Complete genome sequencing and evolutionary analysis of dengue virus serotype 1 isolates from an outbreak in Kerala, South India

In this study, dengue virus (DENV) isolates from a localized, small-scale, non-seasonal dengue outbreak were genetically characterized. The outbreak occurred during the pre-monsoon months (April-May) in a medical college campus in Kerala, South India in 2009 affecting 76 people. Analysis of 39 viral RNA positive serum samples by a serotype specific reverse-transcription polymerase chain reaction identified dengue virus serotype 1 (DENV1) as the causative strain. Formation of a distinct genetic clade was revealed in the initial phylogenetic analysis using nucleotide sequences of a partial (303 bp) Capsid-Pre-membrane protein (C-PrM) coding region of 37 outbreak strains. The sequences of these strains clustered with that of the Genotype III DENV-1 strains from India, and 32 among them formed a single major sub-clade. Whole-genome sequencing (10,693 bp) of two strains (RGCB585/2009 and RGCB592/2009) selected from this major sub-clade, and subsequent phylogenetic analysis using the full-length coding region sequence showed that the sequences grouped with that of the isolates from Thailand (1980), Comoros (1993), Singapore (1993), and Brunei (2005) among the Indo-Pacific isolates. The sequences of the two strains had a nucleotide identity of 97-98 % and an amino acid identity of 98-99 % with these closely related strains. Maximum amino acid similarity was shown with the Singapore 8114/93 isolate (99.6 %). Four mutations-L46M in the capsid, D278N in the NS1, L123I, and L879S in the NS5 protein coding regions-were seen as signature substitutions uniformly in RGCB585/2009 and RGCB592/2009; in another isolate from Kerala (RGCB419/2008) and in the Brunei isolate (DS06-210505). These four isolates also had in common a 21-nucleotide deletion in the hyper-variable region of the 3'-non-translated region. This first report on the complete genome characterization of DENV-1 isolates from India reveals a dengue outbreak caused by a genetically different viral strain. The results point to the possibility of exotic introduction of these circulating viral strains in the region.

Differential gene expression analysis of in vitro duck hepatitis B virus infected primary duck hepatocyte cultures

Background

The human hepatitis B virus (HBV), a member of the hepadna viridae, causes acute or chronic hepatitis B, and hepatocellular carcinoma (HCC). The duck hepatitis B virus (DHBV) infection, a dependable and reproducible model for hepadna viral studies, does not result in HCC unlike chronic HBV infection. Information on differential gene expression in DHBV infection might help to compare corresponding changes during HBV infection, and to delineate the reasons for this difference.

Findings

A subtractive hybridization cDNA library screening of in vitro DHBV infected, cultured primary duck hepatocytes (PDH) identified cDNAs of 42 up-regulated and 36 down-regulated genes coding for proteins associated with signal transduction, cellular respiration, transcription, translation, ubiquitin/proteasome pathway, apoptosis, and membrane and cytoskeletal organization. Those coding for both novel as well as previously reported proteins in HBV/DHBV infection were present in the library. An inverse modulation of the cDNAs of ten proteins, reported to play role in human HCC, such as that of Y-box binding protein1, Platelet-activating factor acetylhydrolase isoform 1B, ribosomal protein L35a, Ferritin, α-enolase, Acid α-glucosidase and Caspase 3, copper-zinc superoxide dismutase (CuZnSOD), Filamin and Pyruvate dehydrogenase, was also observed in this in vitro study.

Conclusions

The present study identified cDNAs of a number of genes that are differentially modulated in in vitro DHBV infection of primary duck hepatocytes. Further correlation of this differential gene expression in in vivo infection models would be valuable to understand the little known aspects of the hepadnavirus biology.

Functional characterization of the CC chemokine RANTES from Pekin duck (Anas platyrhynchos)

RANTES (Regulated upon Activation, Normal T-cell Expressed and Secreted) is a key pro-inflammatory cytokine that belongs to the CC-group of chemokines. The present study was carried out to functionally characterize the previously identified RANTES homologue in domestic duck (GenBank Accession No. AY641435). Recombinant duck RANTES was expressed in Escherichia coli-based and HEK293T cell-based systems. A tRNA supplementation strategy was required to express the protein in E. coli due to the presence of rare codons. In biological assays using HEK293T cell-expressed protein, RANTES was found to mediate chemotaxis of DT-40 chicken B cells and primary duck splenocytes at a concentration of 0.505μg/ml (0.6μM). Immunostaining of the migrated splenocytes using anti-duck CD4 and CD8 monoclonal antibodies and subsequent flow cytometric analysis showed enhanced chemotaxis of CD8+ cells. The recombinant RANTES exhibited in vitro antiviral activity by inhibiting infection of chicken embryo fibroblast cells with duck enteritis virus (DEV) at the same concentration. The effect could be neutralized by rabbit anti-duck RANTES polyclonal serum. The mechanism seems to be direct on viral particles as evidenced by the need for co-incubation of RANTES with DEV prior to the infection for antiviral activity, and also by the enhanced binding of DEV to E. coli expressed purified RANTES on ELISA-based assays. Our results show that the duck RANTES has overlapping biological properties with its mammalian orthologue, and also has possible functional cross-reactivity with chicken immune cells indicated by the chemotaxis of DT-40 cells.

Molecular characterization of Chikungunya virus isolates from clinical samples and adult Aedes albopictus mosquitoes emerged from larvae from Kerala, South India

Chikungunya virus (CHIKV), an arthritogenic alphavirus, is transmitted to humans by infected Aedes (Ae.) aegypti and Ae.albopictus mosquitoes. In the study, reverse-transcription PCR (RT PCR) and virus isolation detected CHIKV in patient samples and also in adult Ae.albopictus mosquitoes that was derived from larvae collected during a chikungunya (CHIK) outbreak in Kerala in 2009. The CHIKV strains involved in the outbreak were the East, Central and South African (ECSA) genotype that had the E1 A226V mutation. The viral strains from the mosquitoes and CHIK patients from the same area showed a close relationship based on phylogenetic analysis. Genetic characterization by partial sequencing of non-structural protein 2 (nsP2; 378 bp), envelope E1 (505 bp) and E2 (428 bp) identified one critical mutation in the E2 protein coding region of these CHIKV strains. This novel, non-conservative mutation, L210Q, consistently present in both human and mosquito-derived samples studied, was within the region of the E2 protein (amino acids E2 200-220) that determines mosquito cell infectivity in many alpha viruses. Our results show the involvement of Ae. albopictus in this outbreak in Kerala and appearance of CHIKV with novel genetic changes. Detection of virus in adult mosquitoes, emerged in the laboratory from larvae, also points to the possibility of transovarial transmission (TOT) of mutant CHIKV strains in mosquitoes.

Genetic characterization of dengue virus serotypes causing concurrent infection in an outbreak in Ernakulam, Kerala, South India

Dengue fever, a mosquito-borne viral infection, causes significant morbidity and has become endemic in the Indian subcontinent. Virus strains currently circulating in many parts of the country are not well studied at the molecular level. In the present study, genetic characterization of virus strains from a dengue outbreak that occurred in and around a tertiary care hospital in Ernakulam, Kerala in the year 2008 has been reported. By reverse transcription polymerase chain reaction (RT-PCR), 37 out of 75 (49.3%) clinically suspected cases were positive for dengue viral RNA. Among these, 21 (56.8%) samples showed concurrent infection with multiple serotypes of the virus. Majority of the combined infections were caused by dengue serotype 2 and 3. Co-infections with type 1 and 2 in two patients, and type 1, 2 and 3 in one patient were also observed. The core-pre-Membrane (CprM) junction nucleotide sequencing and phylogenetic analysis revealed that the type 1 strains were related to the viral strains reported from Delhi-2001 and Gwalior-2002 dengue outbreaks, while the type 2 strains were related to the strains from Gwalior-2001 epidemic. Sequences of type 3 strains did not show clear relation to any of the previous Indian isolates, and in the phylogenetic analysis, they formed a distinct lineage within the Indian type 3 strains. This study indicates hyperendemicity of dengue in the region with the presence of multiple serotypes and high rates of co-infection, and local genomic evolution of the viral strains involved in this outbreak.

Genetic characterization of 2006-2008 isolates of Chikungunya virus from Kerala, South India, by whole genome sequence analysis

Chikungunya virus (CHIKV), a positive-stranded alphavirus, causes epidemic febrile infections characterized by severe and prolonged arthralgia. In the present study, six CHIKV isolates (2006 RGCB03, RGCB05; 2007 RGCB80, RGCB120; 2008 RGCB355, RGCB356) from three consecutive Chikungunya outbreaks in Kerala, South India, were analyzed for genetic variations by sequencing the 11798 bp whole genome of the virus. A total of 37 novel mutations were identified and they were predominant in the 2007 and 2008 isolates among the six isolates studied. The previously identified E1 A226V critical mutation, which enhances mosquito adaptability, was present in the 2007 and 2008 samples. An important observation was the presence of two coding region substitutions, leading to nsP2 L539S and E2 K252Q change. These were identified in three isolates (2007 RGCB80 and RGCB120; 2008 RGCB355) by full-genome analysis, and also in 13 of the 31 additional samples (42%), obtained from various parts of the state, by sequencing the corresponding genomic regions. These mutations showed 100% co-occurrence in all these samples. In phylogenetic analysis, formation of a new genetic clade by these isolates within the East, Central and South African (ECSA) genotypes was observed. Homology modeling followed by mapping revealed that at least 20 of the identified mutations fall into functionally significant domains of the viral proteins and are predicted to affect protein structure. Eighteen of the identified mutations in structural proteins, including the E2 K252Q change, are predicted to disrupt T-cell epitope immunogenicity. Our study reveals that CHIK virus with novel genetic changes were present in the severe Chikungunya outbreaks in 2007 and 2008 in South India.