Molecular epidemiology of novel swine origin influenza virus (S-OIV) from Gwalior, India, 2009

<p>Abstract</p> <p>Background</p> <p>The H1N1pandemic virus is a newly emergent human influenza A virus that is closely related to a number of currently circulating pig viruses in the 'classic North American' and 'Eurasian' swine influenza virus lineages and thus referred as S-OIV. Since the first reports of the virus in humans in April 2009, H1N1 virus has spread to 168 countries and overseas territories. India also witnessed severe H1N1 pandemic virus epidemic with considerable morbidity and mortality in different parts starting from May 2009.</p> <p>Findings</p> <p>The suspected swine flu outbreak from Gwalior India during October- December 2009 was confirmed through S-OIV HA gene specific RT-LAMP and real time RT-PCR. Positive samples through CDC real time and Lamp assay were further processed for isolation of the virus. Full HA gene sequencing of the H1N1 isolates of Gwalior, India revealed 99% homology with California and other circulating novel swine flu viruses. Three major changes were observed at nucleotide level, while two major amino acid shifts were observed at the position C9W and I30M corresponding to the ORF with prototype strain. The HA gene sequence phylogeny revealed the circulation of two genetically distinct lineages belonging to <it>Clade VII </it>and <it>Clade I </it>of S-OIV.</p> <p>Conclusions</p> <p>Our findings also supported the earlier report about circulation of mixed genogroups of S-OIV in India. Therefore continuous monitoring of the genetic makeup of this newly emergent virus is essential to understand its evolution within the country.</p

Refractoriness of Indian Aedes aegypti to Oral Infection with Yellow Fever Virus 17D Strain

Yellow fever virus (YFV) is the causative agent of yellow fever. It is one of the most important hemorrhagic arboviral infection of global public health significance. It is categorised under category ‘C’ of potential bioterrorism agent. Effect of geographical variation on vector competence in Ae. aegypti has been well documented for several viruses including YFV. In the present study, the vector competence of Ae. aegypti mosquitoes collected from Gwalior, India for YFV 17D vaccine strain was evaluated to understand the risk of its transmission. Further the risk associated with transmission of YFV 17D vaccine strain from viremic vaccinees to mosquitoes and subsequently to naive individuals was assessed. Ae. aegypti were orally infected with high titer of YFV 17D strain and the infection status was investigated at 7 and 14 day post infection (dpi) using a highly sensitive quantitative RT-PCR assay. None of the Ae. aegypti mosquito orally infected with YFV 17D strain was found to be positive for YFV. The infection rate was found to be zero per cent at both 7 dpi and 14 dpi. These results demonstrated the inability of the YFV 17D strain to cause infection or replication in the midgut of Ae. aegypti. Due to the highly attenuated replication of this strain in Ae. aegypti midgut, there is a minimal risk of its transmission. Further, it is unlikely for a mosquito that feeds on a viremic vaccine to get infected with this vaccine strain. The risk of transmission of YFV 17D strain by Indian Ae. aegypti mosquitoes is negligible. Further vector competence study using epidemic strain of YFV will aid in risk assessment analysis of YFV in India

Appearance of E1: A226V mutant Chikungunya virus in Coastal Karnataka, India during 2008 outbreak

Chikungunya has resurged in the form of unprecedented explosive epidemic in 2006 after a long gap in India affecting 1.39 million of persons. The disease continued for the next two consecutive years affecting 59,535 and 64,548 persons during 2007 and 2008 respectively. The 2008 outbreak being the second largest among these three years the information regarding the etiology and the mutations involved are useful for further control measures. Among the 2008 outbreaks the Coastal Karnataka accounts for the 46,510 persons. An in-depth investigation of Chikungunya epidemic of Coastal Karnataka, India, 2008 by serology, virus isolation, RT-PCR and genome sequencing revealed the presence and continued circulation of A226V mutant Chikungunya virus. The appearance of this mutant virus was found to be associated with higher prevalence of vector Aedes albopictus and the geographical proximity of coastal Karnataka with the adjoining Kerala state. This is the first report regarding the appearance of this mutation in Karnataka state of India. The present study identified the presence and association of A226V mutant virus with Chikungunya outbreak in India during 2008

Development and evaluation of one step single tube multiplex RT-PCR for rapid detection and typing of dengue viruses

<p>Abstract</p> <p>Background</p> <p>Dengue is emerging as a major public health concern in many parts of the world. The development of a one-step, single tube, rapid, and multiplex reverse transcription polymerase chain reaction (M-RT-PCR) for simultaneous detection and typing of dengue virus using serotype specific primers during acute phase of illness is reported.</p> <p>Results</p> <p>An optimal assay condition with zero background was established having no cross-reaction with closely related members of flavivirus (Japanese encephalitis, West Nile, Yellow fever) and alphavirus (Chikungunya). The feasibility of M-RT-PCR assay for clinical diagnosis was validated with 620 acute phase dengue patient sera samples of recent epidemics in India. The comparative evaluation <it>vis a vis </it>conventional virus isolation revealed higher sensitivity. None of the forty healthy serum samples screened in the present study revealed any amplification, thereby establishing specificity of the reported assay for dengue virus only.</p> <p>Conclusion</p> <p>These findings clearly suggested that M-RT-PCR assay reported in the present study is the rapid and cost-effective method for simultaneous detection as well as typing of the dengue virus in acute phase patient serum samples. Thus, the M-RT-PCR assay developed in this study will serve as a very useful tool for rapid diagnosis and typing of dengue infections in endemic areas.</p

Vertical Transmission of Chikungunya virus in Aedes aegypti Mosquitoes from Northern India

Chikungunya virus is now recognised as a resurging arbovirus of global public health significance, with their circulation in both new and old world. It is horizontally transmitted among vertebrates by Aedes mosquitoes. So far, the existence of vertical transmission of Chikungunya virus in Aedes vector is riddled with conflicting reports. In this study, presence of Chikungunya virus was detected in adult Aedes aegypti mosquitoes that emerged from field-collected larvae from Gwalior, northern India during 2010. This was further confirmed through nucleotide sequencing that revealed the presence of novel east central south African (ECSA) genotype of Chikungunya virus. This provides molecular evidence for vertical transmission of Chikungunya virus in mosquitoes in nature, which may have important consequences for viral survival during inter-epidemic period and adverse climatic conditions

Molecular and Virological Investigation of a Focal Chikungunya Outbreak in Northern India

Chikungunya (CHIK) fever is one of the most important arboviral infections of medical significance. The objective of the present study is to identify and characterize the etiology of a focal febrile arthritis outbreak from Gwalior, northern India, during October-November 2010. A detailed virological (isolation) and molecular (end-point RT-PCR, quantitative RT-PCR, and nucleotide sequencing) investigation of this outbreak was carried out by collecting and studying 52 clinical samples and 15 mosquito pools from the affected region. The investigation revealed the presence of CHIK viral RNA in 29% of clinical samples and 13% mosquito pool by RT-PCR. The quantification of CHIK viral RNA in samples varied from 102.50to 106.67 copies/mL, as demonstrated through quantitative RT-PCR. In addition, six CHIK viruses were isolated from RT-PCR positive samples. The nucleotide sequences of partial E1 gene of five representative CHIK viruses were deciphered, which revealed that all the viral strains from this outbreak belong to the recently emerging ECS African genotype. Identification of Chikungunya virus ECSA African genotype as the etiology of the present outbreak confirms the continued circulation of the novel genotype, since 2006, in India. The identification of CHIK virus inAedes aegyptialso confirmed it as the major vector in northern India.</jats:p

The evaluation of prospects for human and saltwater crocodile (Crocodylus porosus) conflict: the case of coastal Bhitarkanika National Park, India

The preservation of biodiversity and managing human-wildlife conflicts are significant problems associated with conservation worldwide. The evaluation of the human-saltwater crocodile (Crocodylus porosus) conflict around the Bhitarkanika National Park revealed an overview of attacks on humans. In this study, it was found that between 2019 and 2025, a total of 28 fatal attacks were reported in the area adjacent to the National Park. It is also highlighted that the past 25 years of government investment policies in C. porosus conservation have led to a significant increase in the number of C. porosus individuals by approximately 36.4 individuals per year over this period of 25 years. The total population follows a moderately complex to highly nonlinear trend. The adult C. porosus follows a moderately nonlinear trend and the sub-adult follows a highly complex trend. The Combined population of both the adults and sub-adults increases by 12.6 individuals per year, revealing significant growth. A key aspect of this study is the difficulty of recovering and conserving large predator populations due to the inherent risk they pose to people and their livelihoods. The findings of the study will aid in creating strategies to reduce the risk of HWC

Phylogenetic studies reveal existence of multiple lineages of a single genotype of DENV-1 (genotype III) in India during 1956–2007

<p>Abstract</p> <p>Background</p> <p>Dengue virus type 1 (DENV-1) have been mostly circulating silently with dominant serotypes DENV-2 and DENV-3 in India. However recent times have marked an increase in DENV-1 circulation in yearly outbreaks. Many studies have not been carried out on this virus type, leaving a lacunae pertaining to the circulating genotypes, since its earliest report in India. In the present study, we sequenced CprM gene junction of 13 DENV-1 isolated from Delhi and Gwalior (North India) between 2001–2007 and one 1956 Vellore isolate as reference. For comparison, we retrieved 11 other Indian and 70 global reference sequences from NCBI database, making sure that Indian and global isolates from all decades are available for comparative analysis.</p> <p>Results</p> <p>The region was found to be AT rich with no insertion or deletion. Majority of the nucleotide substitutions were silent, except 3 non-conservative amino acid changes (I → T, A → T and L → S at amino acid positions 59,114 and 155 respectively) in the Indian DENV-1 sequences, sequenced in this study. Except two 1997–98 Delhi isolates, which group in genotype I; all other Indian isolates group in genotype III. All Indian genotype III DENV-1 exhibited diversity among them, giving rise to at least 4 distinct lineages (India 1–4) showing proximity to isolates from diverse geographic locations.</p> <p>Conclusion</p> <p>The extensive phylogenetic analysis revealed consistent existence of multiple lineages of DENV-1 genotype III during the last 5 decades in India.</p

Structural and genomic evolutionary dynamics of Omicron variant of SARS-CoV-2 circulating in Madhya Pradesh, India

The SARS-CoV-2 Omicron (B.1.1.529) variant emerged in early November 2021 and its rapid spread created fear worldwide. This was attributed to its increased infectivity and escaping immune mechanisms. The spike protein of Omicron has more mutations (&gt;30) than any other previous variants and was declared as the variant of concern (VOC) by the WHO. The concern among the scientific community was huge about this variant, and a piece of updated information on circulating viral strains is important in order to better understand the epidemiology, virus pathogenicity, transmission, therapeutic interventions, and vaccine development. A total of 710 samples were processed for sequencing and identification up to a resolution of sub-lineage. The sequence analysis revealed Omicron variant with distribution as follows: B.1.1, B.1.1.529, BA.1, BA.2, BA.2.10, BA.2.10.1, BA.2.23, BA.2.37, BA.2.38, BA.2.43, BA.2.74, BA.2.75, BA.2.76, and BA.4 sub-lineages. There is a shift noted in circulating lineage from BA.1 to BA.2 to BA.4 over a period from January to September 2022. Multiple signature mutations were identified in S protein T376A, D405N, and R408S mutations, which were new and common to all BA.2 variants. Additionally, R346T was seen in emerging BA.2.74 and BA.2.76 variants. The emerging BA.4 retained the common T376A, D405N, and R408S mutations of BA.2 along with a new mutation F486V. The samples sequenced were from different districts of Madhya Pradesh and showed a predominance of BA.2 and its variants circulating in this region. The current study identified circulation of BA.1 and BA.1.1 variants during initial phase. The predominant Delta strain of the second wave has been replaced by the Omicron variant in this region over a period of time. This study successfully deciphers the dynamics of the emergence and replacement of various sub-lineages of SARS-CoV-2 in central India on real real-time basis