Genomic surveillance of SARS-CoV-2 by sequencing the RBD region using Sanger sequencing from North Kerala

Next Generation Sequencing (NGS) is the gold standard for the detection of new variants of SARS-CoV-2 including those which have immune escape properties, high infectivity, and variable severity. This test is helpful in genomic surveillance, for planning appropriate and timely public health interventions. But labs with NGS facilities are not available in small or medium research settings due to the high cost of setting up such a facility. Transportation of samples from many places to few centers for NGS testing also produces delays due to transportation and sample overload leading in turn to delays in patient management and community interventions. This becomes more important for patients traveling from hotspot regions or those suspected of harboring a new variant. Another major issue is the high cost of NGS-based tests. Thus, it may not be a good option for an economically viable surveillance program requiring immediate result generation and patient follow-up. The current study used a cost-effective facility which can be set up in a common research lab and which is replicable in similar centers with expertise in Sanger nucleotide sequencing. More samples can be processed at a time and can generate the results in a maximum of 2 days (1 day for a 24 h working lab). We analyzed the nucleotide sequence of the Receptor Binding Domain (RBD) region of SARS-CoV-2 by the Sanger sequencing using in-house developed methods. The SARS-CoV-2 variant surveillance was done during the period of March 2021 to May 2022 in the Northern region of Kerala, a state in India with a population of 36.4 million, for implementing appropriate timely interventions. Our findings broadly agree with those from elsewhere in India and other countries during the period.

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.

POS1262 A COHORT STUDY OF COVID-19 RELATED MULTISYSTEM INFLAMMATORY SYNDROME IN CHILDREN AND ADOLESCENTS FROM MULTIPLE TERTIARY CARE CENTRES IN SOUTH INDIA

Background:

After the peak of COVID 19 pandemic, a surge of cases with multi-system involvement and hyperinflammatory state was reported in children, at multiple tertiary care centers across the world. (1) This COVID-19 associated multisystem inflammatory syndrome in children and adolescents is also known as multisystem inflammatory syndrome in children (MIS-C). There is a paucity of literature of clinical profile of MIS-C patients from India.

Objectives:

To study the clinical manifestations and treatment outcomes of COVID-19 related multisystem inflammatory syndrome in children (MIS-C) and adolescents.

Methods:

It was a cohort study including cases defnied as per the case definitions of MIS-C by World Health Organisation (WHO) or Centre for Disease Control and Prevention(CDC).(2)The clinical parameters, laboratory parameters (including inflammatory markers, D dimer and NT ProBNP), electrocardiogram, 2D echocardiogram, course in hospital, and immediate outcomes were noted.

Results:

Twenty five patients (male-14) with a mean age of 6.22 ±4.25 years and a mean body mass index of 16.21 ±3.36 kg/m2 were enrolled on the study. Average length of hospital stay was 8.12±5.76 days. Associated comorbidities were present in 4 of our patients (16%). Figure 1 shows the frequency of clinical features in our study patients. Table 1 shows the clinical, laboratory, imaging findings, disease course and outcomes.

Figure 1.

Frequency of clinical features in our MIS-C cohort patients

Table 1.

Clinical characteristics of MIS-C patients (n)=25

Clinical Phenotypes:Incomplete/ Atypical Kawasaki Disease (KD)18 (72%)Macrophage activation syndrome (MAS)11 (44%)Unexplained Shock13 (52%)Fever with gastrointestinal symptoms17 (68%)Fever with neurological symptoms9 (36%)Fever with respiratory symptoms5 (20%)COVID chronology:MISC with acute COVID 19 with MAS1 (4%)MISC with acute COVID 19 with incomplete/atypical KD1 (4%)COVID 19 tests:COVID 19 RTPCR positive2 (8%)COVID 19 RTPCR negative23 (92%)COVID 19 IgG positive20 (80%)COVID 19 IgM positive6 (24%)COVID 19 IgG and IgM both positive2 (8%)COVID 19 IgG and IgM not done4 (16%)Other laboratory investigations(Peak/ trough values):Anaemia20 (80%)Leukopenia2 (8%)Thrombocytopenia6 (24%)Pancytopenia2 (8%)Positive CRP23 (92%)High Procalcitonin9 (36%)High ferritin10 (40%)High D- dimer17 (68%)High NT ProBNP23 (92%)Hypoalbuminemia14 (56%)Sterile pyuria7 (28%)Proteinuria4 (16%)Cardiac assessment:Abnormal Electrocardiogram (ECG)5 (20%)Abnormal Echocardiography15 (60%)Coronary dilation/prominence/non-tapering9 (36%)Coronary aneurysm1 (4%)LAD Z score (Mean±SD)2.12 ± 1.11Decreased Ejection fraction (EF)5 (20%)Systolic Dysfunction5 (20%)Pericardial effusion9 (36%)Global/septal hypokinesia4 (16%)Mitral Valve regurgitation3 (12%)Complete heart block1 (4%)

Twenty patients (80%) had severe illness requiring intensive care. Fourteen patients (56%) required inotropic support, 8 patients (32%) required supplemental oxygen, 5 patients (20%) required mechanical ventilation and 2 patients (8%) expired. A total of 23 patients (92%) received pulse steroids followed by oral/iv steroids, 22 patients (88%) received IVIG (2g/kg) and 3 patients (12%) required anticoagulation.

Conclusion:

Our MIS-C cohort had varied clinical manifestations ranging from the mild cutaneous and gastrointestinal symptoms to fatal multiorgan dysfunctions. In contrast to western cohorts, our study cohort had higher number of patients from younger age group and lower BMI.

References:

[1]Ahmed M, Advani S, Moreira A, Zoretic S, Martinez J, Chorath K et al. Multisystem inflammatory syndrome in children: A systematic review. EClinicalMedicine. 2020;26:100527.

[2]Jiang L, Tang K, Levin M, Irfan O, Morris S, Wilson K et al. COVID-19 and multisystem inflammatory syndrome in children and adolescents. The Lancet Infectious Diseases. 2020;20(11):e276-e288.

Disclosure of Interests:

None declared

Some ecological aspects and potential threats to an intertidal gastropod, Umbonium vestiarium

Kalbadevi Bay in Ratgnairi has been identified as potential site for placer mining along the west coast of India. Since, U. vestiarium is a keystone species of the region; study on some ecological aspect was carried. The paper also discusses the possible impact of beach sand mining and other threats to this ecologically important gastropod. Seasonal sampling was carried in 2004-2005 at 13 transects by quadrate method. U. vestiarium was restricted to mid and low tide zone of Station 1-3 and 8-10 located at the north and south ends of the beach. Abundance was highest at Station 10 MT (16 to 12488 ind m(-2)). Based on the size-frequency, it may be considered that U. vestiarium like other tropical fauna recruit during monsoon. Eleven different colour patterns of U. vestiarium were observed. However, average individual size was larger in the samples collected from the north (stn. 1-3) end of the beach. The fastidious nature and sporadic distribution of U. vestiarium make them vulnerable to natural and anthropogenic disturbance.

A comparative study of macrobenthic community from harbours along the central west coast of India

Harbours are heavily stressed coastal habitats characterised by high concentration of contaminant and low diversity of benthic community. The west coast of India harbours most of the major harbours compared to the east coast. Very few studies have compared the macrobenthic community between different Indian harbours. The present study was therefore conducted in three important harbour (Ratnagiri, Goa, Karwar) along the central west coast of India. The paper discusses the health status of the three harbours diagnosed using various biotic indices. Sediment samples were collected using van Veen grab (0.11 m(2)) on board CRV Sagar Sukti. A total of 55 macrobenthic taxa were identified and were numerically dominated by polychaete. Biomass was high (0.14-145.7 g m(-2)) and was made largely by echiurans (>80%). Overall, polychaete dominated the macrobenthic diversity. Opportunistic P.pinnata, Notomastus sp. and Mediomastus sp., dominated the macrobenthic community responding to the increased in the harbour. Biotic indices (Polychaete:Amphipod ratio, ABC curve and geometric class abundance) and the dominance of opportunistic species indicate that, the three harbours are under stress from anthropogenic activities.

Ecotoxicological effect of grounded MV River Princess on the intertidal benthic organisms off Goa

The ecotoxicological effects of oil spill from the grounded vessel MV River Princess on the intertidal benthic organisms of Sinquerim-Candolim beach at Goa were investigated. An intertidal expanse of 1 km on either side of the grounded vessel was selected to evaluate the concentration of total petroleum hydrocarbon (TPH) in the sediment and its effects on the composition, abundance and diversity of micro-, meio- and macrobenthos. TPH in the intertidal sediment ranged from 7.8 to 89 microg g(-1) (mean 35.44+/-26.35 SD). Microbenthos comprised of microalgae, protozoans and juvenile forms of meiobenthos. Apart from juvenile nematodes, which were abundant, Coscinodiscus spp., Navicula spp., and Nitzschia spp. representing microalgae were also observed in microbenthic samples. Meiobenthos was represented by 13 taxa and their total density ranged between 92 and 1057 nos. 10 cm(-2). Maximum meiobenthic abundance of 1057 nos. 10 cm(-2) was observed at Sinquerim. Nematodes were the dominant meiobenthic taxa followed by turbellarians and harpacticoid copepods. The macrobenthos was numerically dominated by polychaetes, followed by crustaceans whereas bivalve molluscs were less represented. There was substantial increase in the petroleum concentration in the beach sediment compared to the previously reported values and highest TPH (89 microg g(-1) sediment) values were in the vicinity of the grounded vessel. The polychaete/amphipod ratio and cumulative and partial dominance abundance-biomass curves showed significant negative impact of TPH on macrofauna. The benthic community structure also showed measurable changes, as there was significant decrease (60%) in the number of species. Given that the microalgal counts were low in sediment, it is assumed that the intertidal meiofauna was possibly using oil-degrading bacteria as alternate food source. In conclusion, the results reported here suggest that the grounded ore carrier is not only detrimental to the beach community, that may take longer time for recovery, but also affects the beach morphology which may have long-term impact on local fishery.