ICMR Virus Unit

Kolkata, India

ICMR Virus Unit

Kolkata, India

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Biswas A.,ICMR Virus Unit | Banerjee A.,ICMR Virus Unit | Banerjee A.,Saint Louis University | Chandra P.K.,ICMR Virus Unit | And 10 more authors.
Journal of Medical Virology | Year: 2011

Mutations in the basal core promoter (BCP) and precore (PC) regions are associated with persistent and intermittently high hepatitis B virus (HBV) replication in several patients. The variability in the functional domains of BCP and PC region of HBV and their association with disease progression and clinical outcome were assessed in Eastern India, an unique region where three HBV genotypes, A, D, and C are prevalent among the same ethnic group. PCR amplification and direct sequencing of BCP and PC region was done on sera obtained from 130 HBsAg positive subjects with different clinical presentations. Associations of the apparent risk factors with clinical advancement were evaluated by statistical methods including multiple logistic regression analyses (MLR). HBV genotype A was present in 33.08%, C in 25.38%, and D in 41.54% cases. Genotypes A and C were associated with higher rate of T1762/A1764 mutations than the most predominant genotype D. HBeAg negative state was associated with considerably higher rate of C1753 mutation. T1762/A1764 along with C1753 was common among cirrhosis and T1762/A1764 without C1753 was frequent among chronic liver disease cases. No significant association was found between A1896 point mutation and clinical status. Multivariate analysis revealed that T1762/A1764 double mutation, HBV/A, age ≥25 years, C1753 and A1899 were critical factors for clinical advancement while age ≥25 years and C1753 as significant predictor for cirrhosis in comparison with chronic liver disease. In conclusion, the analysis of the BCP variability may help in monitoring the progression towards advanced liver disease in Eastern Indian patients. © 2010 Wiley-Liss, Inc.


Panigrahi R.,ICMR Virus Unit | Majumder S.,Calcutta Medical College and Hospital | Gooptu M.,Calcutta Medical College and Hospital | Biswas A.,ICMR Virus Unit | And 7 more authors.
Annals of Hepatology | Year: 2012

Background. The prevalence of occult HBV, defined by the presence of HBV DNA in individuals with anti-bodies to HBV core antigen and with absence of HBV surface antigen, but its clinical significance and viro-logical features in HIV-infected patients is still unclear. Aim. To investigate the prevalence, clinical significance and molecular characterization of occult hepatitis B virus infection in ART-Naive HIV-positive individuals. Material and methods. Among the 1077 HIV-infected patients with different risk factors for HIV infection, 297 were HBsAg-ve ART-naive, of them 112 was randomly selected for the study. HBV DNA was tested by in-house PCR and quantified by qPCR. Molecular characterization was performed by sequencing the envelope and overlapping polymerase genes. Results. We found the prevalence of occult HBV to be 10.7% among a randomly selected group of HBsAg-ve/antiHBc+ve HIV-infected patients. Overall 33.9% (38 of 112) of the patients were antiHBc positive indicating exposure to HBV infection. HBV DNA was detected in 12/38 (31.5%) antiHBc positive samples and 50% of them had CD4 T cell count < 200 cells/mm3. HCV coinfec-tion was low (2.7%). No surrogate marker for OBI could be identified. Presence of antiHBs antibodies did not rule out OBI. Liver biopsy in six cases showed varying stages of chronic hepatitis. Several mutations were detected but not the common immune escape mutant G145R. Conclusion. In conclusion the preva-lence of OBI was significantly high among HIV coinfected patients, which highlights the importance of HBV DNA testing in these patients and indicates need for further prospective studies in larger cohorts to assess its clinical significance.


Biswas A.,ICMR Virus Unit | Panigrahi R.,ICMR Virus Unit | Banerjee A.,ICMR Virus Unit | Pal M.,University of Calcutta | And 3 more authors.
Infection, Genetics and Evolution | Year: 2012

The presence of three different HBV genotypes (A, C and D) in Eastern India provided us a unique opportunity to study HBV pre-S mutants in these genotypes and subtypes among the same ethnic population. Furthermore, we also aimed to investigate the association of the HBV pre-S mutation with clinical outcome. Pre-S1-S2 and S gene was amplified and sequenced from 86 HBsAg positive study subjects with varying clinical manifestation. The genetic variability in the pre-S region (mutations) was studied with respect to different HBV genotypes, subtypes and different clinical categories. Six different types of HBV pre-S mutations were detected in 25 cases (29.07%), among which pre-S2 start codon mutation (28.0%) and pre-S2 deletion (24.0%) were most common. Pre-S mutation was highest in HBV/C (7/18; 38.89%) followed by HBV/A (9/27; 33.33%) and HBV/D (9/40; 22.50%). Pre-S1 deletion is common in HBV/D, whereas pre-S2 start codon mutation and pre-S2 deletions are frequent among HBV/A and HBV/C, respectively. Interestingly, in HBV/A and HBV/C the tendency of mutation/deletion increases from pre-S1 to pre-S2 region while in HBV/D the opposite tendency was observed. A significantly higher association of pre-S mutation (p= 0.013) and pre-S2 deletion/ablation (p= 0.016) was found among the HBeAg negative cases. Pre-S1 deletion and pre-S2 deletion were common among the ASC and CLD cases respectively, while pre-S2 start codon mutation was significantly associated with cirrhosis (p< 0.05). The study underscores the association of types of pre-S mutations with particular HBV genotype and clinical outcome in the study population. © 2012 Elsevier B.V.


Taraphdar D.,ICMR virus unit | Sarkar A.,ICMR virus unit | Bhattacharya M.K.,Indian National Institute of Cholera and Enteric Diseases | Chatterjee S.,ICMR virus unit
Asian Pacific Journal of Tropical Medicine | Year: 2010

Objective: To investigate the outbreak of unknown fever at Siliguri town, Darjeeling District on request from the State Health Department, Government of West Bengal. Methods: Investigations were made to the affected wards, Sub Divisional Hospital and the nursing homes of Siliguri Town. Duration of illness was 3-5 days. Interesting observations were made in some cases which had gastrointestinal disorders with high serum glutamate pyruvate transaminase (SGPT) and serum glutamic oxaloacetic transaminase (SGOT) levels. A total of 69 blood samples and 7 throat swabs (in Minimum Essential Media) were collected and brought to the ICMR Virus Unit, Kolkata for analysis. Mosquitoes from different affected areas were collected for the identification of the definite vector. Results: Amongst the 69 blood samples, 42 (60.86%) were positive to IgM antibody against dengue virus by Mac enzyme-linked immunosorbent assay (ELISA) test. No IgM antibody to Japanese encephalitis virus was detected among the collected blood samples. Based on the clinical symptoms, presence of IgM antibody to dengue virus and identification of Aedes mosquito, it amply proves that, the illness of those cases were due to dengue virus infection. Conclusions: Based on clinical-epidemiological observations of the investigations the possibility of a communicable disease of viral origin, the detection of IgM antibody and the identification of Aedes egypti, and the potential circulation of denge virus in Siliguri town for the first time were all suggested. © 2010.


Sarkar A.,ICMR virus unit | Taraphdar D.,ICMR virus unit | Chatterjee S.,ICMR virus unit
Archives of Clinical Microbiology | Year: 2010

Background: In the year 2002, an investigation was conducted for the diagnosis of an unknown fever outbreak in the District of West Midnapore, West Bengal; on request of the Director of Medical Education, Govt. of West Bengal. In the year 2004, again unknown fever outbreak took place in some other area of same district and that too was investigated on request of the State Medical Department. The recurrence of same episode in the year 2007 was investigated by the local medical team and the collected serum samples were sent to us for laboratory based conformation. Methods and findings: During the first episode (2002), a total of 1158 fever cases were reported with 7 deaths, which spread all over the district since 2nd week of May till 15th July, 2002. In the second episode (2004), 792 cases were reported and 2 deaths were recorded. A total of 781 acute sera samples could be collected during these three consecutive out breaks. The samples were collected from the patients with clinical features of fever with head ache, body ache, nausea, retro orbital pain, abdominal pain and rashes of duration 2-7 days, which is closely related with the symptoms of dengue infection. Only 195 convalescent sera were made available. Acute samples were tested for the presence of dengue specific IgM antibodies by ELISA method. There was a significantly higher incidence of fever cases in children belonging to the age group up to 10 years. No virus could be isolated from the acute sera collected from fever cases. The results of serological survey showed the presence of IgM antibodies to Dengue virus in only in 446 (57%) of the acute cases. Amongst the195 convalescent sera, four fold rise of HAI Antibody titre to Dengue virus was observed only in 77 (39%). Conclusion: Analysis of the epidemiological and serological findings of different years revealed that the out breaks were due to Dengue infection. Children up to 10 years of age in this district were mostly affected during these out breaks. © iMedPub.


Chakraborty A.,ICMR Virus Unit
BMJ case reports | Year: 2012

The authors report a case of a 47-year-old cytomegalovirus (CMV) immunoglobulin G (IgG) seropositive male patient with end stage renal disease who received a live renal transplant from a CMV IgG seropositive donor. Six months post-transplantation, the patient presented with reduced renal allograft function associated with fever, severe breathlessness, new onset jaundice and pancytopenia. His CMV DNA PCR came positive. Hepatitis C virus (HCV) RNA PCR also came positive (genotype I) though anti-HCV test performed before and after transplantation was negative. The patient was treated with oral valganciclovir and showed improvement of his clinical condition and was subsequently discharged under supervised therapy. However, the patient could not be treated for HCV because of risk of renal allograft rejection. The authors suggest oral valganciclovir for management of CMV infection and proper detection and eradication of HCV before renal transplantation to avoid future complications and prolongation of allograft survival.


Datta S.,Defence Research Laboratory Tezpur | Chatterjee S.,Defence Research Laboratory Tezpur | Veer V.,Defence Research Laboratory Tezpur | Chakravarty R.,ICMR Virus Unit
Journal of Clinical and Experimental Hepatology | Year: 2012

Hepatitis B virus (HBV) infection is one of the major global health problems, especially in economically under-developed or developing countries. HBV infection can lead to a number of clinical outcomes including chronic infection, cirrhosis and liver cancer. It ranks among the top 10 causes of death, being responsible for around 1 million deaths every year. Despite the availability of a highly efficient vaccine and potent antiviral agents, HBV infection still remains a significant clinical problem, particularly in those high endemicity areas where vaccination of large populations has not been possible due to economic reasons. Although HBV is among the smallest viruses in terms of virion and genome size, it has numerous unique features that make it completely distinct from other DNA viruses. It has a partially double stranded DNA with highly complex genome organization, life cycle and natural history. Remarkably distinct from other DNA viruses, it uses an RNA intermediate called pregenomic RNA (pgRNA) and reverse transcriptase for its genome replication. Genome replication is accomplished by a complex mechanism of primer shifting facilitated by direct repeat sequences encoded in the genome. Further, the genome has evolved in such a manner that every single nucleotide of the genome is used for either coding viral proteins or used as regulatory regions or both. Moreover, it utilizes internal in-frame translation initiation codons, as well as different reading frames from the same RNA to generate different proteins with diverse functions. HBV also shows considerable genetic variability which has been related with clinical outcomes, replication potential, therapeutic response etc. This review aims at reviewing fundamental events of the viral life cycle including viral replication, transcription and translation, from the molecular standpoint, as well as, highlights the clinical relevance of genetic variability of HBV. © 2012 INASL.


PubMed | Nil Ratan Sarkar Medical College and Hospital, Calcutta National Medical College, ICMR Virus Unit and Infectious Diseases & Beliaghata General Hospital
Type: Journal Article | Journal: Journal of medical virology | Year: 2016

Dengue virus infection is a major cause of morbidity within the endemic tropical and subtropical regions of the world. Dengue virus has four distinct serotypes with specific clinical manifestations. In this study, we observed the changing pattern of dengue serotypes, age-wise dengue infection and useful sero-detection methods needed in a dengue endemic region. We identified dengue serotypes during a period of 5 years among patients with dengue symptoms visiting one of the largest tertiary care infectious disease hospitals of eastern India in Kolkata. A total of 433 dengue RNA positive samples were isolated from 712 acute dengue suspected cases. Age wise distribution highlighted the susceptible age group being >21 years (24.02%) followed by 11-15 years (21.71%) and 5-10 years (21.02%) of the total infected population. Higher numbers of infected cases were found within females as they are involved in more indoor works. The period of study experienced two dengue outbreaks one in 2008 and another in 2012. For early dengue detection, NS1 was found to be more confirmatory than IgM ELISA regarding sensitivity and specificity. DENV-1, 2, and 4 serotypes were the common circulating strains from 2008 until 2010, after which DENV-3 serotype infections rise and led to a massive dengue outbreak in Kolkata with increased numbers of DHF and DSS cases in 2012. The finding within our study emphasizes the public health importance of such prospective surveillance programs with respect to the changing dengue viral etiology and serotypes. J. Med. Virol. 88:1697-1702, 2016. 2016 Wiley Periodicals, Inc.


PubMed | ICMR Virus Unit
Type: | Journal: Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases | Year: 2016

Recombination in RNA virus is a rare event in the survival and evolution to evade host immune system. This is increasing within high risk group population (HRG) due to super infection that occurs by continuous sharing of common drug equipment by HCV infected or HIV-HCV co-infected recurrent drug users. Recombination causes impediment to vaccine development and therapeutic intervention as standard HCV treatment is still genotype specific. Blood samples of 194 people who inject drugs (PWID) were collected from an Opioid Substitution Therapy Centre in Kolkata, India. HCV sero-reactivity was checked by ELISA. Detection of HCV RNA by nested RT-PCR and genotyping by DNA sequencing were done. Phylogenetic analysis, Simplot, Bootscan plot, Recombination Detection Program were used for recombinant strain identification. Out of 80 HCV sero-reactive samples, 77 were RNA positive (96.25%). Out of 74 HIV mono-infected individuals, 12 HCV sero-nonreactive samples were HCV RNA positive. Out of total 89 RNA positive samples, 64 paired partial core and NS5B region (71.9%) were sequenced by Sangers method. Two major genotypes (1 and 3), four subtypes and an inter-genotype recombinant strain (3a/1a) with a novel breakpoint in the NS4B coding region were found.


PubMed | Defence Research Laboratory Tezpur and ICMR Virus Unit
Type: Journal Article | Journal: Journal of clinical and experimental hepatology | Year: 2015

Hepatitis B virus (HBV) infection is one of the major global health problems, especially in economically under-developed or developing countries. HBV infection can lead to a number of clinical outcomes including chronic infection, cirrhosis and liver cancer. It ranks among the top 10 causes of death, being responsible for around 1million deaths every year. Despite the availability of a highly efficient vaccine and potent antiviral agents, HBV infection still remains a significant clinical problem, particularly in those high endemicity areas where vaccination of large populations has not been possible due to economic reasons. Although HBV is among the smallest viruses in terms of virion and genome size, it has numerous unique features that make it completely distinct from other DNA viruses. It has a partially double stranded DNA with highly complex genome organization, life cycle and natural history. Remarkably distinct from other DNA viruses, it uses an RNA intermediate called pregenomic RNA (pgRNA) and reverse transcriptase for its genome replication. Genome replication is accomplished by a complex mechanism of primer shifting facilitated by direct repeat sequences encoded in the genome. Further, the genome has evolved in such a manner that every single nucleotide of the genome is used for either coding viral proteins or used as regulatory regions or both. Moreover, it utilizes internal in-frame translation initiation codons, as well as different reading frames from the same RNA to generate different proteins with diverse functions. HBV also shows considerable genetic variability which has been related with clinical outcomes, replication potential, therapeutic response etc. This review aims at reviewing fundamental events of the viral life cycle including viral replication, transcription and translation, from the molecular standpoint, as well as, highlights the clinical relevance of genetic variability of HBV.

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