Nineteen nucleotides in the variable region of 3' non-translated region are dispensable for the replication of dengue type 1 virus in vitro

Sofosbuvir Suppresses the Genome Replication of DENV1 in Human Hepatic Huh7 Cells

Dengue virus (DENV) causes dengue fever and dengue hemorrhagic fever, and DENV infection kills 20,000 people annually worldwide. Therefore, the development of anti-DENV drugs is urgently needed. Sofosbuvir (SOF) is an effective drug for HCV-related diseases, and its triphosphorylated metabolite inhibits viral RNA synthesis by the RNA-dependent RNA polymerase (RdRp) of HCV. (2'R)-2'-Deoxy-2'-fluoro-2'-methyluridine (FMeU) is the dephosphorylated metabolite produced from SOF. The effects of SOF and FMeU on DENV1 replication were analyzed using two DENV1 replicon-based methods that we previously established. First, a replicon-harboring cell assay showed that DENV1 replicon replication in human hepatic Huh7 cells was decreased by SOF but not by FMeU. Second, a transient replicon assay showed that DENV1 replicon replication in Huh7 cells was decreased by SOF; however, in hamster kidney BHK-21 cells, it was not suppressed by SOF. Additionally, the replicon replication in Huh7 and BHK-21 cells was not affected by FMeU. Moreover, we assessed the effects of SOF on infectious DENV1 production. SOF suppressed infectious DENV1 production in Huh7 cells but not in monkey kidney Vero cells. To examine the substrate recognition of the HCV and DENV1 RdRps, the complex conformation of SOF-containing DENV1 RdRp or HCV RdRp was predicted using AlphaFold 2. These results indicate that SOF may be used as a treatment for DENV1 infection.

Mutations in the 3' non-coding region of a no-known vector flavivirus Yokose virus increased its replication ability in mosquito C6/36 cells

Yokose virus (YOKV) is a bat-associated no-known vector flavivirus group member. We investigated the replication ability of YOKV in mosquito-derived C6/36 cells. YOKV grew in C6/36 cells, but its kinetics of YOKV was markedly slower than those of other mosquito-borne flaviviruses. Transmission electron microscopy indicated an extremely small number of viral particles in YOKV-infected C6/36 cells. Mosquito-borne Japanese encephalitis virus prM-E-bearing chimeric YOKV failed to propagate efficiently in C6/36 cells. We isolated C6/36-adapted YOKV and identified nucleotide mutations in the adapted YOKV. Mutations detected in the 3' non-coding region of the adapted YOKV were critical for the enhanced proliferation ability of the virus. Moreover, the growth of the original and adapted YOKV in C6/36 cells was remarkably increased by shifting the culture temperature from 28 to 36 °C. Thus, our results demonstrate the potential of YOKV to propagate in mosquito cells and support its classification as a mosquito-borne flavivirus.

Identification of an Arylnaphthalene Lignan Derivative as an Inhibitor against Dengue Virus Serotypes 1 to 4 (DENV-1 to -4) Using a Newly Developed DENV-3 Infectious Clone and Replicon

Dengue virus (DENV) is the most widespread arbovirus, causing symptoms ranging from dengue fever to severe dengue, including hemorrhagic fever and shock syndrome. Four serotypes of DENV (DENV-1 to -4) can infect humans; however, no anti-DENV drug is available. To facilitate the study of antivirals and viral pathogenesis, here we developed an infectious clone and a subgenomic replicon of DENV-3 strains for anti-DENV drug discovery by screening a synthetic compound library. The viral cDNA was amplified from a serum sample from a DENV-3-infected individual during the 2019 epidemic; however, fragments containing the prM-E-partial NS1 region could not be cloned until a DENV-3 consensus sequence with 19 synonymous substitutions was introduced to reduce putative Escherichia coli promoter activity. Transfection of the resulting cDNA clone, plasmid DV3syn, released an infectious virus titer of 2.2 × 102 focus-forming units (FFU)/mL. Through serial passages, four adaptive mutations (4M) were identified, and addition of 4M generated recombinant DV3syn_4M, which produced viral titers ranging from 1.5 × 104 to 6.7 × 104 FFU/mL and remained genetically stable in transformant bacteria. Additionally, we constructed a DENV-3 subgenomic replicon and screened an arylnaphthalene lignan library, from which C169-P1 was identified as exhibiting inhibitory effects on viral replicon. A time-of-drug addition assay revealed that C169-P1 also impeded the internalization process of cell entry. Furthermore, we demonstrated that C169-P1 inhibited the infectivity of DV3syn_4M, as well as DENV-1, DENV-2, and DENV-4, in a dose-dependent manner. This study provides an infectious clone and a replicon for the study of DENV-3 and a candidate compound for future development against DENV-1 to -4 infections. IMPORTANCE Dengue virus (DENV) is the most prevalent mosquito-transmitted virus, and there is no an anti-dengue drug. Reverse genetic systems representative of different serotype viruses are invaluable tools for the study of viral pathogenesis and antiviral drugs. Here, we developed an efficient infectious clone of a clinical DENV-3 genotype III isolate. We successfully overcame the instability of flavivirus genome-length cDNA in transformant bacteria, an unsolved issue for construction of cDNA clones of flaviviruses, and adapted this clone to efficiently produce infectious viruses following plasmid transfection of cell culture. Moreover, we constructed a DENV-3 subgenomic replicon and screened a compound library. An arylnaphthalene lignan, C169-P1, was identified as an inhibitor of virus replication and cell entry. Finally, we demonstrated that C169-P1 exhibited a broad-spectrum antiviral effect against the infections with DENV-1 to -4. The reverse genetic systems and the compound candidate described here facilitate the study of DENV and related RNA viruses.

Evolutionary dynamics of dengue virus in India

More than a hundred thousand dengue cases are diagnosed in India annually, and about half of the country's population carries dengue virus-specific antibodies. Dengue propagates and adapts to the selection pressures imposed by a multitude of factors that can lead to the emergence of new variants. Yet, there has been no systematic analysis of the evolution of the dengue virus in the country. Here, we present a comprehensive analysis of all DENV gene sequences collected between 1956 and 2018 from India. We examine the spatio-temporal dynamics of India-specific genotypes, their evolutionary relationship with global and local dengue virus strains, interserotype dynamics and their divergence from the vaccine strains. Our analysis highlights the co-circulation of all DENV serotypes in India with cyclical outbreaks every 3-4 years. Since 2000, genotype III of DENV-1, cosmopolitan genotype of DENV-2, genotype III of DENV-3 and genotype I of DENV-4 have been dominating across the country. Substitution rates are comparable across the serotypes, suggesting a lack of serotype-specific evolutionary divergence. Yet, the envelope (E) protein displays strong signatures of evolution under immune selection. Apart from drifting away from its ancestors and other contemporary serotypes in general, we find evidence for recurring interserotype drift towards each other, suggesting selection via cross-reactive antibody-dependent enhancement. We identify the emergence of the highly divergent DENV-4-Id lineage in South India, which has acquired half of all E gene mutations in the antigenic sites. Moreover, the DENV-4-Id is drifting towards DENV-1 and DENV-3 clades, suggesting the role of cross-reactive antibodies in its evolution. Due to the regional restriction of the Indian genotypes and immunity-driven virus evolution in the country, ~50% of all E gene differences with the current vaccines are focused on the antigenic sites. Our study shows how the dengue virus evolution in India is being shaped in complex ways.

Association of Dengue Virus Serotypes 1&2 with Severe Dengue Having Deletions in Their 3′Untranslated Regions (3′UTRs)

Dengue virus infections are recorded as hyper-endemic in many countries, including India. Research pertaining to the reasons for frequent outbreaks and severe dengue is ongoing. Hyderabad city, India, has been recorded as a ‘hotspot’ for dengue virus infections. Dengue virus strains circulating over the past few years in Hyderabad city have been characterized at the molecular level to analyze the serotype/genotypes; 3′UTRs were further amplified and sequenced. The disease severity in patients infected with dengue virus strains with complete and 3′UTR deletion mutants was analyzed. Genotype I of the serotype 1 replaced genotype III, which has been circulating over the past few years in this region. Coincidentally, the number of dengue virus infections significantly increased in this region during the study period. Nucleotide sequence analysis suggested twenty-two and eight nucleotide deletions in the 3′UTR of DENV-1. The eight nucleotide deletions observed in the case of DENV-1 3′UTR were the first reported in this instance. A 50 nucleotide deletion was identified in the case of the serotype DENV-2. Importantly, these deletion mutants were found to cause severe dengue, even though they were found to be replication incompetent. This study emphasized the role of dengue virus 3′UTRs on severe dengue and emerging outbreaks.

Amino Acid at Position 166 of NS2A in Japanese Encephalitis Virus (JEV) is Associated with In Vitro Growth Characteristics of JEV

We previously showed that the growth ability of the Japanese encephalitis virus (JEV) genotype V (GV) strain Muar is clearly lower than that of the genotype I (GI) JEV strain Mie/41/2002 in murine neuroblastoma cells. Here, we sought to identify the region in GV JEV that is involved in its low growth potential in cultured cells. An intertypic virus containing the NS1-3 region of Muar in the Mie/41/2002 backbone (NS1-3^Muar) exhibited a markedly diminished growth ability in murine neuroblastoma cells. Moreover, the growth rate of a Muar NS2A-bearing intertypic virus (NS2A^Muar) was also similar to that of Muar in these cells, indicating that NS2A of Muar is one of the regions responsible for the Muar-specific growth ability in murine neuroblastoma cells. Sequencing analysis of murine neuroblastoma Neuro-2a cell-adapted NS1-3^Muar virus clones revealed that His-to-Tyr mutation at position 166 of NS2A (NS2A¹⁶⁶) could rescue the low replication ability of NS1-3^Muar in Neuro-2a cells. Notably, a virus harboring a Tyr-to-His substitution at NS2A¹⁶⁶ (NS2A^Y166H) showed a decreased growth ability relative to that of the parental virus Mie/41/2002, whereas an NS2A^Muar-based mutant virus, NS2A^Muar-H166Y, showed a higher growth ability than NS2A^Muar in Neuro-2a cells. Thus, these results indicate that the NS2A¹⁶⁶ amino acid in JEV is critical for the growth and tissue tropism of JEV in vitro.

E and prM proteins of genotype V Japanese encephalitis virus are required for its increased virulence in mice

We previously showed that the Japanese encephalitis virus (JEV) genotype V (GV) strain Muar exhibits significantly higher virulence in mice than the genotype I (GI) JEV strain Mie/41/2002. In this study, we attempted to identify the region responsible for the increased virulence of GV JEV using recombinant intertypic and single mutant JEVs. Intertypic viruses containing the GV E region in the Mie/41/2002 backbone showed increased pathogenicity in mice. The amino acid at position 123 in the E protein (E123) of the Mie/41/2002 and GV JEVs was serine and histidine, respectively. A serine-to-histidine substitution at E123 of the Mie/41/2002 increased its virulence. However, histidine-to-serine changes at E123 in the intertypic mutants with the GV E region remained highly virulent. GV Muar prM-bearing mutants were also highly pathogenic in mice. Our results suggest that the E and prM proteins of GV JEV are responsible for the highly virulent characteristics of GV JEV.

Identification of inhibitors of dengue viral replication using replicon cells expressing secretory luciferase

Dengue virus (DENV) is the causative agent of dengue fever (DF), dengue haemorrhagic fever (DHF), and dengue shock syndrome (DSS) and continues to be a public health problem in the tropical and subtropical areas. However, there is currently no antiviral treatment for DENV infection. In this study, our aim was to develop a stable reporter replicon cell system that supports constant viral RNA replication in cultured cells. The isolated replicon cells exhibited high levels of luciferase activity in the culture supernatant concomitant with expression of virus-encoded NS1, NS3 and NS5 proteins in the cells. The NS1, NS3 proteins and dsRNA were detected in the replicon cells by immunofluorescence analysis. Furthermore, the anti-DENV inhibitors ribavirin and bromocriptine significantly reduced the luciferase activity in a dose-dependent manner. High-throughput screening with a compound library using the stably-transfected replicon cells showed a Z' factor value of 0.57. Our screening yielded several candidates including one compound that has already shown anti-DENV activity. Taken together, our results demonstrate that this DENV subgenomic replicon cell system expressing a secretory luciferase gene can be useful for the high-throughput screening of anti-DENV compounds and the analysis of the replication mechanism of the DENV RNA.

Stearoyl-CoA desaturase-1 is required for flavivirus RNA replication

Dengue virus (DENV) is the most prevalent human arthropod-borne virus and causes severe problems worldwide, mainly in tropical and sub-tropical regions. However, there is no specific antiviral drug against DENV infection. We and others recently reported that stearoyl-CoA desaturase-1 (SCD1) inhibitor showed potent suppression of hepatitis C virus replication. In this study, we examined the impact of SCD1 on DENV replication. We found that SCD1 inhibitors (MK8245 and #1716) dramatically suppressed DENV replication in a dose-dependent manner without cytotoxicity. This anti-DENV efficacy was observed against all four DENV serotypes and other flaviviruses, including Zika virus and Japanese encephalitis virus. A subgenomic replicon system of DENV was used to confirm that SCD1 inhibitor suppressed viral RNA replication. Interestingly, exogenous supplementation of unsaturated fatty acids resulted in recovery of the DENV titer even in the presence of SCD1 inhibitor, suggesting that fatty acid biosynthesis contributes to DENV genome replication. These findings indicate that SCD1 is a novel host factor required for DENV replication, and SCD1 inhibitor is a potential candidate for treating dengue fever.

An estrogen antagonist, cyclofenil, has anti-dengue-virus activity

Dengue virus (DENV) infections are a major cause of morbidity and mortality in tropical and subtropical areas. Several compounds that act against DENV have been studied in clinical trials to date; however, there have been no compounds identified that are effective in reducing the severity of the clinical manifestations. To explore anti-DENV drugs, we examined small molecules that interact with DENV NS1 and inhibit DENV replication. Cyclofenil, which is a selective estrogen receptor modulator (SERM) and has been used clinically as an ovulation-inducing drug, showed an inhibitory effect on DENV replication in mammalian cells but not in mosquito cells. Other SERMs also inhibited DENV replication in mammalian cells, but cyclofenil showed the weakest cytotoxicity among these SERMs. Cyclofenil also inhibited the replication of Zika virus. A time-of-addition assay suggested that cyclofenil may interfere with two stages of the DENV life cycle: the translation-RNA synthesis and assembly-maturation stages. However, the level of intracellular infectious particles decreased more drastically after treatment with cyclofenil than the viral RNA level did, indicating that the assembly-maturation stage might be the main target of cyclofenil. In electron microscopy analysis, many aggregated particles were detected in DENV-infected cells in the presence of cyclofenil, supporting the possibility that cyclofenil impedes the process of assembly and maturation of DENV.

Highly Selective Transmission Success of Dengue Virus Type 1 Lineages in a Dynamic Virus Population: An Evolutionary and Fitness Perspective

Arbovirus transmission is modulated by host, vector, virus, and environmental factors. Even though viral fitness plays a salient role in host and vector adaptation, the transmission success of individual strains in a heterogeneous population may be stochastic. Our large-scale molecular epidemiological analyses of a dengue virus type 1 population revealed that only a subset of strains (16.7%; n = 6) were able to sustain transmission, despite the population being widely dispersed, dynamic, and heterogeneous. The overall dominance was variable even among the “established” lineages, albeit sharing comparable evolutionary characteristics and replication profiles. These findings indicated that virological parameters alone were unlikely to have a profound effect on the survival of viral lineages, suggesting an important role for non-viral factors in the transmission success of lineages. Our observations, therefore, emphasize the strategic importance of a holistic understanding of vector, human host, and viral factors in the control of vector-borne diseases.

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The sustained transmission of dengue virus 1 lineages is highly selective

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The overall dominance is variable even among the “established” lineages

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The lineage dominance is not merely determined by virus evolution and fitness

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The non-viral factors play an important role in the survival of virus lineages

A single amino acid substitution in the NS4B protein of Dengue virus confers enhanced virus growth and fitness in human cells in vitro through IFN-dependent host response

Dengue virus (DENV) replication between mosquito and human hosts is hypothesized to be associated with viral determinants that interact in a differential manner between hosts. However, the understanding of inter-host viral determinants that drive DENV replication and growth between hosts is limited. Through the use of clinical isolates, we identified an amino acid variation of Ala, Met and Val at position 116 of DENV-1 NS4B. While the proportion of virus with the NS4B-116V variant remained constantly high in serial passages in a mosquito cell line, populations of the NS4B-116M and NS4B-116A variants became dominant after serial passages in mammalian cell lines. Using recombinant DENV-1 viruses, the Val to Ala or Met alteration at position NS4B-116 (rDENV-1-NS4B-116A and rDENV-1-NS4B-116M) resulted in enhanced virus growth in human cells in comparison to the clone with Val at NS4B-116 (rDENV-1-NS4B-116V). However, the reverse phenomenon was observed in a mosquito cell line. Additionally, in a human cell line, differential levels of IFN-α/β and IFN-stimulated gene expressions (IFIT3, IFI44L, OAS1) suggested that the enhanced viral growth was dependent on the ability of the NS4B protein to hamper host IFN response during the early phase of infection. Overall, we identified a novel and critical viral determinant at the pTMD3 of NS4B region that displayed differential effects on DENV replication and fitness in human and mosquito cell lines. Taken together, the results suggest the importance of the NS4B protein in virus replication and adaptation between hosts.

Identification of Compound-B, a novel anti-dengue virus agent targeting the non-structural protein 4A

Dengue virus (DENV) is the causative agent of dengue fever and dengue hemorrhagic fever/dengue shock syndrome. At present, no antiviral drugs are available for treatment DENV infections. In this study, a screening system based on a DENV-infected cell-based assay identified a novel anti-DENV agent with a benzimidazole skeleton, named Compound-B, which demonstrated antiviral activity specific to four DENV serotypes (EC₅₀: 1.32-4.12 μM). Analysis of a single amino acid substitution of Compound-B-resistant DENV2 revealed that mutation C87S in the non-structural protein 4A (NS4A) contributes to resistance to Compound-B.

Complete Genome Characterization of the 2017 Dengue Outbreak in Xishuangbanna, a Border City of China, Burma and Laos

A dengue outbreak abruptly occurred at the border of China, Myanmar, and Laos in June 2017. By November 3rd 2017, 1184 infected individuals were confirmed as NS1-positivein Xishuangbanna, a city located at the border. To verify the causative agent, complete genome information was obtained through PCR and sequencing based on the viral RNAs extracted from patient samples. Phylogenetic trees were constructed by the maximum likelihood method (MEGA 6.0). Nucleotide and amino acid substitutions were analyzed by BioEdit, followed by RNA secondary structure prediction of untranslated regions (UTRs) and protein secondary structure prediction in coding sequences (CDSs). Strains YN2, YN17741, and YN176272 were isolated from local residents. Stains MY21 and MY22 were isolated from Burmese travelers. The complete genome sequences of the five isolates were 10,735 nucleotides in length. Phylogenetic analysis classified all five isolates as genotype I of DENV-1, while isolates of local residents and Burmese travelers belonged to different branches. The three locally isolates were most similar to the Dongguan strain in 2011, and the other two isolates from Burmese travelers were most similar to the Laos strain in 2008. Twenty-four amino acid substitutions were important in eight evolutionary tree branches. Comparison with DENV-1SS revealed 658 base substitutions in the local isolates, except for two mutations exclusive to YN17741, resulting in 87 synonymous mutations. Compared with the local isolates, 52 amino acid mutations occurred in the CDS of two isolates from Burmese travelers. Comparing MY21 with MY22, 17 amino acid mutations were observed, all these mutations occurred in the CDS of non-structured proteins (two in NS1, 10 in NS2, two in NS3, three in NS5). Secondary structure prediction revealed 46 changes in the potential nucleotide and protein binding sites of the CDSs in local isolates. RNA secondary structure prediction also showed base changes in the 3′UTR of local isolates, leading to two significant changes in the RNA secondary structure. To our knowledge, this study is the first complete genome analysis of isolates from the 2017 dengue outbreak that occurred at the border areas of China, Burma, and Laos.

Hirsutine, an Indole Alkaloid of Uncaria rhynchophylla, Inhibits Late Step in Dengue Virus Lifecycle

Dengue virus (DENV) is transmitted to humans by Aedes mosquitoes and is a public health issue worldwide. No antiviral drugs specific for treating dengue infection are currently available. To identify novel DENV inhibitors, we analyzed a library of 95 compounds and 120 extracts derived from crude drugs (herbal medicines). In the primary screening, A549 cells infected with DENV-1 were cultured in the presence of each compound and extract at a final concentration of 10 μM (compound) and 100 μg/mL (extract), and reduction of viral focus formation was assessed. Next, we eliminated compounds and extracts which were cytotoxic using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Hirsutine, an indole alkaloid of Uncaria rhynchophylla, was identified as a potent anti-DENV compound exhibiting high efficacy and low cytotoxicity. Hirsutine showed antiviral activity against all DENV serotypes. Time-of-drug-addition and time-of-drug-elimination assays indicated that hirsutine inhibits the viral particle assembly, budding, or release step but not the viral translation and replication steps in the DENV lifecycle. A subgenomic replicon system was used to confirm that hirsutine does not restrict viral genome RNA replication. Hirsutine is a novel DENV inhibitor and potential candidate for treating dengue fever.

Novel antiviral activity of bromocriptine against dengue virus replication

Dengue virus (DENV) infectious disease is a major public health problem worldwide; however, licensed vaccines or specific antiviral drugs against this infection are not available. To identify novel anti-DENV compounds, we screened 1280 pharmacologically active compounds using focus reduction assay. Bromocriptine (BRC) was found to have potent anti-DENV activity and low cytotoxicity (half maximal effective concentration [EC50], 0.8-1.6 μM; and half maximal cytotoxicity concentration [CC50], 53.6 μM). Time-of-drug-addition and time-of-drug-elimination assays suggested that BRC inhibits translation and/or replication steps in the DENV life cycle. A subgenomic replicon system was used to verify that BRC restricts RNA replication step. Furthermore, a single amino acid substitution (N374H) was detected in the NS3 protein that conferred resistance to BRC. In summary, BRC was found to be a novel DENV inhibitor and a potential candidate for the treatment of DENV infectious disease.

Whole Genome Sequencing-Based Molecular Epidemiologic Analysis of Autochthonous Dengue Virus Type 1 Strains Circulating in Japan in 2014

Cases of autochthonous infections of dengue virus type 1 (DENV-1) were detected in Japan after a 70-year period devoid of dengue outbreaks. We previously showed that E gene sequences are identical in 11 of the 12 DENV-1 strains autochthonous to Japan. However, the E sequence represents only 14% of the DENV-1 genome. In the present study, we have sequenced the entire genome of 6 autochthonous DENV-1 strains that were isolated from patients during the 2014 outbreak. Sequencing of 5 Yoyogi group strains with identical E sequences and 1 Shizuoka strain with a different E sequence revealed that the first Yoyogi group strain differed from the Shizuoka strain by 18 amino acid residues. Furthermore, 2 Yoyogi group strains had different genomic sequences while the other 3 had identical genomes. Phylogenetic analyses indicated that the Hyogo strain, a Yoyogi group strain, was the first to diverge from the other 4 Yoyogi group strains. The E gene sequence of the Yoyogi group strains exhibits the highest homology to those of the strains isolated in Malaysia and Singapore between 2013 and 2014. The patient infected with the Hyogo strain visited Malaysia before the onset of dengue fever, suggesting that this was a case of dengue infection imported from Malaysia.

Highly divergent dengue virus type 1 genotype sets a new distance record

Dengue viruses (DENVs) are the leading cause of mosquito-borne viral disease of humans. They exist in both endemic and sylvatic ecotypes. In 2014, a viremic patient who had recently visited the rainforests of Brunei returned to Australia displaying symptoms consistent with DENV infection. A unique DENV strain was subsequently isolated from the patient, which we propose belongs to a new genotype within DENV serotype 1 (DENV-1). Bayesian evolutionary phylogenetic analysis suggests that the putative sylvatic DENV-1 Brunei 2014 (Brun2014) is the most divergent DENV-1 yet recorded and increases the time to the most recent common ancestor (MRCA) for DENV-1 from ≈120 years to ≈315 years. DENV-1 classification of the Brun2014 strain was further supported by monoclonal antibody serotyping data. Phenotypic characterization demonstrated that Brun2014 replication rates in mosquito cells and infection rates in Aedes aegypti mosquitoes were not significantly different from an epidemic DENV-1 strain. Given its ability to cause human illness and infect Ae. aegypti, potential urban spillover and clinical disease from further Brun2014 transmission cannot be discounted.

Full-length infectious clone of a low passage dengue virus serotype 2 from Brazil

Full-length dengue virus (DENV) cDNA clones are an invaluable tool for many studies, including those on the development of attenuated or chimeric vaccines and on host-virus interactions. Furthermore, the importance of low passage DENV infectious clones should be highlighted, as these may harbour critical and unique strain-specific viral components from field-circulating isolates. The successful construction of a functional Brazilian low passage DENV serotype 2 full-length clone through homologous recombination reported here supports the use of a strategy that has been shown to be highly useful by our group for the development of flavivirus infectious clones and replicons.

Establishment and characterization of two new cell lines from the mosquito Armigeres subalbatus (Coquillett) (Diptera: Culicidae)

Armigeres subalbatus (Coquillett) is a medically important mosquito and a model species for immunology research. We successfully established two cell lines from the neonate larvae of A. subalbatus using two different media. To our knowledge, this is the first report of an established Armigeres mosquito cell line. The cell lines, designated as Ar-3 and Ar-13, consist of adherent and diploid cells with compact colonies. Both these cell lines grow slowly after passage at a split ratio of 1:5 and a population doubling time of 2.7 and 3.0 d, respectively. Random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) was used to confirm that these lines correspond to the species of origin and are clearly distinct from seven other insect cell lines. Furthermore, reverse-transcription PCR was used to demonstrate that the Ar-3 cell line is susceptible to the Japanese encephalitis virus and two insect flaviviruses associated with Culex and Aedes mosquitoes but relatively insensitive to dengue virus. These data indicate that the newly established cell lines are cellular models of A. subalbatus as well as beneficial tools for the propagation of viruses associated with the Armigeres mosquito.

Analysis of Mosquito-Borne Flavivirus Superinfection in Culex tritaeniorhynchus (Diptera: Culicidae) Cells Persistently Infected with Culex Flavivirus (Flaviviridae)

Superinfection exclusion is generally defined as a phenomenon in which a pre-existing viral infection prevents a secondary viral infection; this has also been observed in infections with mosquito-borne viruses. In this study, we examined the superinfection exclusion of the vertebrate-infecting flaviviruses, Japanese encephalitis virus (JEV) and dengue virus (DENV), by stable and persistent infection with an insect-specific flavivirus, Culex flavivirus (CxFV), in a Culex tritaeniorhynchus Giles cell line (CTR cells). Our experimental system was designed based on the premise that wild Cx. tritaeniorhynchus mosquitoes naturally infected with CxFV are superinfected with JEV by feeding on JEV-infected animals. As a result, we found no evidence of the superinfection exclusion of both JEV and DENV by pre-existing CxFV infection at the cellular level. However, JEV superinfection induced severe cytopathic effects on persistently CxFV-infected CTR cells. These observations imply the possibility that JEV superinfection in CxFV-infected Cx. tritaeniorhynchus mosquitoes has an adverse effect on their fitness.

Complete genome sequencing and evolutionary phylogeography analysis of Indian isolates of Dengue virus type 1

Dengue is now hyper-endemic in most parts of south and southeast Asia including India. The northern India particularly national capital New Delhi witnessed major Dengue outbreaks with Dengue virus type 1 (DENV-1) as the dominant serotype since last five years. This study was initiated to decipher the complete genome information of recently circulating DENV-1 (2009-2011) along with the prototype Indian DENV-1, isolated in 1956. Further extensive ML phylogenetic and Bayesian phylogeography analysis was carried out to investigate the evolution of this virus and understand its spatiotemporal diffusion across the globe. The complete genome analysis revealed deletion of a unique 21-nucleotide stretch in the 3' un-translated region of recent Indian DENV-1. The north Indian DENV-1 revealed up to 5.2% nucleotide sequence difference compared to recent isolates from southern India. Selection pressure analysis revealed positive selection in few amino acid sites of both structural and non-structural proteins. The molecular phylogeny classified the Indian DENV-1 into genotype III, which is also known as cosmopolitan genotype. The northern and southern Indian DENV-1 were grouped into distinct clades. The molecular clock analysis estimated a mean evolutionary rate of 7.08×10(-4) substitutions/site/year for cosmopolitan genotype. The phylogeography analysis revealed that the cosmopolitan genotype DENV-1 originated ∼1938 in India and subsequently spread globally. The diffusion of virus from India to Caribbean and South America was confirmed through SPREAD analysis. This study also confirmed the temporal displacement of different clades of DENV-1 in India over last five decades.

Genetic analysis of West Nile virus isolates from an outbreak in Idaho, United States, 2006-2007

West Nile virus (WNV) appeared in the U.S. in 1999 and has since become endemic, with yearly summer epidemics causing tens of thousands of cases of serious disease over the past 14 years. Analysis of WNV strains isolated during the 2006–2007 epidemic seasons demonstrates that a new genetic variant had emerged coincidentally with an intense outbreak in Idaho during 2006. The isolates belonging to the new variant carry a 13 nt deletion, termed ID-Δ13, located at the variable region of the 3′UTR, and are genetically related. The analysis of deletions and insertions in the 3′UTR of two major lineages of WNV revealed the presence of conserved repeats and two indel motifs in the variable region of the 3′UTR. One human and two bird isolates from the Idaho 2006–2007 outbreaks were sequenced using Illumina technology and within-host variability was analyzed. Continued monitoring of new genetic variants is important for public health as WNV continues to evolve.

Natural infection of cynomolgus monkeys with dengue virus occurs in epidemic cycles in the Philippines

To investigate the potential role of non-human primates (NHPs) in a dengue virus (DENV) epidemic, we conducted serological and genomic studies using plasma samples collected from 100 cynomolgus monkeys (Macaca fascicularis) in an animal breeding facility in the Philippines. An ELISA revealed 21 monkeys with a positive IgM reaction and 19 positive for IgG. Five of the monkeys were positive for both IgM and IgG. Of the 21 IgM-positive samples, a neutralization assay identified seven containing DENV-specific antibodies. We amplified the viral non-structural 1 (NS1) gene in two and the envelope (E) gene in one of these seven samples by RT-PCR. Phylogenetic analyses revealed that these DENV genes belonged to the epidemic DENV-2 family, not the sylvatic DENV family. These results suggest that NHPs may serve as a reservoir of epidemic DENV; therefore, the ecology of the urban DENV infection cycle should be investigated in these animals in detail.

Replacement of conserved or variable sequences of the mosquito-borne dengue virus 3' UTR with homologous sequences from Modoc virus does not change infectivity for mosquitoes

The genus Flavivirus includes both vector-borne and no known vector (NKV) species, but the molecular determinants of transmission mode are not known. Conserved sequence differences between the two groups occur in 5' and 3' UTRs. To investigate the impact of these differences on transmission, chimeric genomes were generated, in which UTRs, UTRs+capsid, or the upper 3' UTR stem-loop of mosquito-borne dengue virus (DENV) were replaced with homologous regions from NKV Modoc virus (MODV); the conserved pentanucleotide sequence (CPS) was also deleted from the DENV genome. Virus was not recovered following transfection of these genomes in three different cell types. However, DENV genomes in which the CPS or variable region (VR) of the 3' UTR were replaced with MODV sequences were recovered and infected Aedes aegypti mosquitoes with similar efficiencies to DENV. These results demonstrate that neither vector-borne CPS nor VR is required for vector-borne transmission.

Construction of an infectious cDNA clone of Culex flavivirus, an insect-specific flavivirus from Culex mosquitoes

Culex flavivirus (CxFV) is an insect-specific flavivirus that has recently been detected in various Culex spp. mosquitoes worldwide. Here, we report the successful construction of a full-length infectious cDNA clone of a Tokyo strain, CxFV-NIID21. The full-length CxFV-NIID21 cDNA was cloned into the low-copy-number plasmid pMW119, which was stably amplified in Escherichia coli. Transfection of a mosquito cell line with in vitro-transcribed RNA from the cDNA clone resulted in the production of recombinant progeny virus with growth properties, cytopathogenicity, and virion morphology similar to the parental virus.

Identification and characterization of the short variable region of the Japanese encephalitis virus 3' NTR

Since the 1980s, the Japanese encephalitis virus (JEV) variants with slightly short variable regions (VR) of the 3' non-translated region (NTR) have been found; however, the implications of these short VR remain unclear. We recently identified two novel types of short VR (5 and 9 nt shorter than that of major group of genotype I JEV strains) of genotype I JEV isolates. To elucidate the impact of these short VR on the replication and virulence of JEV, we generated five recombinant JEV viruses: M41-d5 and M41-d9 have deletions in the VR that correspond to those observed in some recent JEV isolates, M41-d5d9 has both the 5- and 9-nt deletions in the VR, M41-d27 has a large deletion that encompasses both the 5- and 9-nt deletion regions, and M41-a13 has a 13-nt sequence insertion of the genotype III JEV strain Beijing-1 into the parent genotype I JEV strain Mie/41/2002 genome. The recombinant viruses and the parent virus, except for the M41-d27 mutant, showed similar growth properties in mammalian and mosquito cell lines. Mouse challenge experiments indicated that no significant differences among the recombinant viruses M41-d5d9, M41-d27, M41-a13, and the parent virus. Our results suggest that the short VR in JEV 3' NTR do not affect its growth in vitro or its pathogenicity in mice.

An amino acid substitution (V3I) in the Japanese encephalitis virus NS4A protein increases its virulence in mice, but not its growth rate in vitro

Our previous studies have shown that the Japanese encephalitis virus (JEV) strain Mie/40/2004 is the most virulent of the strains isolated by us in Japan from 2002 to 2004. Comparison of the amino acid sequence of Mie/40/2004 with those of low-virulence strains revealed that an isoleucine residue at position 3 of the Mie/40/2004 NS4A protein may increase viral pathogenicity. A recombinant virus with a single valine-to-isoleucine substitution (V3I) at position 3 in the low-virulence Mie/41/2002 background (rJEV-Mie41-NS4AV3I) exhibited increased virulence in mice compared with the Mie/41/2002 parent strain. The V3I mutation did not affect virus growth in several cell lines. These results demonstrate that the isoleucine at position 3 in the NS4A protein of Mie/40/2004 is responsible for its high virulence in vivo. This is the first report to show that an amino acid substitution in a flavivirus NS4A protein alters viral pathogenicity in mice.

Restoration of replication-defective dengue type 1 virus bearing mutations in the N-terminal cytoplasmic portion of NS4A by additional mutations in NS4B

Flavivirus NS4A has an N-terminal hydrophilic cytoplasmic portion; however, the role of this portion remains poorly understood. In this study, we show that a recombinant dengue type 1 virus (DENV-1) in which a subportion (amino acids 27-34) of the N-terminal portion of NS4A is replaced by the corresponding region from Japanese encephalitis virus (JEV) is defective in replication. Using the defective mutant clone NS4A(27-34(JEV)), we recovered suppressor mutant viruses that carry various non-synonymous mutations. Site-directed mutational analysis indicated that a single non-synonymous mutation in NS4B that is found in the suppressor viruses is sufficient to restore NS4A(27-34(JEV)). Recombinant DENV-1 with single mutations in NS4B had increased growth properties as compared to the wild-type virus and NS4A(27-34(JEV)) virus bearing the same NS4B mutation. Collectively, our results suggest that the NS4B mutation enhanced the growth of DENV-1, irrespective of the sequence of the 27-34 subportion NS4A.

Molecular genetic relationship of the 3' untranslated region among Thai dengue-3 virus, Bangkok isolates, during 1973-2000

Dengue virus serotype 3 (DENV-3) was associated with severe dengue epidemics in Thailand during 1973-1999. We studied Thai DENV-3 viruses isolated from hospitalized children in Bangkok with differing disease severity during that period. Viruses were sequenced at their 5' and 3' untranslated regions (UTRs), which are regions that play a pivotal role in viral replication. Our results indicated that the primary sequences as well as the secondary structures at both ends of Thai DENV-3 viruses were highly conserved over almost three decades. We found nucleotide insertions and deletions at the variable region (VR) that is located just downstream of the nonstructural protein 5 (NS5) stop codon among these viruses. The phylogenetic tree derived from the size heterogeneity of VR in the 3' UTR divided DENV-3 into four genotypes, and Thai DENV-3 viruses in this study belonged to genotype II. The replication efficiency of the candidate viruses with different lengths at the VR were assessed in the mosquito (C6/36) and human (HepG2) cell lines. Our results show that the viruses with nucleotide insertions at VR replicated better than the virus that contained deletions. Our findings indicate that Thai DENV-3 demonstrated a remarkable conservation of nucleotides over 28 years. Correlation with disease severity suggests that both primary sequences and secondary structures of the 3' UTR do not appear correlated with disease severity in humans.

Molecular aspects of Dengue virus replication

Dengue virus (DENV)--a mosquito transmitted pathogen--is the causative agent of Dengue fever, the most important arboviral disease of humans, which affects an estimated 50-100 million people annually. Despite the high morbidity and mortality associated with DENV infections, an effective DENV vaccine and antiviral therapies are still missing. An improved understanding of the molecular mechanisms underlying the different steps of the DENV replication cycle, for example, genome replication and virus maturation, could help to develop such substances. Over the past several years, many important findings have been published with respect to a better understanding of DENV replication. In this review we will highlight recent insights into the molecular mechanisms of the viral replication cycle.

Reverse genetics and the study of dengue virus

Dengue virus infection causes the most important arthropod-borne disease of humans. Currently, there are no dengue vaccines or antiviral therapies in clinical use, although their development is a global health priority. Using a technique known as ‘reverse genetics’, the dengue virus RNA genome can be manipulated, either by the introduction of specific mutations or the deletion and/or substitution of entire genes. This has led to the production of novel recombinant viruses that have potential as vaccines and the production of noninfectious viral subgenomes (termed replicons) useful for drug screening. Reverse genetics is also an invaluable tool for studying the role of dengue virus RNA elements and proteins in replication and pathogenesis. This review describes the contribution of reverse genetics to dengue virus research to date, highlighting the potential use of this technology in the development of effective control measures against dengue in the future.

Characterization of Asn130-to-Ala mutant of dengue type 1 virus NS1 protein

The nonstructural protein 1 (NS1) of flavivirus has two N-glycosylation sites that are thought to be important for viral replication. Effects of NS1 glycosylation site mutations on viral replication have been reported in several flaviviruses, but the results have differed. In this report, we examined the role of glycosylation site of NS1 on the replication of dengue type 1 virus (DENV-1). DENV-1 production was not detectable when full-length DENV-1 RNA, which has an N-glycosylation site Asn130-to-Ala (Asn130Ala) mutation in NS1, was transfected into mammalian and mosquito cells. However, replication and secretion of recombinant DENV-1 with the NS1 Asn130Ala mutation were recovered by exogenously expressed wild-type DENV-1 NS1. A growth kinetics experiment showed that propagation of wild-type DENV-1 was prevented by NS1 Asn130Ala mutant expression in trans. Our results suggest that Asn130 of the DENV-1 NS1 is important for viral replication in both mammalian and mosquito cells.

A PCR-based protocol for generating West Nile virus replicons

A new protocol for the generation of West Nile virus (WNV) replicons was developed. Fragmented cDNAs that covered the entire WNV RNA sequence, except the sequence corresponding to nucleotides 190-2379, were amplified separately by polymerase chain reactions (PCRs) using primer set franking with overlapping sequences of 40-50 bp at the 5'- and the 3'-ends of each fragment. All amplified fragments were mixed together and annealed to each other at the overlapping sequences. The annealed-DNA fragments were elongated by DNA polymerase and amplified by short-cycle PCRs to generate full-sized WNV replicon cDNAs. The WNV replicons were transcribed in vitro using the replicon cDNAs as templates. When the in vitro-transcribed replicon was introduced into mammalian cells, the viral envelope protein and viral positive- and negative-strand RNAs were detected in the replicon-transfected cells. It is noteworthy that the synthesis of the replicon cDNAs and the replicons took just 1 week, and that the use of a high-fidelity DNA polymerase afforded stability to the sequence of the synthetic replicon.

Characterization of the variable region in the 3' non-translated region of dengue type 1 virus

The first 84 nt in the 3' non-translated region (3' NTR) of dengue type 1 virus (DENV-1) exhibit lower levels of conservation than the other regions; this region is named the variable region (VR). The VR is further divided into two subregions: a 5'-terminal hypervariable region (HVR) and a 3'-terminal semi-variable region (SVR). Recent reports suggested that the VR of DENV-2 is required for efficient virus growth in mammalian cells. To investigate whether this is also true for the VR of DENV-1, deletion or replacement mutations were introduced into the VR by using recombinant DENV-1 cDNA clones. Recombinant viruses with deletion of either or both subregions exhibited reduced growth properties compared with the original virus. Mutants with incompletely reversed or unrelated sequences in the HVR demonstrated growth properties similar to those of the original virus. However, a replacement mutation in the SVR did not cause recovery of growth properties. Furthermore, the amount of viral RNA was decreased in Vero cells infected with the growth-attenuated mutant viruses. Results of reporter translation assays suggest that VR mutations may not affect the translation process of DENV-1. These data indicate that the VR is important for DENV-1 replication and is associated with the accumulation of DENV-1 RNA in mammalian cells, and that the HVR and SVR in the VR may have different roles in DENV-1 replication.

Rapid fixation of a distinctive sequence motif in the 3' noncoding region of the clade of West Nile virus invading North America

Phylogenetic analysis of complete genomes of West Nile virus (WNV) by a variety of methods supported the hypothesis that North American isolates of WNV constitute a monophyletic group, together with an isolate from Israel and one from Hungary. We used ancestral sequence reconstruction in order to obtain evidence for evolutionary changes that might be correlated with increased virulence in this clade (designated the N.A. clade). There was one amino acid change (I-->T at residue 356 of the NS3 protein) that occurred in the ancestor of the N.A. clade and remained conserved in all N.A. clade genomes analyzed. There were four changes in the upstream portion of the 3' noncoding region (the AT-enriched region) that occurred in the ancestor of the N.A. clade and remained conserved in all N.A. clade genomes analyzed, changes predicted to alter RNA secondary structure. The AT-enriched region showed a higher rate of substitution in the branch ancestral to the N.A. clade, relative to polymorphism, than did the remainder of the noncoding regions, synonymous sites in coding regions, or nonsynonymous sites in coding regions. The high rate of occurrence of fixed nucleotide substitutions in this region suggests that positive Darwinian selection may have acted on this portion of the 3'NCR and that these fixed changes, possibly in concert with the amino acid change in NS3, may underlie phenotypic effects associated with increased virulence in North American WNV.

Novel dengue virus type 1 from travelers to Yap State, Micronesia

Dengue virus type 1 (DENV-1), which was responsible for the dengue fever outbreak in Yap State, Micronesia, in 2004, was isolated from serum samples of 4 dengue patients in Japan. Genome sequencing demonstrated that this virus belonged to genotype IV and had a 29-nucleotide deletion in the 3´ noncoding region.