Cat Scratch Disease of the Breast/Axilla: Recognition of a Rare Disease and Approaches for Differential Diagnosis.

Cat scratch disease rarely presents as a breast or axillary mass mimicking carcinoma both clinically and radiologically. Diagnosing breast/axillary cat scratch disease is challenging due to its rarity and nonspecific findings. Here, we reported 2 patients with breast cat scratch disease and reviewed 14 patients with cat scratch disease involving breast/axilla from the past 30 years.

Evolution of the SARS-CoV-2 pandemic in India.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a bat-derived betacoronavirus, that emerged around December 2019. In spite of the lesser genomic diversity of CoVs in general, a steady accumulation of mutations spread over its genome have been noted, resulting in the emergence of several clades and lineages. Majority of these mutations are random and non-functional changes; however a few variants of concern (VOC) and variants of interest (VOI) designated by the WHO since late 2020 have implications to diagnostics, pathogenicity and immune escape.

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.

Perspectives for repurposing drugs for the coronavirus disease 2019.

The newly emerged 2019 novel coronavirus (CoV), named as severe acute respiratory syndrome CoV-2 (SARS-CoV-2), like SARS-CoV (now, SARS-CoV-1) and Middle East respiratory syndrome CoV (MERS-CoV), has been associated with high infection rates with over 36,405 deaths. In the absence of approved marketed drugs against coronaviruses, the treatment and management of this novel CoV disease (COVID-19) worldwide is a challenge. Drug repurposing that has emerged as an effective drug discovery approach from earlier approved drugs could reduce the time and cost compared to de novo drug discovery.

Full-genome sequences of the first two SARS-CoV-2 viruses from India.

Background & Objectives: Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally affected 195 countries. In India, suspected cases were screened for SARS-CoV-2 as per the advisory of the Ministry of Health and Family Welfare. The objective of this study was to characterize SARS-CoV-2 sequences from three identified positive cases as on February 29, 2020.

Chikungunya phylogeography reveals persistent global transmissions of the Indian Ocean Lineage from India in association with mutational fitness.

Since the resurgence of chikungunya virus (CHIKV) in India in 2005, the Indian subcontinent sublineage of the Indian Ocean lineage (IOL) has continued transmission in India and also radiation from India causing additional outbreaks in surrounding countries. This study was undertaken for an in-depth understanding of the evolutionary dynamics of the IOL, the global transmission routes in the Indian context and possible association with mutational fitness. The whole genome sequencing of Indian isolates representing CHIKV outbreaks (2014-2018) from selected States of India was carried out, followed by phylogeography analysis of the IOL using the Bayesian Markov chain Monte Carlo method and selection pressure analysis.

Phylogeography of Kyasanur Forest Disease virus in India (1957-2017) reveals evolution and spread in the Western Ghats region.

The Kyasanur Forest Disease (KFD) has become a major public health problem in the State of Karnataka, India where the disease was first identified and in Tamil Nadu, Maharashtra, Kerala, and Goa covering the Western Ghats region of India. The incidence of positive cases and distribution of the Kyasanur Forest Disease virus (KFDV) in different geographical regions raises the need to understand the evolution and spatiotemporal transmission dynamics. Phylogeography analysis based on 48 whole genomes (46 from this study) and additionally 28 E-gene sequences of KFDV isolated from different regions spanning the period 1957-2017 was thus undertaken.

Whole-genome-based characterization of three human Rotavirus C strains isolated from gastroenteritis outbreaks in Western India and a provisional intra-genotypic lineage classification system.

The number of whole-genome sequences of human rotavirus C (RVC) strains available in public databases is recently increasing. Thus far from India only a single whole genome of human RVC of a sporadic case was available. In this study, nearly full-length genome sequencing and phylogenetic analyses of three RVC strains isolated from three different gastroenteritis outbreaks during 2010-2014 in Western India was carried out.

Molecular mechanism by which residues at position 481 and 546 of measles virus hemagglutinin protein define CD46 receptor binding using a molecular docking approach.

The hemagglutinin (H) protein of measles viruses (MeV) mediates binding to the cellular receptors, CD46,human signaling lymphocyte activation molecule and nectin-4. Vaccine strains primarily contain H-proteins possessing MeV-H: Y481 and can utilize CD46. Reports suggest that a single amino acid change in MeV-H at position 481 in wild type strains renders them inefficient in utilizing CD46.

Selection of avian influenza A (H9N2) virus with reduced susceptibility to neuraminidase inhibitors oseltamivir and zanamivir.

Identification of amino-acid substitutions in the neuraminidase (NA) of low-pathogenic avian influenza (AI) H9N2 viruses is important to study the susceptibility to NA inhibitors (NAI). To identify mutations under NAI selective pressure, the virus was serially passaged with increasing levels of either oseltamivir or zanamivir in ovo, and the growth of the viruses in the presence and absence of NAI's compared. Mutations R292 K in the presence of oseltamivir and E119D in presence of zanamivir were observed within passage one and two respectively.

Global spatiotemporal transmission dynamics of measles virus clade D genotypes in the context of the measles elimination goal 2020 in India.

Measles viruses (MeV) circulating in India mainly belong to genoypes D4 and D8 of clade D. In the context of measles elimination goal 2020 in India, molecular clock and phylogeography studies would help to identify the timescales of evolution and track the transmission pathways of MeV. We used nucleoprotein gene sequences (n = 756) from GenBank, representing 86 countries (1973-2016), to study the spatiotemporal transmission dynamics of clade D.

Genetic characterization of chikungunya viruses isolated during the 2015-2017 outbreaks in different states of India, based on their E1 and E2 genes.

During 2015-2017, chikungunya virus (CHIKV) showed a resurgence in several parts of India with Karnataka, Maharashtra and New Delhi accounting for a majority of the cases. E2-E1 gene based characterization revealed Indian subcontinent sublineage strains possessing Aedes aegypti mosquito-adaptive mutations E1: K211E and E2:V264A, with the 211 site positively selected. Novel mutational sites E1: K16E/Q, E1: K132Q/T, E1: S355T, E2: C19R and E2:S185Y could be associated with epitopes or virulence determining domains.

Computational analysis of the effect of polymerase acidic (PA) gene mutation F35L in the 2009 pandemic influenza A (H1N1) virus on binding aspects of mononucleotides in the endonuclease domain.

An F35L mutation in the N-terminal domain of the polymerase acidic protein (PA-Nter), which contains the active site of the endonuclease, has been reported to result in higher polymerase activity in mouse-adapted strains of the 2009 pandemic influenza A H1N1 virus. We modeled wild and mutant complexes of uridine 5'-monophosphate (UMP) as the endonuclease substrate and performed molecular dynamics simulations. The results demonstrated that the F35L mutation could result in a changed orientation of a helix containing active site residues and improve the ligand affinity in the mutant strain.

A molecular modelling approach to understand the effect of co-evolutionary mutations (V344M, I354L) identified in the PB2 subunit of influenza A 2009 pandemic H1N1 virus on m7GTP ligand binding.

The cap binding domain of the polymerase basic 2 (PB2) subunit of influenza polymerases plays a critical role in mediating the 'cap-snatching' mechanism by binding the 5' cap of host pre-mRNAs during viral mRNA transcription. Monitoring variations in the PB2 protein is thus vital for evaluating the pathogenic potential of the virus. Based on selection pressure analysis of PB2 gene sequences of the pandemic H1N1 (pH1N1) viruses of the period 2009-2014, we identified a site, 344V/M, in the vicinity of the cap binding pocket showing evidence of adaptive evolution and another co-evolving residue, 354I/L, in close vicinity.

Genomic characterization of coxsackievirus type B3 strains associated with acute flaccid paralysis in south-western India.

Acute flaccid paralysis (AFP) associated with coxsackievirus type B3 (CV-B3) of the species Enterovirus B is an emerging concern worldwide. Although CV-B3-associated AFP in India has been demonstrated previously, the genomic characterization of these strains is unreported. Here, CV-B3 strains detected on the basis of the partial VP1 gene in 10 AFP cases and five asymptomatic contacts identified from different regions of south-western India during 2009-2010 through the Polio Surveillance Project were considered for complete genome sequencing and characterization.

Molecular dynamics simulation of the effects of single (S221P) and double (S221P and K216E) mutations in the hemagglutinin protein of influenza A H5N1 virus: a study on host receptor specificity.

Avian influenza viruses of subtype H5N1 circulating in animals continue to pose threats to human health. The binding preference of the viral surface protein hemagglutinin (HA) to sialosaccharides of receptors is an important area for understanding mutations in the receptor binding site that could be the cause for avian-to-human transmission. In the present work, we studied the effect of two receptor binding site mutations, S221P singly and in combination with another mutation K216E in the HA protein of influenza A H5N1 viruses.

Phylogeographic analysis of Japanese encephalitis virus in India (1956-2012).

Japanese encephalitis virus (JEV) isolates from India phylogenetically belong to two genotypes, III and I. We used envelope gene sequences from GenBank, representing different states of India and other countries, to study the spatiotemporal transmission histories of these two JEV genotypes separately. Genotype III was found to have been successively introduced in the 1930s, 1950s and 1960s, followed by genotype I twice around 2003-2006.

Molecular mechanism of the enhanced viral fitness contributed by secondary mutations in the hemagglutinin protein of oseltamivir resistant H1N1 influenza viruses: modeling studies of antibody and receptor binding.

The envelope protein hemagglutinin (HA) of influenza viruses is primarily associated with host antibody and receptor interactions. The HA protein is known to maintain a functional balance with neuraminidase (NA), the other major envelope protein. Prior to 2007-2008, human seasonal H1N1 viruses possessing the NA H274Y mutation, which confers oseltamivir resistance, generally had low growth capability.

Global phylogeography of Dengue type 1 and 2 viruses reveals the role of India.

Patterns in virus dispersal and epidemiology of viral diseases can be revealed by phylogeographic studies. Currently knowledge about phylogeography of Dengue virus (DENV) Types 1 and 2 is limited. We carried out the phylogeographic analyses for DENV-1 and DENV-2, by the Bayesian Markov Chain Monte Carlo (MCMC) approach, with emphasis on Indian isolates in relation to the global evolutionary dynamics of the viruses.

Genetic characterization and molecular clock analyses of the Crimean-Congo hemorrhagic fever virus from human and ticks in India, 2010-2011.

A nosocomial outbreak of Crimean Congo hemorrhagic fever (CCHF) was reported among humans in Ahmadabad district, Gujarat, India during January, 2011. In the present study we provide the complete genomic sequences of four CCHFV isolates derived from two human patients and two pools of Hyalomma anatolicum ticks during the period of this outbreak and the complete S segment sequence of two retrospective human serum samples, positive for CCHFV in 2010. Sequence-based molecular characterization of the Indian CCHFV showed that they possessed the functional motifs known to occur in the S, M and L gene segment products as in other CCHF viruses.