Detection and isolation of SARS-CoV-2 Eta variant from the international travelers and local residents of India

International travel has been the major source for the rapid spread of new SARS‐CoV‐2 variants across the globe. During SARS‐CoV‐2 genomic surveillance, a total of 212 SARS‐CoV‐2 positive clinical specimens were sequenced using next‐generation sequencing. A complete SARS‐CoV‐2 genome could be retrieved from 90 clinical specimens. Of them, 14 sequences belonged to the Eta variant from clinical specimens of international travelers (n = 12) and local residents (n = 2) of India, and 76 belonged to other SARS‐CoV‐2 variants. Of all the Eta‐positive specimens, the virus isolates were obtained from the clinical specimens of six international travelers. Many variants of interest have been found to cause substantial community transmission or cluster infections. The detection of this variant with lethal E484K mutation across the globe and India necessitates persistent genomic surveillance of the SARS‐CoV‐2 variants, which would aid in taking preventive action.

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.

Comparable neutralization of SARS-CoV-2 Delta AY.1 and Delta with individuals sera vaccinated with BBV152

Sera of COVID-19 naive vaccinees, COVID-19 recovered cases with vaccination and breakthrough cases demonstrated 1.3, 2.5 and 1.9-fold reduction in neutralization titers against Delta and 1.5, 3.5, 2.8-fold against Delta AY.1 compared to B.1 respectively. However, high neutralization titers would still effectively protect against Delta, Delta AY.1 and B.1.617.3 variants.

A case with SARS-CoV-2 reinfection from India

A healthcare worker presented with fever, cough, headache and tested positive by SARS-CoV-2 real time reverse transcriptase polymerase chain reaction (qRT-PCR). He got admitted to hospital and recovered after 14 days. After 2 months, as a screening protocol considering the high risk setup he got tested and again found to be positive for SARS-CoV-2 by qRT-PCR. Our patient had detectable levels of Anti-SARS-CoV-2 IgG antibodies during the reinfection but found negative for Neutralizing antibodies (NAb). Our findings suggest that the person after the initial infection might not develop the desired protective immunity to prevent the reinfection as demonstrated by absence of NAb.

Neutralization of VUI B.1.1.28 P2 variant with sera of COVID-19 recovered cases and recipients of Covaxin an inactivated COVID-19 vaccine

Our study has shown 1.09 and 1.92 fold reductions in the neutralizing titer with sera of individuals with natural infection and Covaxin vaccine recipients against B.1.1.28.2 variant.

Neutralization of Beta and Delta variant with sera of COVID-19 recovered cases and vaccinees of inactivated COVID-19 vaccine BBV152/Covaxin

SARS-CoV-2 variant of concern mainly Delta and Beta is global public health concern due to its impact on existing vaccines. Here, we assessed the neutralization of sera from COVID-19 recovered cases and BBV152 vaccinees against Beta and Delta variants. BBV152 vaccine found to confer significant protection against both the variants.

Experiences of Indian Council of Medical Research with tick-borne zoonotic infections: Kyasanur Forest disease & Crimean-Congo haemorrhagic fever in India with One Health focus

Emergence and re-emergence of several pathogens have been witnessed by this century in the form of outbreaks, epidemics and pandemics. In India, the influencing factor that promotes dissemination of emerging and re-emerging viral infections is the biogeographical zones: a megadiverse country, characterized by varied geographical, climatic conditions and ever-changing socio-economical and geopolitical issues. These influence the movement of humans and animals and add layers of complexity for the identification and timely management of infectious diseases. This review focuses on two tick-borne infections: Crimean-Congo haemorrhagic fever (CCHF) and Kyasanur forest disease (KFD). In the last two decades, these viruses have emerged and caused outbreaks in different parts of India. KFD virus was initially identified in 1957 and was known to be endemic in Karnataka State while CCHF virus was first identified during 2010 in Gujarat State, India. These viruses have managed to emerge in new areas within the last decade. With changing epidemiology of these arboviruses, there is a probability of the emergence of these viruses from new areas in future. The investigations on these two diseases under the One Health focus involved early detection, quickly developing diagnostic tools, identifying stakeholders, capacity building by developing collaboration with major stakeholders to understand the epidemiology and geographical spread in domestic animal reservoirs and tick vectors in the affected areas, developing laboratory network, providing diagnostic reagents and biosafety and laboratory diagnosis training to the network laboratories to control these diseases.

Comparison of the immunogenicity & protective efficacy of various SARS-CoV-2 vaccine candidates in non-human primates

BACKGROUND & OBJECTIVES

The COVID-19 pandemic has emerged as a global public health crisis and research groups worldwide are engaged in developing vaccine candidates to curb its transmission, with a few vaccines having progressed to advanced stages of clinical trials. The aim of this systematic review was to compare immunogenicity and protective efficacy of various SARS-CoV-2 vaccine candidates tested in non-human primate (NHP) models.

METHODS

Literature on effect of SARS-CoV-2 vaccines in NHP models reported on PubMed and preprint platforms (medRxiv and bioRxiv) till October 22, 2020, was searched with the following terms: coronavirus vaccine, COVID-19 vaccine, SARS-CoV-2 vaccine, nonhuman primate, and rhesus macaque.

RESULTS

Our search yielded 19 studies, which reported immune response elicited by 18 vaccine candidates in NHP. All the vaccines induced detectable neutralizing antibody (NAb) titres in the serum of vaccinated animals, with some showing effective viral clearance from various organs. The vaccinated animals also showed nil to mild histopathological changes in their lungs compared to placebo groups in the trials that performed necropsy.

INTERPRETATION & CONCLUSIONS

Our findings highlighted onset of quick immunogenicity and protective efficacy of mRNA-1273, followed by Ad26.CoV2.S, NVX-CoV2373, BNT162b2, RBD and BBV152 vaccine candidates in preclinical trials as compared to the others. NHP data also showed correlation with clinical trial data available for a few vaccines. Preclinical trials of COVID-19 vaccine candidates in NHPs yielded promising results, with some candidates faring better than others.

Immunogenicity and protective efficacy of inactivated SARS-CoV-2 vaccine candidate, BBV152 in rhesus macaques

The COVID-19 pandemic is a global health crisis that poses a great challenge to the public health system of affected countries. Safe and effective vaccines are needed to overcome this crisis. Here, we develop and assess the protective efficacy and immunogenicity of an inactivated SARS-CoV-2 vaccine in rhesus macaques. Twenty macaques were divided into four groups of five animals each. One group was administered a placebo, while three groups were immunized with three different vaccine candidates of BBV152 at 0 and 14 days. All the macaques were challenged with SARS-CoV-2 fourteen days after the second dose. The protective response was observed with increasing SARS-CoV-2 specific IgG and neutralizing antibody titers from 3^rd-week post-immunization. Viral clearance was observed from bronchoalveolar lavage fluid, nasal swab, throat swab and lung tissues at 7 days post-infection in the vaccinated groups. No evidence of pneumonia was observed by histopathological examination in vaccinated groups, unlike the placebo group which exhibited interstitial pneumonia and localization of viral antigen in the alveolar epithelium and macrophages by immunohistochemistry. This vaccine candidate BBV152 has completed Phase I/II (NCT04471519) clinical trials in India and is presently in phase III, data of this study substantiates the immunogenicity and protective efficacy of the vaccine candidates.

Isolation and characterization of the new SARS-CoV-2 variant in travellers from the United Kingdom to India: VUI-202012/01 of the B.1.1.7 lineage

We have isolated the new severe acute respiratory syndrome coronavirus-2 variant of concern 202 012/01 from the positive coronavirus disease 2019 cases that travelled from the UK to India in the month of December 2020. This emphasizes the need for the strengthened surveillance system to limit the local transmission of this new variant.

Preparedness of public health-care system for Zika virus outbreak: An Indian perspective

Zika virus is a mosquito-borne flavivirus that has emerged recently and affected in many countries. Since its discovery in Uganda in 1947, two major outbreaks were reported from Yap Islands in 2007 and French Polynesia in 2013. In 2015, the first case of ZIKV infection was confirmed from Brazil followed by a report of cases from American and Caribbean countries. In February 2016, the World Health Organization declared ZIKV infection a Public Health Emergency of International Concern. India reported the first Zika case in 2017. Subsequently, 157 laboratory-confirmed cases of ZIKV including 63 pregnant women were reported from Rajasthan, India in 2018. Since 2014, many countries took initiatives to boost their public health system to combat ZIKV. However, there is still scope for the improvement. This review describes ZIKV outbreaks, diagnostic challenges, surveillance and control measures in India and the future perspective to deal with the ZIKV outbreak in India.

Isophthaloyl-Based Selective Fluorescence Receptor for Zn (II) Ion in Semi-Aqueous Medium

A novel Isophthaloyl-based symmetrical (12E,21E)-N1',N3'-bis(2-hydroxybenzylidene) isophthalohydrazide, receptor (1) was synthesized and characterized using various spectroscopic technique. The reorganization ability of receptor (1) was evaluated in semi-aqueous medium and shows significant enhancement in fluorescence intensity for Zn (II) ion over various metal ions in CH₃CN:H₂O (1:1, v/v). The 1:2 binding stoichiometry between receptor (1) and Zn (II) ion was established using Job's plot and the proposed complex structure was calculated by applying Density Functional Theory (DFT) method. The binding constant (K_a) of receptor (1) with Zn (II) ion was established with the Benesi-Hildebrand plot, Scatchard and Connor's plot and the values are 1.00 × 10⁴ M^-1, 1.05× 10⁴ M^-1 and 1.05× 10⁴ M^-1 respectively. The limit of detection (LOD) and limit of quantification (LOQ) of receptor (1) and Zn (II) ion was 0.292 μM and 0.974 μM respectively. The binding mode was due to photo-induced electron transfer (PET) and the coordination of Zn (II) ion with C = N hydroxyl group of receptor (1). Electrochemical analysis of metal free receptor (1) and with Zn (II) ion also confirmed the formation of complex.

Crimean Congo hemorrhagic fever serosurvey in humans for identifying high-risk populations and high-risk areas in the endemic state of Gujarat, India

Background

Crimean Congo Hemorrhagic Fever (CCHF) is a highly infectious zoonotic disease of humans transmitted by Hyalomma ticks. Earlier studies have shown CCHF seroprevalence in livestock throughout India, yet sporadic outbreaks have been recorded mostly from the Gujarat state of India since 2011. Occupational vulnerability to CCHF for animal handlers, veterinarians, abattoir workers, and healthcare workers has been documented. The current study was planned to determine the seroprevalence of CCHF with an intention to identify the high -risk population and high -risk areas from Gujarat state, India.

Methods

Based on the socio-clinical data, the human population of Gujarat was divided into eight categories viz. A: CCHF affected person/house/close contact, B: Neighborhood contacts, C: Animal handlers, D: General population, E: Farmers, F: Abattoir workers, G: Veterinarian, H: Healthcare workers. A total of 4978 human serum samples were collected from 33 districts of Gujarat during year 2015, 2016 and 2017. All the samples were screened for the presence of anti-CCHFV IgG using indigenously developed anti-CCHFV IgG ELISA. Univariate regression analysis was performed to recognize significant risk factors for CCHF seropositivity.

Results

Twenty-five serum samples were found to be positive with an overall CCHF human seropositivity of 0.5% (95% CI 0.30–0.74%). Gender predisposition to CCHF prevalence was observed in males (OR: 2.80; p-value: 0.020). The risk for seropositivity increased sevenfold when a person was in contact or neighbor with a CCHF case (OR 7.02; p-value: < 0.0001). No significant difference in seropositivity was observed within different age groups. Veterinarians, healthcare workers, and control group were found to be seronegative for CCHF.

Conclusions

In-spite of CCHF sporadic outbreaks reported in Gujarat, the seropositivity for CCHF in the state was low as compared to other endemic countries. Males, close contacts and neighbors were identified as a high-risk population for CCHF infection. To recognize the high-risk area, tick screening and animal serosurvey would be a wiser choice. The study also suggests circulation and under diagnoses of CCHFV in the naïve regions of Gujarat.

Identification and characterization of novel mosquito-borne (Kammavanpettai virus) and tick-borne (Wad Medani) reoviruses isolated in India

In 1954, a virus named Wad Medani virus (WMV) was isolated from Hyalomma marginatum ticks from Maharashtra State, India. In 1963, another virus was isolated from Sturnia pagodarum birds in Tamil Nadu, India, and named Kammavanpettai virus (KVPTV) based on the site of its isolation. Originally these virus isolates could not be identified with conventional methods. Here we describe next-generation sequencing studies leading to the determination of their complete genome sequences, and identification of both virus isolates as orbiviruses (family Reoviridae). Sequencing data showed that KVPTV has an AT-rich genome, whereas the genome of WMV is GC-rich. The size of the KVPTV genome is 18 234 nucleotides encoding proteins ranging 238-1290 amino acids (aa) in length. Similarly, the size of the WMV genome is 16 941 nucleotides encoding proteins ranging 214-1305 amino acids in length. Phylogenetic analysis of the VP1 gene, along with the capsid genes VP5 and VP7, revealed that KVPTV is likely a novel mosquito-borne virus and WMV is a tick-borne orbivirus. This study focuses on the phylogenetic comparison of these newly identified orbiviruses with mosquito-, tick- and Culicoides-borne orbiviruses isolated in India and other countries.