This page has only limited features, please log in for full access.
Several reports have highlighted the contributions of host factors such as age, gender and co-morbidities such as diabetes, hypertension and coronary heart disease in determining COVID-19 disease severity. However, inspite of initial efforts at understanding the contributions of SARS-CoV-2 variants, most were unable to delineate causality. Hence, in this study we re-visited the contributions of different clades of viruses (G, GR and GH) along with other attributes in explaining the disparity in mortality rates among countries. A total of 26,642 high quality SARS-CoV-2 sequences were included and the A23,403G (S:D614G) variant was found to be in linkage disequilibrium with C14,408 U (RdRp: P323L). Linear regression analyses revealed increase in age [Odds ratio: 1.055 (p-value 0.000358)] and higher frequency of clade-G viruses [Odds ratio: 1.029(p-value 0.000135)] could explain 37.43% of the differences in mortality rates across the 58 countries (Multiple R-squared: 0.3743). Next, Machine-Learning algorithms LogitBoost and AdaboostM1 were applied to determine whether countries belonging to high/low mortality groups could be classified using the same attributes and accurate classification was achieved in 70.69% and 62.07% of the countries, respectively. Further, evolutionary analyses of the Indian viral population (n = 662) were carried out. Allele frequency spectrum, nucleotide diversity (π) values and negative Tajima's D values across ORFs were indicative of population expansion. Network analysis revealed the presence of two major clusters of viral haplotypes, namely, clade-G and a variant of clade L [Lv] having the RdRp:A97V amino acid change. Clade-G genomes were found to be evolving more rapidly and were also found in higher proportions in three states with highest mortality rates namely, Gujarat, Madhya Pradesh and West Bengal. Thus, the findings of this study and results from in vitro studies highlighting the role of these variants in increasing transmissibility and altering response to antivirals reflect the role of viral factors in disease prognosis.
Bhaswati Pandit; Samsiddhi Bhattacharjee; Bornali Bhattacharjee. Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. Infection, Genetics and Evolution 2021, 90, 104734 -104734.
AMA StyleBhaswati Pandit, Samsiddhi Bhattacharjee, Bornali Bhattacharjee. Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. Infection, Genetics and Evolution. 2021; 90 ():104734-104734.
Chicago/Turabian StyleBhaswati Pandit; Samsiddhi Bhattacharjee; Bornali Bhattacharjee. 2021. "Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India." Infection, Genetics and Evolution 90, no. : 104734-104734.
The first Indian cases of COVID-19 caused by SARS-Cov-2 were reported in February 29, 2020 with a history of travel from Wuhan, China and so far above 4500 deaths have been attributed to this pandemic. The objectives of this study were to characterize Indian SARS-CoV-2 genome-wide nucleotide variations, trace ancestries using phylogenetic networks and correlate state-wise distribution of viral haplotypes with differences in mortality rates. A total of 305 whole genome sequences from 19 Indian states were downloaded from GISAID. Sequences were aligned using the ancestral Wuhan-Hu genome sequence (NC_045512.2). A total of 633 variants resulting in 388 amino acid substitutions were identified. Allele frequency spectrum, and nucleotide diversity (π) values revealed the presence of higher proportions of low frequency variants and negative Tajima’s D values across ORFs indicated the presence of population expansion. Network analysis highlighted the presence of two major clusters of viral haplotypes, namely, clade G with the S:D614G, RdRp: P323L variants and a variant of clade L [Lv] having the RdRp:A97V variant. Clade G genomes were found to be evolving more rapidly into multiple sub-clusters including clade GH and GR and were also found in higher proportions in three states with highest mortality rates namely, Gujarat, Madhya Pradesh and West Bengal.
Bornali Bhattacharjee; Bhaswati Pandit. Phylogenetic clustering of the Indian SARS-CoV-2 genomes reveals the presence of distinct clades of viral haplotypes among states. 2020, 1 .
AMA StyleBornali Bhattacharjee, Bhaswati Pandit. Phylogenetic clustering of the Indian SARS-CoV-2 genomes reveals the presence of distinct clades of viral haplotypes among states. . 2020; ():1.
Chicago/Turabian StyleBornali Bhattacharjee; Bhaswati Pandit. 2020. "Phylogenetic clustering of the Indian SARS-CoV-2 genomes reveals the presence of distinct clades of viral haplotypes among states." , no. : 1.
Indiscriminate use of antibiotics has resulted in a catastrophic increase in the levels of antibiotic resistance in India. Hospitals treat critical bacterial infections and thus can serve as reservoirs of multidrug resistant (MDR) bacteria. Hence, this study was conducted to gauge the prevalence patterns of MDR bacteria in hospital wastewater. Water samples collected from 11 hospitals and 4 environmental sources belonging to 5 most-densely populated districts of West Bengal, India were grown on MacConkey and Eosin Methylene Blue agar. A total of 84 (hospital-associated = 70, environmental water sources = 14) isolates were characterized. The predominant species found in water from hospital-associated areas (HAA) were Acinetobacter baumannii (22.9%), Escherichia coli (28.6 %), and Klebsiella pneumoniae (25.7%). Greater than 75% of the HAA isolates were found to be mcr-1 gene negative and colistinresistant. Meropenem non-susceptibility was also high among the HAA isolates at 58.6%, with the presence of the carbapenemase gene and blaNDM in 67.1% of the non-susceptible isolates. Among the three predominant species, significantly higher numbers of E. coli isolates were found to be non-susceptible to meropenem ((80%), p-value = 0.00432) and amikacin (AK (90%), p-value = 0.00037). This study provides evidence for the presence of high numbers of colistin-resistant and carbapenem-hydrolyzing Proteobacteriain hospital wastewater.
Taniya Bardhan; Madhurima Chakraborty; Bornali Bhattacharjee. Prevalence of Colistin-Resistant, Carbapenem-Hydrolyzing Proteobacteria in Hospital Water Bodies and Out-Falls of West Bengal, India. International Journal of Environmental Research and Public Health 2020, 17, 1007 .
AMA StyleTaniya Bardhan, Madhurima Chakraborty, Bornali Bhattacharjee. Prevalence of Colistin-Resistant, Carbapenem-Hydrolyzing Proteobacteria in Hospital Water Bodies and Out-Falls of West Bengal, India. International Journal of Environmental Research and Public Health. 2020; 17 (3):1007.
Chicago/Turabian StyleTaniya Bardhan; Madhurima Chakraborty; Bornali Bhattacharjee. 2020. "Prevalence of Colistin-Resistant, Carbapenem-Hydrolyzing Proteobacteria in Hospital Water Bodies and Out-Falls of West Bengal, India." International Journal of Environmental Research and Public Health 17, no. 3: 1007.
: Carbapenem resistant Klebsiella pneumoniae has been highlighted to be a critical pathogen by the World Health Organization. The objectives of this study were to assess the efficacy of lactic acid (LA) against planktonic cells and biofilms formed by carbapenem-hydrolyzing K. pneumoniae isolates obtained from the nares of preterm neonates. Time-kill assays with graded percentages of (v/v) LA in water were initially carried out against planktonic cells of a meropenem (MRP)-resistant K. pneumoniae isolate, JNM11.C4. The efficacy parameters such as optimal incubation time and minimum inhibitory concentration were determined by comparing colony-forming unit counts (log(10)CFU). Scanning electron microscopy was used to visualize cell damage. Likewise, JNM11.C4 biofilms were treated with graded series of (v/v) LA. Six carbapenem-hydrolyzing isolates were next used to validate the results. A reduction of 3.6 ± 0.6 log(10) CFU/mL in JNM11.C4 planktonic cells and >3 ± 0.03log(10) CFU/mL in biofilm-forming cells were observed using 0.225% and 2% LA, respectively, after three hours. Similar decreases in viable cell-counts were observed both in the case of planktonic (˃3.6 ± 0.3log(10) CFU/mL) and biofilm-forming cells (3.8 ± 0.3log(10) CFU/mL) across all the six clinical isolates. These results indicate that LA is an effective antimicrobial against planktonic carbapenem-hydrolyzing K. pneumoniae cells and biofilms.
Taniya Bardhan; Madhurima Chakraborty; Bornali Bhattacharjee. Bactericidal Activity of Lactic Acid against Clinical, Carbapenem-Hydrolyzing, Multi-Drug-Resistant Klebsiella pneumoniae Planktonic and Biofilm-Forming Cells. Antibiotics 2019, 8, 181 .
AMA StyleTaniya Bardhan, Madhurima Chakraborty, Bornali Bhattacharjee. Bactericidal Activity of Lactic Acid against Clinical, Carbapenem-Hydrolyzing, Multi-Drug-Resistant Klebsiella pneumoniae Planktonic and Biofilm-Forming Cells. Antibiotics. 2019; 8 (4):181.
Chicago/Turabian StyleTaniya Bardhan; Madhurima Chakraborty; Bornali Bhattacharjee. 2019. "Bactericidal Activity of Lactic Acid against Clinical, Carbapenem-Hydrolyzing, Multi-Drug-Resistant Klebsiella pneumoniae Planktonic and Biofilm-Forming Cells." Antibiotics 8, no. 4: 181.
Bornali Bhattacharjee; Taniya Bardhan; Madhurima Chakraborty; Manjari Basu. Resistance profiles and resistome mapping of multidrug resistant carbapenem-hydrolyzing Klebsiella pneumoniae strains isolated from the nares of preterm neonates. International Journal of Antimicrobial Agents 2018, 53, 535 -537.
AMA StyleBornali Bhattacharjee, Taniya Bardhan, Madhurima Chakraborty, Manjari Basu. Resistance profiles and resistome mapping of multidrug resistant carbapenem-hydrolyzing Klebsiella pneumoniae strains isolated from the nares of preterm neonates. International Journal of Antimicrobial Agents. 2018; 53 (4):535-537.
Chicago/Turabian StyleBornali Bhattacharjee; Taniya Bardhan; Madhurima Chakraborty; Manjari Basu. 2018. "Resistance profiles and resistome mapping of multidrug resistant carbapenem-hydrolyzing Klebsiella pneumoniae strains isolated from the nares of preterm neonates." International Journal of Antimicrobial Agents 53, no. 4: 535-537.
Human papillomavirus type 16 (HPV16), a member of the Papillomaviridae family, is the primary etiological agent of cervical cancer. Here, we report the complete genome sequences of four HPV16 Asian American variants and four European variants, isolated from cervical biopsies and scrapings in India.
Paramita Mandal; Bornali Bhattacharjee; Shrinka Sen; Amrapali Bhattacharya; Rahul Roy Chowdhury; Nidhu Ranjan Mondal; Sharmila Sengupta. Complete Genome Sequences of Eight Human Papillomavirus Type 16 Asian American and European Variant Isolates from Cervical Biopsies and Lesions in Indian Women. Genome Announcements 2016, 4, e00243-16 .
AMA StyleParamita Mandal, Bornali Bhattacharjee, Shrinka Sen, Amrapali Bhattacharya, Rahul Roy Chowdhury, Nidhu Ranjan Mondal, Sharmila Sengupta. Complete Genome Sequences of Eight Human Papillomavirus Type 16 Asian American and European Variant Isolates from Cervical Biopsies and Lesions in Indian Women. Genome Announcements. 2016; 4 (3):e00243-16.
Chicago/Turabian StyleParamita Mandal; Bornali Bhattacharjee; Shrinka Sen; Amrapali Bhattacharya; Rahul Roy Chowdhury; Nidhu Ranjan Mondal; Sharmila Sengupta. 2016. "Complete Genome Sequences of Eight Human Papillomavirus Type 16 Asian American and European Variant Isolates from Cervical Biopsies and Lesions in Indian Women." Genome Announcements 4, no. 3: e00243-16.
Human cytomegalovirus (HCMV) exhibits surprisingly high genomic diversity during natural infection although little is known about the limits or patterns of HCMV diversity among humans. To address this deficiency, we analyzed genomic diversity among congenitally infected infants. We show that there is an upper limit to HCMV genomic diversity in these patient samples, with ∼25% of the genome being devoid of polymorphisms. These low diversity regions were distributed across 26 loci that were preferentially located in DNA-processing genes. Furthermore, by developing, to our knowledge, the first genome-wide mutation and recombination rate maps for HCMV, we show that genomic diversity is positively correlated with these two rates. In contrast, median levels of viral genomic diversity did not vary between putatively single or mixed strain infections. We also provide evidence that HCMV populations isolated from vascular compartments of hosts from different continents are genetically similar and that polymorphisms in glycoproteins and regulatory proteins are enriched in these viral populations. This analysis provides the most highly detailed map of HCMV genomic diversity in human hosts to date and informs our understanding of the distribution of HCMV genomic diversity within human hosts.
Nicholas Renzette; Cornelia Pokalyuk; Laura Gibson; Bornali Bhattacharjee; Mark R. Schleiss; Klaus Hamprecht; Aparecida Y. Yamamoto; Marisa M Mussi-Pinhata; William J. Britt; Jeffrey D. Jensen; Timothy F. Kowalik. Limits and patterns of cytomegalovirus genomic diversity in humans. Proceedings of the National Academy of Sciences 2015, 112, E4120 -E4128.
AMA StyleNicholas Renzette, Cornelia Pokalyuk, Laura Gibson, Bornali Bhattacharjee, Mark R. Schleiss, Klaus Hamprecht, Aparecida Y. Yamamoto, Marisa M Mussi-Pinhata, William J. Britt, Jeffrey D. Jensen, Timothy F. Kowalik. Limits and patterns of cytomegalovirus genomic diversity in humans. Proceedings of the National Academy of Sciences. 2015; 112 (30):E4120-E4128.
Chicago/Turabian StyleNicholas Renzette; Cornelia Pokalyuk; Laura Gibson; Bornali Bhattacharjee; Mark R. Schleiss; Klaus Hamprecht; Aparecida Y. Yamamoto; Marisa M Mussi-Pinhata; William J. Britt; Jeffrey D. Jensen; Timothy F. Kowalik. 2015. "Limits and patterns of cytomegalovirus genomic diversity in humans." Proceedings of the National Academy of Sciences 112, no. 30: E4120-E4128.
International audienceThe inflammatory cytokine IL-1β is critical for host responses against many human pathogens. Here, we define Group B Streptococcus (GBS)-mediated activation of the Nod-like receptor-P3 (NLRP3) inflammasome in macrophages. NLRP3 activation requires GBS expression of the cytolytic toxin, β-hemolysin, lysosomal acidification, and leakage. These processes allow the interaction of GBS RNA with cytosolic NLRP3. The present study supports a model in which GBS RNA, along with lysosomal components including cathepsins, leaks out of lysosomes and interacts with NLRP3 to induce IL-1β production
Rahul Gupta; Shubhendu Ghosh; Brian Monks; Rosane B. DeOliveira; Te-Chen Tzeng; Parisa Kalantari; Anubhab Nandy; Bornali Bhattacharjee; Jennie Chan; Fabianno Ferreira; Vijay Rathinam; Shruti Sharma; Egil Lien; Neal Silverman; Kate Fitzgerald; Arnaud Firon; Patrick Trieu-Cuot; Philipp Henneke; Douglas T. Golenbock. RNA and β-Hemolysin of Group B Streptococcus Induce Interleukin-1β (IL-1β) by Activating NLRP3 Inflammasomes in Mouse Macrophages. Journal of Biological Chemistry 2014, 289, 13701 -13705.
AMA StyleRahul Gupta, Shubhendu Ghosh, Brian Monks, Rosane B. DeOliveira, Te-Chen Tzeng, Parisa Kalantari, Anubhab Nandy, Bornali Bhattacharjee, Jennie Chan, Fabianno Ferreira, Vijay Rathinam, Shruti Sharma, Egil Lien, Neal Silverman, Kate Fitzgerald, Arnaud Firon, Patrick Trieu-Cuot, Philipp Henneke, Douglas T. Golenbock. RNA and β-Hemolysin of Group B Streptococcus Induce Interleukin-1β (IL-1β) by Activating NLRP3 Inflammasomes in Mouse Macrophages. Journal of Biological Chemistry. 2014; 289 (20):13701-13705.
Chicago/Turabian StyleRahul Gupta; Shubhendu Ghosh; Brian Monks; Rosane B. DeOliveira; Te-Chen Tzeng; Parisa Kalantari; Anubhab Nandy; Bornali Bhattacharjee; Jennie Chan; Fabianno Ferreira; Vijay Rathinam; Shruti Sharma; Egil Lien; Neal Silverman; Kate Fitzgerald; Arnaud Firon; Patrick Trieu-Cuot; Philipp Henneke; Douglas T. Golenbock. 2014. "RNA and β-Hemolysin of Group B Streptococcus Induce Interleukin-1β (IL-1β) by Activating NLRP3 Inflammasomes in Mouse Macrophages." Journal of Biological Chemistry 289, no. 20: 13701-13705.
Populations of human cytomegalovirus (HCMV), a large DNA virus, are highly polymorphic in patient samples, which may allow for rapid evolution within human hosts. To understand HCMV evolution, longitudinally sampled genomic populations from the urine and plasma of 5 infants with symptomatic congenital HCMV infection were analyzed. Temporal and compartmental variability of viral populations were quantified using high throughput sequencing and population genetics approaches. HCMV populations were generally stable over time, with ∼88% of SNPs displaying similar frequencies. However, samples collected from plasma and urine of the same patient at the same time were highly differentiated with approximately 1700 consensus sequence SNPs (1.2% of the genome) identified between compartments. This inter-compartment differentiation was comparable to the differentiation observed in unrelated hosts. Models of demography (i.e., changes in population size and structure) and positive selection were evaluated to explain the observed patterns of variation. Evidence for strong bottlenecks (>90% reduction in viral population size) was consistent among all patients. From the timing of the bottlenecks, we conclude that fetal infection occurred between 13–18 weeks gestational age in patients analyzed, while colonization of the urine compartment followed roughly 2 months later. The timing of these bottlenecks is consistent with the clinical histories of congenital HCMV infections. We next inferred that positive selection plays a small but measurable role in viral evolution within a single compartment. However, positive selection appears to be a strong and pervasive driver of evolution associated with compartmentalization, affecting ≥34 of the 167 open reading frames (∼20%) of the genome. This work offers the most detailed map of HCMV in vivo evolution to date and provides evidence that viral populations can be stable or rapidly differentiate, depending on host environment. The application of population genetic methods to these data provides clinically useful information, such as the timing of infection and compartment colonization. The large, dsDNA virus Human cytomegalovirus (HCMV) is the most genetically complex viral pathogen of humans. HCMV populations are highly variable, which may allow the virus to evolve in human hosts on short timescales. We tested this hypothesis by longitudinally sampling HCMV populations from the urine and/or plasma of congenitally infected infants. We found that HCMV is generally stable within a compartment, but rapidly evolves when crossing host compartments. In fact, HCMV sampled from two compartments of the same host is as different as HCMV collected from unrelated hosts. We used mathematical modeling and population genetic analysis to show that both a bottleneck (i.e., a reduction in population size) associated with compartment colonization as well as positive selection are necessary to explain the observed differences between compartments. We also conclude from these data that fetal infection in these patients occurred between 13–18 weeks gestational age, consistent with the timing of symptomatic congenital HCMV infections. This study is the most detailed investigation of DNA virus evolution in human hosts to date, provides a framework for the study of other viral infections using similar techniques, and will aid in the development of new antiviral therapies and vaccines.
Nicholas Renzette; Laura Gibson; Bornali Bhattacharjee; Donna Fisher; Mark R. Schleiss; Jeffrey D. Jensen; Timothy F. Kowalik. Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection. PLoS Genetics 2013, 9, e1003735 .
AMA StyleNicholas Renzette, Laura Gibson, Bornali Bhattacharjee, Donna Fisher, Mark R. Schleiss, Jeffrey D. Jensen, Timothy F. Kowalik. Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection. PLoS Genetics. 2013; 9 (9):e1003735.
Chicago/Turabian StyleNicholas Renzette; Laura Gibson; Bornali Bhattacharjee; Donna Fisher; Mark R. Schleiss; Jeffrey D. Jensen; Timothy F. Kowalik. 2013. "Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection." PLoS Genetics 9, no. 9: e1003735.
We tested the hypothesis that (i) synonymous variations within the coding regions, and (ii) variations within the non-coding regions of HPV, influence cervical cancer (CaCx) pathogenesis under the impact of intact HPV16 genomes. Whole genome sequence analysis of HPV16 isolates within 70 CaCx cases and 25 non-malignant samples revealed that synonymous variations were significantly higher within the E6 (p = 0.014), E5 (p = 0.001) and L2 (p = 0.0002) genes of HPV16 isolates within cases, compared to isolates within non-malignant samples. All of the 25 (100%) humanized codons identified within L2 ORF of the samples analyzed, were harbored by CaCx cases, while 8 out of 25 (32%) were harbored by HPV16 positive non-malignant samples (p = 3.87105E-07). L2 (mRNA and protein) expression was evident only among cases with episomal viral genomes and L2 mRNA expression correlated significantly with E2 gene copy numbers suggesting expression from all episomal genomes. Among such cases, Asian American (AA) isolates portrayed all of the humanized codons (100%; 4–6/sample) recorded within L2, which was significantly higher (p = 2.02E-7) compared to the European (E) isolates (22.8%; none or 1–2/sample). Additionally, majority of E variant isolates within cases (54/57; 94.7%) portrayed a variation (T4228C) within the short non-coding region (NCR2) between E5 and L2 genes, which portrays a weak promoter activity specific for L2 mRNA expression. This resulted in loss of 9 out of 14 miRNA binding sites (hsa-miR-548 family), despite the significant overexpression of miR548a-5p and miR548d-5p among such cases (28.64 and 36.25 folds, respectively), in comparison to HPV negative control samples. The findings exemplify the biological relevance of sequence variations in HPV16 genomes and highlight that episomal HPV16 in CaCx cases employ multiple mechanisms to sustain L2 expression, thereby justifying the potential role of L2 in such cancers, as opposed to those harboring viral integration.
Paramita Mandal; Bornali Bhattacharjee; Damayanti Das Ghosh; Nidhu Ranjan Mondal; Rahul Roy Chowdhury; Sudipta Roy; Sharmila Sengupta. Differential Expression of HPV16 L2 Gene in Cervical Cancers Harboring Episomal HPV16 Genomes: Influence of Synonymous and Non-Coding Region Variations. PLOS ONE 2013, 8, e65647 .
AMA StyleParamita Mandal, Bornali Bhattacharjee, Damayanti Das Ghosh, Nidhu Ranjan Mondal, Rahul Roy Chowdhury, Sudipta Roy, Sharmila Sengupta. Differential Expression of HPV16 L2 Gene in Cervical Cancers Harboring Episomal HPV16 Genomes: Influence of Synonymous and Non-Coding Region Variations. PLOS ONE. 2013; 8 (6):e65647.
Chicago/Turabian StyleParamita Mandal; Bornali Bhattacharjee; Damayanti Das Ghosh; Nidhu Ranjan Mondal; Rahul Roy Chowdhury; Sudipta Roy; Sharmila Sengupta. 2013. "Differential Expression of HPV16 L2 Gene in Cervical Cancers Harboring Episomal HPV16 Genomes: Influence of Synonymous and Non-Coding Region Variations." PLOS ONE 8, no. 6: e65647.
This study was undertaken to decipher the interdependent roles of (i) methylation within E2 binding site I and II (E2BS-I/II) and replication origin (nt 7862) in the long control region (LCR), (ii) expression of viral oncogene E7, (iii) expression of the transcript (E7-E1∧E4) that encodes E2 repressor protein and (iv) viral load, in human papillomavirus 16 (HPV16) related cervical cancer (CaCx) pathogenesis. The results revealed over-representation (p<0.001) of methylation at nucleotide 58 of E2BS-I among E2-intact CaCx cases compared to E2-disrupted cases. Bisulphite sequencing of LCR revealed overrepresentation of methylation at nucleotide 58 or other CpGs in E2BS-I/II, among E2-intact cases than E2-disrupted cases and lack of methylation at replication origin in case of both. The viral transcript (E7-E1∧E4) that produces the repressor E2 was analyzed by APOT (amplification of papillomavirus oncogenic transcript)-coupled-quantitative-RT-PCR (of E7 and E4 genes) to distinguish episomal (pure or concomitant with integrated) from purely integrated viral genomes based on the ratio, E7 CT/E4 CT. Relative quantification based on comparative CT (theshold cycle) method revealed 75.087 folds higher E7 mRNA expression in episomal cases over purely integrated cases. Viral load and E2 gene copy numbers were negatively correlated with E7 CT (p = 0.007) and E2 CT (p<0.0001), respectively, each normalized with ACTB CT, among episomal cases only. The k-means clustering analysis considering E7 CT from APOT-coupled-quantitative-RT-PCR assay, in conjunction with viral load, revealed immense heterogeneity among the HPV16 positive CaCx cases portraying integrated viral genomes. The findings provide novel insights into HPV16 related CaCx pathogenesis and highlight that CaCx cases that harbour episomal HPV16 genomes with intact E2 are likely to be distinct biologically, from the purely integrated viral genomes in terms of host genes and/or pathways involved in cervical carcinogenesis.
Damayanti Das Ghosh; Bornali Bhattacharjee; Shrinka Sen; Laikangbam Premi; Indranil Mukhopadhyay; Rahul Roy Chowdhury; Sudipta Roy; Sharmila Sengupta. Some Novel Insights on HPV16 Related Cervical Cancer Pathogenesis Based on Analyses of LCR Methylation, Viral Load, E7 and E2/E4 Expressions. PLOS ONE 2012, 7, e44678 .
AMA StyleDamayanti Das Ghosh, Bornali Bhattacharjee, Shrinka Sen, Laikangbam Premi, Indranil Mukhopadhyay, Rahul Roy Chowdhury, Sudipta Roy, Sharmila Sengupta. Some Novel Insights on HPV16 Related Cervical Cancer Pathogenesis Based on Analyses of LCR Methylation, Viral Load, E7 and E2/E4 Expressions. PLOS ONE. 2012; 7 (9):e44678.
Chicago/Turabian StyleDamayanti Das Ghosh; Bornali Bhattacharjee; Shrinka Sen; Laikangbam Premi; Indranil Mukhopadhyay; Rahul Roy Chowdhury; Sudipta Roy; Sharmila Sengupta. 2012. "Some Novel Insights on HPV16 Related Cervical Cancer Pathogenesis Based on Analyses of LCR Methylation, Viral Load, E7 and E2/E4 Expressions." PLOS ONE 7, no. 9: e44678.
Human cytomegalovirus (HCMV) has been found in malignant gliomas at variable frequencies with efforts to date focused on characterizing the role(s) of single gene products in disease. Here, we reexamined the HCMV prevalence in malignant gliomas using different methods and began to dissect the genetics of HCMV in tumors. HCMV DNA was found in 16/17 (94%) tumor specimens. Viral DNA copy numbers were found to be low and variable, ranging from 10 2 to 10 6 copies/500 ng of total DNA. The tumor tissues had incongruences between viral DNA copy numbers and protein levels. However, nonlatent protein expression was detected in many tumors. The viral UL83 gene, encoding pp65, was found to segregate into five cancer-associated genotypes with a bias for amino acid changes in glioblastoma multiforme (GBM) in comparison to the low-grade tumors. Deep sequencing of a GBM-associated viral population resulted in 81,224 bp of genome coverage. Sequence analysis revealed the presence of intact open reading frames and higher numbers of high-frequency variations within the repeat long region compared to the unique long region, which harbors many core genes, and the unique short region ( P = 0.001). This observation was in congruence with phylogenetic analyses across replication-competent viral strains in databases. The tumor-associated viral population was less variable (π = 0.1% and π AA = 0.08%) than that observed in other clinical infections. Moreover, 42/46 (91.3%) viral genes analyzed had dN/dS scores of <1, which is indicative of high amino acid sequence conservation. Taken together, these findings raise the possibility that replication-competent HCMV may exist in malignant gliomas.
Bornali Bhattacharjee; Nicholas Renzette; Timothy F. Kowalik. Genetic Analysis of Cytomegalovirus in Malignant Gliomas. Journal of Virology 2012, 86, 6815 -6824.
AMA StyleBornali Bhattacharjee, Nicholas Renzette, Timothy F. Kowalik. Genetic Analysis of Cytomegalovirus in Malignant Gliomas. Journal of Virology. 2012; 86 (12):6815-6824.
Chicago/Turabian StyleBornali Bhattacharjee; Nicholas Renzette; Timothy F. Kowalik. 2012. "Genetic Analysis of Cytomegalovirus in Malignant Gliomas." Journal of Virology 86, no. 12: 6815-6824.
Research has shown that RNA virus populations are highly variable, most likely due to low fidelity replication of RNA genomes. It is generally assumed that populations of DNA viruses will be less complex and show reduced variability when compared to RNA viruses. Here, we describe the use of high throughput sequencing for a genome wide study of viral populations from urine samples of neonates with congenital human cytomegalovirus (HCMV) infections. We show that HCMV intrahost genomic variability, both at the nucleotide and amino acid level, is comparable to many RNA viruses, including HIV. Within intrahost populations, we find evidence of selective sweeps that may have resulted from immune-mediated mechanisms. Similarly, genome wide, population genetic analyses suggest that positive selection has contributed to the divergence of the HCMV species from its most recent ancestor. These data provide evidence that HCMV, a virus with a large dsDNA genome, exists as a complex mixture of genome types in humans and offer insights into the evolution of the virus. Human Cytomegalovirus (HCMV) is a dsDNA virus that is the leading source of birth defects associated with an infectious agent. There is currently no effective HCMV vaccine and few treatment strategies for congenital infections exist. Thus, a better understanding of HCMV infections is warranted. Limited data has shown that HCMV exists as a mixture of a few genotypes in human hosts. Here, we describe our use of high throughput sequencing to study the extent of genome wide variability within HCMV infections sampled from congenital infections. Surprisingly, we find that HCMV populations are as variable as quasispecies RNA viruses; it is commonly believed that DNA viruses are more genetically stable than RNA viruses, and thus produce homogenous populations. Additionally, we find evidence of evolutionary pressures acting on the HCMV genome, both within and among populations. These results provide the first evidence that diversity of DNA virus populations can be comparable to that of RNA virus populations.
Nicholas Renzette; Bornali Bhattacharjee; Jeffrey Jensen; Laura Gibson; Timothy F. Kowalik. Extensive Genome-Wide Variability of Human Cytomegalovirus in Congenitally Infected Infants. PLOS Pathogens 2011, 7, e1001344 .
AMA StyleNicholas Renzette, Bornali Bhattacharjee, Jeffrey Jensen, Laura Gibson, Timothy F. Kowalik. Extensive Genome-Wide Variability of Human Cytomegalovirus in Congenitally Infected Infants. PLOS Pathogens. 2011; 7 (5):e1001344.
Chicago/Turabian StyleNicholas Renzette; Bornali Bhattacharjee; Jeffrey Jensen; Laura Gibson; Timothy F. Kowalik. 2011. "Extensive Genome-Wide Variability of Human Cytomegalovirus in Congenitally Infected Infants." PLOS Pathogens 7, no. 5: e1001344.
We tested the hypothesis that cervical cancers (CaCx) harbor high HPV16 viral load compared to controls and this is influenced by E2 status and age of subjects. Viral load (natural log transformed values) per 100ng genomic DNA was estimated (152 cases and 87 controls) by Taqman assay. Median viral load was significantly higher (Mann-Whitney U test) among cases (17.21) compared to controls (9.86), irrespective of E2 status or upon considering E2 status as a covariate in logistic regression model (p<0.001). Viral load of E2 intact cases (17.80) was significantly higher (p<0.001) compared to those with disrupted E2 (9.78). At equivalent probability of being a case, viral load was higher among individuals (i) of lower age, irrespective of E2 status, and (ii) with intact E2 but of similar age as those with disrupted E2. Thus viral load in association with E2 status and/or age might be of causal relevance in CaCx pathogenesis.
Damayanti Das; Bornali Bhattacharjee; Shrinka Sen; Indranil Mukhopadhyay; Sharmila Sengupta. Association of viral load with HPV16 positive cervical cancer pathogenesis: Causal relevance in isolates harboring intact viral E2 gene. Virology 2010, 402, 197 -202.
AMA StyleDamayanti Das, Bornali Bhattacharjee, Shrinka Sen, Indranil Mukhopadhyay, Sharmila Sengupta. Association of viral load with HPV16 positive cervical cancer pathogenesis: Causal relevance in isolates harboring intact viral E2 gene. Virology. 2010; 402 (1):197-202.
Chicago/Turabian StyleDamayanti Das; Bornali Bhattacharjee; Shrinka Sen; Indranil Mukhopadhyay; Sharmila Sengupta. 2010. "Association of viral load with HPV16 positive cervical cancer pathogenesis: Causal relevance in isolates harboring intact viral E2 gene." Virology 402, no. 1: 197-202.
We re-sequenced HPV16 genome (~6 kb) implicated in cervical carcinogenesis (LCR, E2, E5, E6, E7, L1, L2) to prioritize sequence variants for functional validation as biomarkers, using CaCx cases (n=74) and asymptomatic controls (n=24). Of the nucleotide variations recorded (n=271), non-synonymous changes in L2 region were significantly higher (p=0.005) among cases (2.67%) compared to controls (1.27%). Using SIFT database, 29 non-synonymous changes (frequency=0.01-0.03) predicted as deleterious to protein functions were identified. Haplotype analysis considering 110 polymorphic variations (frequency> or =0.05) within intact viral isolates (53 CaCx cases and 21 controls) using NETWORK software, confirmed Asian-American (AA, 14.86%) and European (E, 85.14%) variants, differing at 78 positions. The E-variants portrayed thirty-six haplotypes, of which, E-12 was most prevalent within cases (38.1%; 16/42) and controls (28.57%; 6/21) harboring polymorphic variations at 10 positions, in contrast to HPV16R. Cases of the E-12 haplotype harbored 7 deleterious mutations distributed within L1 (n=1), E2 (n=1), E5 (n=1), and L2 (n=4), while none within similar controls. Thus rare deleterious variations within genes implicated in productive infection over the E-12 haplotype background of intact HPV16 isolates might be of causal relevance for CaCx development.
Bornali Bhattacharjee; Nidhu Ranjan Mandal; Sudipta Roy; Sharmila Sengupta. Characterization of sequence variations within HPV16 isolates among Indian women: Prediction of causal role of rare non-synonymous variations within intact isolates in cervical cancer pathogenesis. Virology 2008, 377, 143 -150.
AMA StyleBornali Bhattacharjee, Nidhu Ranjan Mandal, Sudipta Roy, Sharmila Sengupta. Characterization of sequence variations within HPV16 isolates among Indian women: Prediction of causal role of rare non-synonymous variations within intact isolates in cervical cancer pathogenesis. Virology. 2008; 377 (1):143-150.
Chicago/Turabian StyleBornali Bhattacharjee; Nidhu Ranjan Mandal; Sudipta Roy; Sharmila Sengupta. 2008. "Characterization of sequence variations within HPV16 isolates among Indian women: Prediction of causal role of rare non-synonymous variations within intact isolates in cervical cancer pathogenesis." Virology 377, no. 1: 143-150.
Human papillomavirus type 16 (HPV-16) E2 protein negatively regulates transcription of the E6 and E7 genes. This study was done to test the hypothesis that methylation of the HPV 16 long control region (LCR) is overrepresented among cervical cancer (CaCx) cases compared to cytologically normal controls harboring intact E2 gene. Methylation of the E2 binding site (E2BS-I), proximal to the P97 promoter, was assessed by HpaII/ MspI restriction digestion while McrBC digestion was used to assess LCR-E6 (7289-540) for 57 CaCx samples and 15 normal controls. E2BS-I methylation was found to be significantly higher (56.14%) in cases compared to (20%) controls [OR(age-adjusted) (95% CI): 4.53 (1.05-19.43) p=0.042]. The difference between cases (54.39%) and controls (40%) with respect to LCR-E6 methylation status [OR(age-adjusted) (95% CI): 1.77(0.5-6.3); p=0.38] was not significant. Sequencing of a randomly selected set of 13 methylated malignant samples revealed absence or rare presence, of methylation at CpGs 7579, 7535, 7683 and 7862 respectively. Methylation was found to be more at CpGs within E2 binding sites proximal to the P97 promoter. These results indicate the involvement of E2 binding site methylation in presence of intact E2, leading to loss of E2 repressor activity in CaCx.
Bornali Bhattacharjee; Sharmila Sengupta. CpG methylation of HPV 16 LCR at E2 binding site proximal to P97 is associated with cervical cancer in presence of intact E2. Virology 2006, 354, 280 -285.
AMA StyleBornali Bhattacharjee, Sharmila Sengupta. CpG methylation of HPV 16 LCR at E2 binding site proximal to P97 is associated with cervical cancer in presence of intact E2. Virology. 2006; 354 (2):280-285.
Chicago/Turabian StyleBornali Bhattacharjee; Sharmila Sengupta. 2006. "CpG methylation of HPV 16 LCR at E2 binding site proximal to P97 is associated with cervical cancer in presence of intact E2." Virology 354, no. 2: 280-285.
We evaluated the status of the HPV16 E2 gene (disrupted or intact), nucleotide sequence alterations within intact E2 genes and LCR of HPV16 isolates in a group of CaCx cases (invasive squamous cell carcinomas, n = 81) and population controls (normal cervical scrapes, n = 27) from Indian women. E2 disruption was detected by amplifying the entire E2 gene with single set of primers, while overlapping primers were used to determine if any particular region got selectively disrupted. Nucleotide variations in E2 and LCR were analyzed by PCR amplification followed by bi-directional sequencing. The associations between the viral factors and CaCx were analyzed using Fisher's Exact or Chi-squared test and interpreted as OR (95% CI) and P values. E2 disruption was significantly higher among the cases [3.38 (1.07–10.72); P = 0.02], which was maximum in the region between nucleotides 3650 and 3872 (DNA-binding region). The European (E) variant was found to be the prevalent subgroup (87.76% among cases and 96.30% among the controls), and the remaining samples were Asian-American variants. Among the E subgroup, variation at position 7450 (T > C) within the E2-binding site-IV was found to be significantly higher among the E2 undisrupted cases (21/37; 56.76%), compared to controls (5/18; 27.78%) [3.41 (1.01–11.55); P = 0.03]. Besides HPV16 E2 disruption, LCR 7450T > C variation within undisrupted E2 of E subgroup appears to be a major factor contributing to the risk of CaCx development in Indian women. Furthermore, polymorphisms in the E2 gene of HPV16 may not be significant for disease risk.
Bornali Bhattacharjee; Sharmila Sengupta. HPV16 E2 gene disruption and polymorphisms of E2 and LCR: Some significant associations with cervical cancer in Indian women. Gynecologic Oncology 2006, 100, 372 -378.
AMA StyleBornali Bhattacharjee, Sharmila Sengupta. HPV16 E2 gene disruption and polymorphisms of E2 and LCR: Some significant associations with cervical cancer in Indian women. Gynecologic Oncology. 2006; 100 (2):372-378.
Chicago/Turabian StyleBornali Bhattacharjee; Sharmila Sengupta. 2006. "HPV16 E2 gene disruption and polymorphisms of E2 and LCR: Some significant associations with cervical cancer in Indian women." Gynecologic Oncology 100, no. 2: 372-378.