly higher in permanent water bodies than in temporary habitats (P<0.05) (high risk of anophelines). The highest pH (≥8.2), dissolved solids (≥0.39) levels showed significantly (P<0.05) decreased larval densities (lower risk of breeding), adjusted with breeding sites and season. Nitrite levels increased (P=0.022) larval densities. Interpretation & conclusions: The present study facilitated estimating the productive period of a larval habitat enabling target larval sources to reduce adult populations. Implementing larviciding strategy before monsoon season is presumably the most cost-effective strategy. The output can be utilized for environmental monitoring of mosquito breeding risk in other malaria endemic areas, particularly where medium/large water bodies are the predominant breeding sites for malaria vectors.

Non-communicable diseases as a major contributor to deaths in 12 tribal districts in India.

Background & objectives: Non-communicable diseases (NCDs) are the leading cause of death in India. Although studies have reported a high prevalence of NCD in tribal populations, there are limited data pertaining mortality due to NCDs. Therefore, in this study we estimated the proportion of deaths due to NCDs among 15 yr and older age group in tribal districts in India. Methods: We conducted a community-based survey in 12 districts (one per State) with more than 50 per cent tribal population. Data were collected using a verbal autopsy tool from the family member of the deceased. The estimated sample size was 452 deaths per district. We obtained the list of deaths for the reference period of one year and updated it during the survey. The cause of death was assigned using the International Classification of Diseases-10 classification and analyzed the proportions of causes of death. The age-standardized death rate (ASRD) was also estimated. Results: We surveyed 5292 deaths among those above 15 years of age. Overall, NCDs accounted for 66 per cent of the deaths, followed by infectious diseases (15%) and injuries (11%). Cardiovascular diseases were the leading cause of death in 10 of the 12 sites. In East Garo Hills (18%) and Lunglei (26%), neoplasms were the leading cause of death. ASRD due to NCD ranged from 426 in Kinnaur to 756 per 100,000 in East Garo Hills. Interpretation & conclusions: The findings of this community-based survey suggested that NCDs were the leading cause of death among the tribal populations in India. It is hence suggested that control of NCDs should be one of the public health priorities for tribal districts in India.

Preparedness of primary & secondary care health facilities for the management of non-communicable diseases in tribal population across 12 districts in India.

Background and objectives: Non-communicable diseases (NCDs) are highly prevalent in the tribal populations; however, there are limited data regarding health system preparedness to tackle NCDs among these populations. We estimated the availability of human resources, equipment, drugs, services and knowledge of doctors for NCD management in the selected tribal districts in India. Methods: A cross-sectional survey was conducted in 12 districts (one from each State) with at least 50 per cent tribal population in Andaman and Nicobar Islands, Himachal Pradesh, Madhya Pradesh, Odisha and eight northeastern States. Primary health centres (PHCs), community health centres (CHCs) and district/sub-district hospitals (DHs) were surveyed and data on screening and treatment services, human resources, equipment, drugs and information systems indicators were collected and analysed. The data were presented as proportions. Results: In the present study 177 facilities were surveyed, including 156 PHCs/CHCs and 21 DHs. DHs and the majority (82-96%) of the PHCs/CHCs provided outpatient treatment for diabetes and hypertension. Overall, 97 per cent of PHCs/CHCs had doctors, and 78 per cent had staff nurses. The availability of digital blood pressure monitors ranged from 35 to 43 per cent, and drugs were either not available or inadequate. Among 213 doctors, three-fourths knew the correct criteria for hypertension diagnosis, and a few correctly reported diabetes diagnosis criteria. Interpretation & conclusions: The results of this study suggest that the health system of the studied tribal districts was not adequately prepared to manage NCDs. The key challenges included inadequately trained workforce and a lack of equipment and drugs. It is suggested that capacity building and, procurement and distribution of equipment, drugs and information systems to track NCD patients should be the key focus areas of national programmes.

TruenatTM - micro real-time-polymerase chain reaction for rapid diagnosis of leptospirosis at minimal resource settings.

Background & objectives: The biological spectrum of leptospirosis ranges from acute undifferentiated febrile illness to severe fatal syndrome or a combination of syndromes. Diagnosis on clinical grounds alone is difficult and depends on laboratory support. However, no confirmatory tests are available, which is rapid and can be performed with minimum facilities available. The objectives of this study were to evaluate the diagnostic utility, accuracy and reproducibility of a rapid real time-PCR based method (TruenatTM) for early diagnosis of leptospirosis, and its usage in low resource settings. Methods: The Truenat™ test was performed using plasma sample collected from confirmed patients and controls. DNA was extracted from plasma samples and the reaction was performed as per the manufacturer's instructions. Leptospiral isolates were also used to assess the performance using different serovars. Results: Evaluation of the Truenat™ test with RT-PCR as the gold standard showed that Truenat™ had a sensitivity of 97.4 per cent and a specificity of 98.6 per cent. The overall agreement with RT-PCR was 98.2 per cent. Interpretation & conclusions: Our results showed that the test would be a useful tool for early diagnosis of leptospirosis in settings with minimal facilities and the test results could be obtained within an hour. This indicates that a specific therapy can be instituted during the early phase of the disease even at peripheral healthcare facilities as well during the outbreaks.

Molecular characterization of chikungunya virus isolates from two localized outbreaks during 2014-2019 in Kerala, India.

After the 2005-2009 chikungunya epidemic, intermittent outbreaks were reported in many parts of India. The outbreaks were caused by either locally circulating strains or imported viruses. Virus transmission routes can be traced by complete genome sequencing studies. We investigated two outbreaks in 2014 and 2019 in Kerala, India. Chikungunya virus (CHIKV) was isolated from the samples, and whole genomes were sequenced for a 2014 isolate and a 2019 isolate. Phylogenetic analysis revealed that the isolates formed a separate group with a 2019 isolate from Pune, Maharashtra, and belonged to the East/Central/South African (ECSA) genotype, Indian subcontinent sublineage of the Indian Ocean Lineage (IOL). A novel mutation at amino acid position 76 of the E2 gene was observed in the group. The phylogenetic results suggest that the outbreaks might have been caused by a virus that had been circulating in India since 2014. A detailed study is needed to investigate the evolution of CHIKV in India.

Detection of Nipah virus in Pteropus medius in 2019 outbreak from Ernakulam district, Kerala, India.

BACKGROUND: In June 2019, Nipah virus (NiV) infection was detected in a 21-year-old male (index case) of Ernakulum, Kerala, India. This study was undertaken to determine if NiV was in circulation in Pteropus species (spp) in those areas where the index case had visit history in 1 month. METHODS: Specialized techniques were used to trap the Pteropus medius bats (random sampling) in the vicinity of the index case area. Throat and rectal swabs samples of 141 bats along with visceral organs of 92 bats were collected to detect the presence of NiV by real-time reverse transcriptase-polymerase chain reaction (qRTPCR). Serum samples of 52 bats were tested for anti-NiV Immunoglobulin (Ig) G antibodies by Enzyme-Linked Immunosorbent Assay (ELISA). The complete genome of NiV was sequenced by next-generation sequencing (NGS) from the tissues and swab samples of bats. RESULTS: One rectal swab sample and three bats visceral organs were found positive for the NiV. Interestingly, 20.68% (12/58) of Pteropus were positive for anti-NiV IgG antibodies. NiV sequences of 18,172; 17,200 and 15,100 nucleotide bps could be retrieved from three Pteropus bats. CONCLUSION: A distinct cluster of NiV sequences, with significant net-evolutionary nucleotide divergence, was obtained, suggesting the circulation of new genotype (I-India) in South India. NiV Positivity in Pteropus spp. of bats revealed that NiV is circulating in many districts of Kerala state, and active surveillance of NiV should be immediately set up to know the hotspot area for NiV infection.

Pooled testing for COVID-19 diagnosis by real-time RT-PCR: A multi-site comparative evaluation of 5- & 10-sample pooling.

BACKGROUND & OBJECTIVES: Public health and diagnostic laboratories are facing huge sample loads for COVID-19 diagnosis by real-time reverse transcription-polymerase chain reaction (RT-PCR). High sensitivity of optimized real-time RT-PCR assays makes pooled testing a potentially efficient strategy for resource utilization when positivity rates for particular regions or groups of individuals are low. We report here a comparative analysis of pooled testing for 5- and 10-sample pools by real-time RT-PCR across 10 COVID-19 testing laboratories in India. METHODS: Ten virus research and diagnostic laboratories (VRDLs) testing for COVID-19 by real-time RT-PCR participated in this evaluation. At each laboratory, 100 nasopharyngeal swab samples including 10 positive samples were used to create 5- and 10-sample pools with one positive sample in each pool. RNA extraction and real-time RT-PCR for SARS-CoV-2-specific E gene target were performed for individual positive samples as well as pooled samples. Concordance between individual sample testing and testing in the 5- or 10-sample pools was calculated, and the variation across sites and by sample cycle threshold (Ct) values was analyzed. RESULTS: A total of 110 each of 5- and 10-sample pools were evaluated. Concordance between the 5-sample pool and individual sample testing was 100 per cent in the Ct value ≤30 cycles and 95.5 per cent for Ctvalues ≤33 cycles. Overall concordance between the 5-sample pooled and individual sample testing was 88 per cent while that between 10-sample pool and individual sample testing was 66 per cent. Although the concordance rates for both the 5- and 10-sample pooled testing varied across laboratories, yet for samples with Ct values ≤33 cycles, the concordance was ≥90 per cent across all laboratories for the 5-sample pools. INTERPRETATION & CONCLUSIONS: Results from this multi-site assessment suggest that pooling five samples for SARS-CoV-2 detection by real-time RT-PCR may be an acceptable strategy without much loss of sensitivity even for low viral loads, while with 10-sample pools, there may be considerably higher numbers of false negatives. However, testing laboratories should perform validations with the specific RNA extraction and RT-PCR kits in use at their centres before initiating pooled testing.

Neutralizing antibody responses to SARS-CoV-2 in COVID-19 patients.

BACKGROUND & OBJECTIVES: The global pandemic caused by SARS-CoV-2 virus has challenged public health system worldwide due to the unavailability of approved preventive and therapeutic options. Identification of neutralizing antibodies (NAb) and understanding their role is important. However, the data on kinetics of NAb response among COVID-19 patients are unclear. To understand the NAb response in COVID-19 patients, we compared the findings of microneutralization test (MNT) and plaque reduction neutralization test (PRNT) for the SARS-CoV-2. Further, the kinetics of NAb response among COVID-19 patients was assessed. METHODS: A total of 343 blood samples (89 positive, 58 negative for SARS-CoV-2 and 17 cross-reactive and 179 serum from healthy individuals) were collected and tested by MNT and PRNT. SARS-CoV-2 virus was prepared by propagating the virus in Vero CCL-81 cells. The intra-class correlation was calculated to assess the correlation between MNT and PRNT. The neutralizing endpoint as the reduction in the number of plaque count by 90 per cent (PRNT90) was also calculated. RESULTS: The analysis of MNT and PRNT quantitative results indicated that the intra-class correlation was 0.520. Of the 89 confirmed COVID-19 patients, 64 (71.9%) showed NAb response. INTERPRETATION & CONCLUSIONS: The results of MNT and PRNT were specific with no cross-reactivity. In the early stages of infection, the NAb response was observed with variable antibody kinetics. The neutralization assays can be used for titration of NAb in recovered/vaccinated or infected COVID-19 patients.

Development of indigenous IgG ELISA for the detection of anti-SARS-CoV-2 IgG.

BACKGROUND & OBJECTIVES: Since the beginning of the year 2020, the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impacted humankind adversely in almost all spheres of life. The virus belongs to the genus Betacoronavirus of the family Coronaviridae. SARS-CoV-2 causes the disease known as coronavirus disease 2019 (COVID-19) with mild-to-severe respiratory illness. The currently available diagnostic tools for the diagnosis of COVID-19 are mainly based on molecular assays. Real-time reverse transcription-polymerase chain reaction is the only diagnostic method currently recommended by the World Health Organization for COVID-19. With the rapid spread of SARS-CoV-2, it is necessary to utilize other tests, which would determine the burden of the disease as well as the spread of the outbreak. Considering the need for the development of such a screening test, an attempt was made to develop and evaluate an IgG-based ELISA for COVID-19. METHODS: A total of 513 blood samples (131 positive, 382 negative for SARS-CoV-2) were collected and tested by microneutralization test (MNT). Antigen stock of SARS-CoV-2 was prepared by propagating the virus in Vero CCL-81 cells. An IgG capture ELISA was developed for serological detection of anti-SARS-CoV-2 IgG in serum samples. The end point cut-off values were determined by using receiver operating characteristic (ROC) curve. Inter-assay variability was determined. RESULTS: The developed ELISA was found to be 92.37 per cent sensitive, 97.9 per cent specific, robust and reproducible. The positive and negative predictive values were 94.44 and 98.14 per cent, respectively. INTERPRETATION & CONCLUSIONS: This indigenously developed IgG ELISA was found to be sensitive and specific for the detection of anti-SARS-CoV-2 IgG in human serum samples. This assay may be used for determining seroprevalence of SARS-CoV-2 in a population exposed to the virus.

Experiential learnings from the Nipah virus outbreaks in Kerala towards containment of infectious public health emergencies in India.

Nipah virus (NiV) outbreak occurred in Kozhikode district, Kerala, India in 2018 with a case fatality rate of 91% (21/23). In 2019, a single case with full recovery occurred in Ernakulam district. We described the response and control measures by the Indian Council of Medical Research and Kerala State Government for the 2019 NiV outbreak. The establishment of Point of Care assays and monoclonal antibodies administration facility for early diagnosis, response and treatment, intensified contact tracing activities, bio-risk management and hospital infection control training of healthcare workers contributed to effective control and containment of NiV outbreak in Ernakulam.

Laboratory preparedness for SARS-CoV-2 testing in India: Harnessing a network of Virus Research & Diagnostic Laboratories.

Background & objectives: An outbreak of respiratory illness of unknown aetiology was reported from Hubei province of Wuhan, People's Republic of China, in December 2019. The outbreak was attributed to a novel coronavirus (CoV), named as severe acute respiratory syndrome (SARS)-CoV-2 and the disease as COVID-19. Within one month, cases were reported from 25 countries. In view of the novel viral strain with reported high morbidity, establishing early countrywide diagnosis to detect imported cases became critical. Here we describe the role of a countrywide network of VRDLs in early diagnosis of COVID-19. Methods: The Indian Council of Medical Research (ICMR)-National Institute of Virology (NIV), Pune, established screening as well as confirmatory assays for SARS-CoV-2. A total of 13 VRDLs were provided with the E gene screening real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay. VRDLs were selected on the basis of their presence near an international airport/seaport and their past performance. The case definition for testing included all individuals with travel history to Wuhan and symptomatic individuals with travel history to other parts of China. This was later expanded to include symptomatic individuals returning from Singapore, Japan, Hong Kong, Thailand and South Korea. Results: Within a week of standardization of the test at NIV, all VRDLs could initiate testing for SARS-CoV-2. Till February 29, 2020, a total of 2,913 samples were tested. This included both 654 individuals quarantined in the two camps and others fitting within the case definition. The quarantined individuals were tested twice - at days 0 and 14. All tested negative on both occasions. Only three individuals belonging to different districts in Kerala were found to be positive. Interpretation & conclusions: Sudden emergence of SARS-CoV-2 and its potential to cause a pandemic posed an unsurmountable challenge to the public health system of India. However, concerted efforts of various arms of the Government of India resulted in a well-coordinated action at each level. India has successfully demonstrated its ability to establish quick diagnosis of SARS-CoV-2 at NIV, Pune, and the testing VRDLs.

Impact of Temperature Variant on Survival of Aedes albopictus Skuse (Diptera: Culicidae): Implications on Thermotolerance and Acclimation.

Aedes albopictus (Skuse 1894) is prevalent in the urban/peri-urban Port Blair, posing a public health threat, during past outbreaks of chikungunya (2006) and dengue (2010). Despite its vector potential, information on the biology is scanty. Therefore, impact of temperature on survival of immature stages, under laboratory conditions, was studied on F1 population of Andamans. Ae. albopictus larvae were exposed to static temperatures viz. 37°C, 39°C, 41°C, 43°C and 45°C, and the lethal time to cause 50% (LT50) and 90% mortality (LT90) was computed. To assess adaptive thermotolerance, larvae exposed (37°C and 39°C) were re-exposed to higher temperatures (43°C and 45°C). All larvae survived at 37°C and 39°C for the entire exposure period of 420 min, while variable mortality was observed at 41°C, 43°C and 45°C. Larvae re-exposed to 43°C and 45°C showed an increase in thermotolerance with respect to non-adapted larvae. The results are discussed in the context of survival, development and distribution.