DP1, a multifaceted synthetic peptide: Mechanism of action, activity and clinical potential

AIMS

Microbial infections remain a leading cause of mortality worldwide, with Staphylococcus aureus (S. aureus) being a prominent etiological agent, responsible for causing persistent bacterial infections in humans. It is a nosocomial, opportunistic pathogen, capable to propagate within the bloodstream and withstand therapeutic interventions. In the current study, a novel, indigenously designed synthetic antimicrobial peptide (sAMP) has been evaluated for its antimicrobial potential to inhibit the growth and proliferation of S. aureus.

MAIN METHODS

The sAMP, designed peptide (DP1) was evaluated for its minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) against a panel of pathogenic bacterial strains. Membrane mechanistic studies were performed by measuring membrane conductivity via dielectric spectroscopy and visualizing changes in bacterial membrane structure through field emission scanning electron microscopy (FE-SEM). Further, DP1 was tested for its in vivo antimicrobial potential in an S. aureus-induced systemic infection model.

KEY FINDINGS

The results indicated that DP1 has the potential to inhibit the growth and proliferation of a broad spectrum of Gram-positive, Gram-negative and multidrug-resistant (MDR) bacterial strains. Strong bactericidal effect attributed to change in electrical conductivity of the bacterial cells leading to membrane disruption was observed through dielectric spectroscopy and FE-SEM micrographs. Further, in the in vivo murine systemic infection study, 50 % reduction in S. aureus bioburden was observed within 1 day of the administration of DP1.

SIGNIFICANCE

The results indicate that DP1 is a multifaceted peptide with potent bactericidal, antioxidant and therapeutic properties. It holds significance as a novel drug candidate to effectively combat S. aureus-mediated systemic infections.

In Vivo Acute Toxicity and Therapeutic Potential of a Synthetic Peptide, DP1 in a Staphylococcus aureus Infected Murine Wound Excision Model

Bacterial infections at the surgical sites are one of the most prevalent skin infections that impair the healing mechanism. They account for about 20% of all types of infections and lead to approximately 75% of surgical-site infection-associated mortality. Several antibiotics, such as cephalosporins, fluoroquinolones, quinolones, penicillin, sulfonamides, etc., that are used to treat such wound infections not only counter infections but also disrupt the normal flora. Moreover, antibiotics, when used for a prolonged duration, may impair the formation of new blood vessels, delay collagen production, or inhibit the migration of certain cells involved in wound repair, leading to an impaired healing process. Therefore, there is a dire need for alternate therapeutic approaches against such infections. Antimicrobial peptides have gained considerable attention as a promising strategy to counter these pathogens and prevent the spread of infection. Recently, we have reported a designed peptide, DP1, and its broad-spectrum in vitro antimicrobial activity against Gram-positive and Gram-negative bacteria. In the present study, in vivo acute toxicity of DP1 was evaluated and even at a high dose (20 mg/kg body weight) of DP1, a 100% survival of mice was observed. Subsequently, a Staphylococcus aureus-infected murine wound excision model was established to assess the wound healing efficacy of DP1. The study revealed significant wound healing vis-a-vis attenuated S. aureus bioburden at the wound site and also controlled the oxidative stress depicting anti-oxidant activity as well. Healing of the infected wounds was also verified by histopathological examination. Based on the results of this study, it can be concluded that DP1 improves wound resolution despite infections and promotes the healing mechanism. Hence, DP1 holds compelling potential as a novel antimicrobial drug that requires further explorations in clinical platforms.

Strategic Approaches to Improvise Peptide Drugs as Next Generation Therapeutics

In recent years, the occurrence of a wide variety of drug-resistant diseases has led to an increase in interest in alternate therapies. Peptide-based drugs as an alternate therapy hold researchers' attention in various therapeutic fields such as neurology, dermatology, oncology, metabolic diseases, etc. Previously, they had been overlooked by pharmaceutical companies due to certain limitations such as proteolytic degradation, poor membrane permeability, low oral bioavailability, shorter half-life, and poor target specificity. Over the last two decades, these limitations have been countered by introducing various modification strategies such as backbone and side-chain modifications, amino acid substitution, etc. which improve their functionality. This has led to a substantial interest of researchers and pharmaceutical companies, moving the next generation of these therapeutics from fundamental research to the market. Various chemical and computational approaches are aiding the production of more stable and long-lasting peptides guiding the formulation of novel and advanced therapeutic agents. However, there is not a single article that talks about various peptide design approaches i.e., in-silico and in-vitro along with their applications and strategies to improve their efficacy. In this review, we try to bring different aspects of peptide-based therapeutics under one article with a clear focus to cover the missing links in the literature. This review draws emphasis on various in-silico approaches and modification-based peptide design strategies. It also highlights the recent progress made in peptide delivery methods important for their enhanced clinical efficacy. The article would provide a bird's-eye view to researchers aiming to develop peptides with therapeutic applications.

Graphical Abstract

Post-operative atrial fibrillation: not just a transient phenomenon

Funding Acknowledgements

Type of funding sources: None.

Background

A high proportion of patients undergoing cardiac surgery develop atrial fibrillation (AF) in the immediate post-operative period. To assess whether this translates into long-term AF, studies have used incidence of stroke as a surrogate marker, however the rhythm has not been directly measured. Our study retrospectively reviewed device checks of patients with permanent cardiac devices who underwent cardiac surgery in order to directly measure AF up to 18 months post cardiac surgery.

Purpose

To assess whether the development AF in the immediate post-operative period relates to the prevalence of longer-term AF after cardiac surgery.

Methods

Patients who had undergone a coronary artery bypass graft (CABG) or valve surgery between January 2011 and March 2020 and who had a pre-existing device or a device inserted within 1 year after surgery were identified. Patients were excluded if they had a congenital cardiac condition or a diagnosis of AF pre-operatively. Patients were categorised as having AF in the immediate post-operative period if AF was coded in the electronic ICU observation chart, mentioned on the discharge summary, or found in a device check <6 weeks post-surgery. Device checks were analysed up to 18 months post-surgery and AF was confirmed if lasting >6 minutes and documented on atrial electrogram (EGM). Comorbidities and operation details were gathered from institutional surgical database and medical notes.

Results

359 patients at our institution met initial criteria. 94 had device checks available and were used for final analysis. Mean follow up duration was 377 days. In total 41 (44%) patients developed AF in the immediate post-operative period. Patients developing post-op AF were older (69 vs. 64 years old, p=0.01) and had a different spread in operation type (CABG only 27% vs. 28%, valve only 51% vs. 68%, combined CABG & valve 22% vs. 4%, p=0.02) but there was no difference in other relevant characteristics (see Table 1). In total, 24 (26%) patients developed longer term AF, with significantly higher proportion in those who developed immediate post-operative AF (see Figure 1). Immediate post-operative AF and hypertension demonstrated a significant association with longer-term AF on univariate regression analysis using a significance value of 0.1. On multivariate analysis only immediate post-operative AF remained significant (odds ratio 3.75 (95% confidence interval 1.38-10.22), p=0.01).

Conclusion

Developing AF in the post-operative period appears to be an independent predictor of developing clinically significant AF up to 18 months after surgery. This is an important finding in identifying patients who may be at higher risk of thromboembolic events. Further research is required to determine the optimal approach, in particular consideration of anticoagulation in this patient group.

The effect of cardiac surgery type on incidence of post-operative atrial fibrillation amongst patients with post-procedural conduction disease

Funding Acknowledgements

Type of funding sources: None.

Background

Approximately 1% of cardiac operations result in post-operative heart block (PoHB). Post -operative atrial fibrillation (PoAF) has been quoted as occurring in 40-50% of combined coronary artery bypass graft (CABG) and valvular procedures, 25% of CABG only and 30% of valve only procedures. The co-existence of PoAF in patients with PoHB, and the link to operation type is less well documented.

Purpose

To investigate characteristics predisposing patients post cardiac surgery for PoHB and PoAF.

Methods

We screened patients who had undergone CABG, aortic or mitral valve replacements (AVR and MVR respectively) or mitral valve repairs at Bristol Royal Infirmary between 1/1/2010 and 1/4/2020. We created a merged surgical and electrophysiological database identifying patients with permanent pacemakers inserted within 30 days of cardiac surgery for PoHB to create our final database. By reviewing electronic notes we identified patients in this cohort who developed PoAF prior to discharge. We excluded patients with congenital heart defects or known prior atrial fibrillation. We then analysed the incidence of both PoHB and PoAF for different operation subtypes.

Results

Of the 10779 operations, 6625 (61%) were CABG-Only, 4124 (38%) were Valve-Only and 1219 (11%) were combined CABG&Valve. In total 85 (0.8%) patients developed PoHB. There was a higher proportion of female patients in the PoHB group but no other demographic differences (See Table 1). In terms of operation type, the PoHB group contained a significantly higher proportion of patients who had undergone AVR (78% vs. 28%, p<0.001). There was also a significant association with operations performed on cardiopulmonary bypass and with longer cross clamp time however this did not remain statistically significant on multivariate analysis. Valve surgery was associated with a higher proportion of patients developing PoHB than CABG, with AVR relating to the highest PoHB rates (AVR 2.0%, MVR 0.9%, CABG 0.2%, p<0.0001). Both mechanical and bioprosthetic AVR were associated with a higher proportion of patients developing PoHB than MVR.

In our cohort 34/85 (41%) patients with POHB developed post-operative AF. After univariate analysis of the patient and operation factors listed in Table 1, only age and body mass index were predictors of development of PoAF after multivariate analysis (age: odds ratio 1.81 (1.02-1.36), p=0.024, BMI: odds ratio 1.09 (1.02-1.17), p=0.01), with no association to surgical parameters.

Conclusion

PoHB occurs commonly following both CABG and valve procedures, with higher incidence in the setting of valve surgery, with our data showing a 2 fold higher chance of PoHB in patients undergoing aortic versus mitral valve replacements. In contrast, there is no clear relationship between type of surgery and development of postoperative atrial fibrillation in this cohort but larger studies are warranted.

QTc interval in survivors of out of hospital cardiac arrest

BACKGROUND

QTc interval (QTc) prolongation is seen on the post-arrest electrocardiogram (ECG) of many out of hospital cardiac arrest (OHCA) survivors. It remains unclear whether this is a transient phenomenon or a manifestation of an underlying arrhythmic substrate. This observational study assessed the trend of QTc in an unselected group of patients presenting with OHCA. We sought to identify any relationship between QTc, gender and aetiology of arrest. We observed whether targeted temperature management (TTM) is associated with malignant arrhythmia.

METHOD

We analysed 60 patients presenting with OHCA to the Bristol Heart Institute during a 20-month period. We measured QTc on admission and assessed for persistence, development and resolution of prolongation at up to 5 time points post-OHCA. Aetiology of arrest was divided into coronary, non-coronary or primary arrhythmic to investigate for patterns in QTc behaviour.

RESULTS

81.7% (49/60) of arrests were attributed to an acute coronary event. 55% (33/60) had QTc prolongation on admission, of which 79% resolved. There were no significant differences in QTc behaviour by aetiology. One patient presenting with a normal QTc, developed prolongation during admission and received a genetic diagnosis of Long QT Syndrome. TTM was employed in 57/60, with no increased incidence of malignant arrhythmia.

CONCLUSIONS

Prolonged QTc on admission does not imply a primary arrhythmic aetiology and resolves in the majority pre-discharge. However, an initial normal QTc post-OHCA does not preclude a diagnosis of Long QT syndrome, highlighting the importance of thorough investigations in these patients. TTM appears safe from a cardiac perspective.

Variations in antibiotic use across India: multi-centre study through Global Point Prevalence survey

The aim of the study was to assess antimicrobial prescribing patterns, and variation in practice, in India. A point prevalence survey (PPS) was conducted in October to December 2017 in 16 tertiary care hospitals across India. The survey included all inpatients receiving an antimicrobial on the day of PPS and collected data were analysed using a web-based application of the University of Antwerp. In all, 1750 patients were surveyed, of whom 1005 were receiving a total of 1578 antimicrobials. Among the antimicrobials prescribed, 26.87% were for community-acquired infections; 19.20% for hospital-acquired infections; 17.24% for medical prophylaxis; 28.70% for surgical prophylaxis; and 7.99% for other or undetermined reasons. Antibiotic prescribing quality indicators, such as reason in notes and post-prescription review score, were low. This PPS showed widespread antibiotic usage, underlining the need for antibiotic stewardship to promote evidence-based practice.

A prospective genome-wide study of prostate cancer metastases reveals association of wnt pathway activation and increased cell cycle proliferation with primary resistance to abiraterone acetate-prednisone

Background

Genomic aberrations have been identified in metastatic castration-resistant prostate cancer (mCRPC), but molecular predictors of resistance to abiraterone acetate/prednisone (AA/P) treatment are not known.

Patients and methods

In a prospective clinical trial, mCRPC patients underwent whole-exome sequencing (n = 82) and RNA sequencing (n = 75) of metastatic biopsies before initiating AA/P with the objective of identifying genomic alterations associated with resistance to AA/P. Primary resistance was determined at 12 weeks of treatment using criteria for progression that included serum prostate-specific antigen measurement, bone and computerized tomography imaging and symptom assessments. Acquired resistance was determined using the end point of time to treatment change (TTTC), defined as time from enrollment until change in treatment from progressive disease. Associations of genomic and transcriptomic alterations with primary resistance were determined using logistic regression, Fisher's exact test, single and multivariate analyses. Cox regression models were utilized for determining association of genomic and transcriptomic alterations with TTTC.

Results

At 12 weeks, 32 patients in the cohort had progressed (nonresponders). Median study follow-up was 32.1 months by which time 58 patients had switched treatments due to progression. Median TTTC was 10.1 months (interquartile range: 4.4-24.1). Genes in the Wnt/β-catenin pathway were more frequently mutated and negative regulators of Wnt/β-catenin signaling were more frequently deleted or displayed reduced mRNA expression in nonresponders. Additionally, mRNA expression of cell cycle regulatory genes was increased in nonresponders. In multivariate models, increased cell cycle proliferation scores (≥ 50) were associated with shorter TTTC (hazard ratio = 2.11, 95% confidence interval: 1.17-3.80; P = 0.01).

Conclusions

Wnt/β-catenin pathway activation and increased cell cycle progression scores can serve as molecular markers for predicting resistance to AA/P therapy.

Abstract P3-08-01: Characteristics, outcomes and prognostic factors of luminal androgen receptor (LAR) triple-negative breast cancer (TNBC)

Background: The LAR subtype is a genomically distinct subset of TNBC. Using a large cohort of non-metastatic TNBC patients (pts) with long term follow-up, we sought to further characterize the clinicopathologic features and outcomes of LAR vs non-LAR TNBC.

Methods: From a cohort of 9982 women with surgically-treated non-metastatic breast cancer, 605 met criteria for TNBC (ER/PR<1% and HER2-negative) by central pathology. RNA extracted from 304 FFPE tumor specimens using the HighPure RNA extraction kit was subjected to TruSeq RNA Access library preparation and sequencing on a HiSeq2500. Adequate RNA was available for 283 pts. Tumors were classified as LAR or non-LAR using a shrunken centroid model, CABAL (Clustering Among BAsal and Luminal androgen receptor). In addition to previously described analyses [Leon-Ferre et al, Breast Cancer Res Treat 2017], immunohistochemical (IHC) androgen receptor (AR) staining was performed and the impact of various parameters on invasive disease-free survival (IDFS) and overall survival (OS) was assessed using Cox proportional hazards models.

Results: 58 (20%) tumors were classified as LAR and 225 (80%) as non-LAR. Compared to non-LAR, LAR pts were older (mean age 65 vs 54) and more often postmenopausal (79%vs53%), both p=0.01. Apocrine histology was more common among LAR tumors (21%vs0%), which were also lower grade (grade3: 69%vs95%) and had lower Ki-67 (Ki-67>15%: 64%vs82%), all p<0.01. Additionally, LAR tumors had lower median stromal tumor infiltrating lymphocytes (TILs, 20%vs25%) and were less frequently lymphocyte-predominant [≥50% stromal or intratumoral TILs (19%vs32%)], although neither reached statistical significance. AR IHC was available for 223 of 283 tumors. Median AR IHC score in LAR was 65% (range 0-100%) vs 0% (range 0-90%) in non-LAR. T/N stage, surgery type, and receipt of adjuvant chemotherapy (AdjCT) or radiotherapy were similar between LAR and non-LAR. LAR pts had shorter IDFS and OS compared to non-LAR (5.6 vs 11.8 yrs and 10.8 vs 20.8 yrs, respectively), although this did not reach statistical significance. Test of proportional hazard assumption was not significant for IDFS or OS (p = 0.30 and 0.09). IDFS estimates were numerically higher in LAR vs non-LAR (80.2%vs70.5%,p = 0.92) at 3yrs post-diagnosis; whereas the opposite was true (40.9%vs55.6%,p = 0.07) after 10yrs. OS estimates at 3 and 5yrs were similar between LAR and non-LAR, but at 10yrs OS was inferior in LAR (40.9%vs66.4%,p = 0.24). In a univariate analysis including both LAR and non-LAR, older age, higher N stage, lower TILs and absence of AdjCT were associated with poorer IDFS and OS. In a multivariate analysis, higher N stage and absence of AdjCT remained associated with both poorer IDFS and OS; while lower stromal TILs were associated with poorer IDFS (p=0.01), and with a trend towards poorer OS (p=0.07).

Conclusions: LAR TNBCs occurred in older women, were lower grade, and had lower TIL density than nonLAR tumors. While significant differences in IDFS or OS were not demonstrated, LAR pts exhibited a numerically lower risk of a disease event at 3yrs, but higher risk by 10yrs compared to nonLAR pts. In the entire cohort, higher N stage, absence of AdjCT and lower TILs were independently associated with poorer outcomes.

Citation Format: Leon-Ferre RA, Polley M-Y, Liu H, Kalari KR, Boughey JC, Liu MC, Cafourek V, Negron V, Ingle JN, Thompson KJ, Tang X, Barman P, Carlson E, Visscher DW, Carter JC, Couch FJ, Goetz MP. Characteristics, outcomes and prognostic factors of luminal androgen receptor (LAR) triple-negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-08-01.

The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response

Response to treatment with selective serotonin reuptake inhibitors (SSRIs) varies considerably between patients. The International SSRI Pharmacogenomics Consortium (ISPC) was formed with the primary goal of identifying genetic variation that may contribute to response to SSRI treatment of major depressive disorder. A genome-wide association study of 4-week treatment outcomes, measured using the 17-item Hamilton Rating Scale for Depression (HRSD-17), was performed using data from 865 subjects from seven sites. The primary outcomes were percent change in HRSD-17 score and response, defined as at least 50% reduction in HRSD-17. Data from two prior studies, the Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomics Study (PGRN-AMPS) and the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study, were used for replication, and a meta-analysis of the three studies was performed (N=2394). Although many top association signals in the ISPC analysis map to interesting candidate genes, none were significant at the genome-wide level and the associations were not replicated using PGRN-AMPS and STAR*D data. The top association result in the meta-analysis of response represents SNPs 5′ upstream of the neuregulin-1 gene, NRG1 (P = 1.20E - 06). NRG1 is involved in many aspects of brain development, including neuronal maturation and variations in this gene have been shown to be associated with increased risk for mental disorders, particularly schizophrenia. Replication and functional studies of these findings are warranted.

Abstract P1-08-10: Integration of next generation sequencing (NGS) and patient derived xenografts (PDX) to identify novel markers of paclitaxel (T) response in the breast cancer genome guided therapy study (BEAUTY)

Background:

Based upon the association between pathologic response and disease free survival, the neoadjuvant setting is increasingly being used for drug development. NGS has identified unique and recurrent genetic alterations in breast cancer (BC) that are potentially targetable; however, the clinical implications are mostly unknown. We developed a prospective neoadjuvant study (BEAUTY) in high risk BC patients (pts) using weekly T followed by anthracycline-based chemo wherein percutaneous tumor biopsies (PTB) are obtained before/during/after chemo for NGS and PDX. Our goal is to identify novel biomarkers/pathways and develop PDX to test new therapeutic approaches.

Methods: Pts underwent PTB at baseline and after 12 wks of T. Response to T was defined based upon 12 week Ki-67: responder (<15%) vs non-responder (≥15%). Pts with histologic response and absence of invasive BC at 12 wks were classified as responders. NGS was performed using PTB/blood DNA (exome) and PTB (RNA seq). MRI response was classified using RECIST criteria. NGS data were used to identify somatic copy number variants (cnvs) and expressed single nucleotide variants (eSNVs). Non-SCID mice (estrogen supplemented) were implanted ≤ 30 minutes with PTB samples.

Results: Of the first 78 pts, 44 have completed T. Here we focus on 18 pts with either triple negative or luminal B BC. Clinical characteristics according to Ki-67 response are shown in Table 1. Comparison of genomic alterations in BEAUTY pts with TCGA identified a greater overlap with copy number gains (73%) compared to deletions (40%), along with similar observations of mutations in TP53, PTEN, RYR2, and AKT1 genes. Association analysis of CNVs and eSNVs between responders/non-responders identified 33 genes (predominantly located in chromosomes 1, 8, 13) and 580 eSNVs (corresponding to 497 genes) with a p < 0.05. Differential gene expression (DGE) analysis of responders/non-responders identified 198 genes with a p-value < 0.05. Integrated analysis of 539 genes (CNVs, eSNVs and DGE) identified pathways such as TGF-beta, Jak-Stat, WNT and NOTCH signalling. PDX take rate was 44% [triple negative (6/10); Luminal B (2/8)]. PDX growth rate was significantly associated with clinical baseline Ki-67 (p = 0.00014).

Conclusion: This is the first prospective study to demonstrate the feasibility of using PTB to obtain both NGS data and PDX in the neoadjuvant setting. PDX take rate is associated with BC subtype and baseline Ki-67. Studies are ongoing to 1) validate genes/pathways associated with treatment response in subsequent BEAUTY pts; 2) genomically characterize and assess PDX in vivo response to T and 3) Use NGS data to prioritize new drugs/drug combinations in PDX.

Funded by Mayo Clinic Center for Individualized Medicine and MC Cancer Center.

Clinical CharacteristicsOverallResponders: 12 week Ki-67 < 15% (n = 9)Non-Responders: 12 week Ki-67 ≥ 15% (n = 9)Median Age495345T stage T2/T314 (78%)7 (78%)7 (78%)Node Positive8 (44%)4 (44%)4 (44%)Triple negative10 (56%)6 (67%)4 (44%)Luminal B8 (44%)3 (33%)5 (56%)Ki-67 after 12 Weeks of T Median 5% (0-11%)Median 35% (17-60%)Complete/Partial MRI Response after T 6 (67%)2 (22%)

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-08-10.

Early onset primary pulmonary cryptococcosis in a renal transplant patient

We report a case of primary pulmonary cryptococcosis in a post-renal transplant patient. A 65-year-old male renal transplant patient was admitted to the hospital with a low grade fever of 1 month, radiologically mimicking tuberculosis (TB). Broncho-alveolar fluid (BAL) shows capsulated yeast, and Cryptococcus neoformans was grown on culture supported by cytology and histopathological examination. Cryptococcal antigen was positive (32-fold) in serum and was negative in cerebrospinal fluid (CSF). The patient was given amphotericin B and 5-flucytosine and clinical improvement was seen on a weekly follow up. The serum cryptococcal antigen test might contribute to the early detection and treatment of pulmonary cryptococcosis. The results of antifungal susceptibility were aid in selecting the drug of choice for treatment.

A rare case of diphyllobothriasis from Pondicherry, South India

Diphyllobothriasis is an intestinal parasitic infection caused by the ingestion of raw fresh-water fish containing the infectious larvae of Diphyllobothrium spp. This infection is uncommon in India. We report a case of diphyllobothriasis that occurred in Pondicherry, India, in a 5-year-old boy hailing from a fishing community. He attended the Pediatric OPD with spontaneous discharge of segments of the adult parasite. The segments (macroscopically and microscopically) were identified as those of Diphyllobothrium latum. The stool examination also revealed characteristic oval eggs.

Changing pattern of human group A rotaviruses: Emergence of G12 as an important pathogen among children in eastern India

BACKGROUND

Rotavirus genotypes, G1-G4 and G9 are associated with childhood diarrhoea throughout the world. In our previous study, we detected G1, G2, G4 and three G12 strains from Kolkata, India.

OBJECTIVES

To study the prevalence of G- and P-genotypes of rotaviruses associated with dehydrating diarrhoea in children admitted to two leading hospitals in eastern India.

STUDY DESIGN

An active surveillance was conducted for elucidation of rotavirus infection in two leading hospitals in Kolkata, West Bengal and Berhampur (GM), Orissa, India, separated by 603km from January 2003 to April 2005. The rotaviruses were detected by RNA electrophoresis in polyacrylamide gels. G- and P-typing of the positive samples were accomplished by amplifying VP7 and VP4 genes by RT-PCR and genotyped by seminested multiplex PCR methods. Sequencing, sequence analysis and phylogenetic analysis of VP7 genes of G12 strains were carried out to understand the variations between the strains isolated from different parts of the world.

RESULTS

The genotypic distribution varied remarkably from our earlier study period (1998-2001) with G1 (53.8%) being the most predominant strain followed by G2 (22.5%), G12 (17.1%), G9 (2.1%) and not a single G3 or G4 isolate was detected separately. 35.2% samples exhibited mixed P-types followed by P[4] (31.7%), P[8] (21.8%) and P[6] (9.8%). The phylogenetic analysis of G12 strains revealed that the G12 strains detected from different parts of the world clustered into three different lineages. Though VP7 sequences of G12 strains isolated from Kolkata and Berhampur are conserved, their P-types were different.

CONCLUSION

During this study period we reported emergence of G12 strains as an important pathogen among children in eastern India, thus necessitating its inclusion in future polyvalent vaccine to control rotavirus diarrhoea.

RT-PCR based diagnosis revealed importance of human group B rotavirus infection in childhood diarrhoea

BACKGROUND

Human group B rotavirus was first identified as causative agent of a large outbreak of severe gastroenteritis affecting more than 1 million people, predominantly adults in China in 1982-1983. In spite of serological evidences for the presence of group B rotavirus in many countries of the world, the virus has been detected only from China, India and Bangladesh, where most of the cases were from adults.

OBJECTIVES

To ascertain the role of group B rotavirus as an aetiological agent of diarrhoea among children in Kolkata, India.

STUDY DESIGN

An active surveillance was conducted for rotavirus infection in children in a leading referral paediatric hospital and a few samples were also collected from adults of another hospital in Kolkata, India over a period of 3 years (2002-2004). After primary screening of rotaviruses by RNA electrophoresis in polyacrylamide gel, 200 of 412 samples negative by PAGE were screened by reverse transcription polymerase chain reaction for group B rotaviruses. The group B rotavirus positives samples were also confirmed by dot-blot hybridization.

RESULT

During the study period, we detected 37 (18.5%) sporadic cases of human group B rotavirus infection in children below 3 years of age of which 15 (7.5%) showed mixed infection with group A rotaviruses by RT-PCR. In dot-blot hybridization studies the RNA of all rotavirus positive samples hybridized with the nonisotopic psoralen-biotin labeled total RNA probe generated from a human group B rotavirus CAL-1 strain confirming the samples as group B rotaviruses.

CONCLUSION

The shift in age preference of group B rotavirus infection from adult to children and mixed infection of group B and group A rotaviruses reveals the importance of group B rotavirus as an etiological agent of childhood diarrhoea. Therefore, future vaccination strategy should include both group A and B rotaviruses to control rotavirus diarrhoea.

Sequencing and sequence analysis of VP7 and NSP5 genes reveal emergence of a new genotype of bovine group B rotaviruses in India

Three bovine group B rotavirus strains were detected from diarrheic calves during a surveillance study of rotaviral diarrhea in West Bengal, India. The sequence analysis of VP7 and NSP5 genes of these strains demonstrates a high degree of sequence variation from other group B rotavirus strains, indicating the emergence of a new genotype.

Emergence of novel human group A rotavirus G12 strains in India

Three rare human G12 strains were detected from diarrheic clinical samples of children (<8 months of age) in Calcutta during a routine surveillance study of rotaviral diarrhea in India. The VP7 genes of G12 strains and their products showed maximum homology (97 to 99% at the nucleotide level and 98% at the amino acid level, respectively) with those of two recently reported G12 strains (from the United States and Thailand) but lesser homology with those of prototype G12 strain L26.

An automated annotation tool for genomic DNA sequences using GeneScan and BLAST

Genomic sequence data are often available well before the annotated sequence is published. We present a method for analysis of genomic DNA to identify coding sequences using the GeneScan algorithm and characterize these resultant sequences by BLAST. The routines are used to develop a system for automated annotation of genome DNA sequences.