Molecular evolution and distribution of dengue viruses type 1 and 2 in nature

Dengue: the risk to developed and developing countries

Dengue viruses are members of the Flaviviridae, transmitted principally in a cycle involving humans and mosquito vectors. In the last 20 years the incidence of dengue fever epidemics has increased and hyperendemic transmission has been established over a geographically expanding area. A severe form, dengue hemorrhagic fever (DHF), is an immunopathologic disease occurring in persons who experience sequential dengue infections. The risk of sequential infections, and consequently the incidence of DHF, has risen dramatically, first in Asia and now in the Americas. At the root of the emergence of dengue as a major health problem are changes in human demography and behavior, leading to unchecked populations of and increased exposure to the principal domestic mosquito vector, Aedes aegypti. Virus-specified factors also influence the epidemiology of dengue. Speculations on future events in the epidemiology, evolution, and biological expression of dengue are presented.

Identification of mosquito-borne flavivirus sequences using universal primers and reverse transcription/polymerase chain reaction

A reverse transcription/polymerase chain reaction (RT/PCR) protocol for the rapid detection and identification of flaviviruses was developed using a set of universal oligonucleotide primers. These primers correspond to sequences in the 3' non-coding region and in the NS5 gene which are highly conserved among the mosquito-borne flaviviruses. The sequences of the resulting amplified products were analysed for dengue 1, dengue 2, dengue 3, dengue 4, Japanese encephalitis, West Nile, yellow fever and Zika viruses, and compared with the published sequences of other flaviviruses. The 291-297 nucleotides corresponding to the C-terminus of NS5 gene showed 56 to 76% similarity, whereas the 3' non-coding region (190 to 421 nucleotides) showed only 20 to 36% similarity. Genetic classification of the Zika virus supported its traditional serological grouping. Recombinant plasmids containing the flavivirus sequences were used in a nucleic acid hybridization test to identify the RT/PCR products derived from viral RNA extracted from experimentally infected mosquitoes. The plasmids were dotted on a strip of nitrocellulose membrane and incubated with the RT/PCR product labelled with digoxigenin during the PCR step. This is a valuable method for the rapid and specific identification of mosquito-borne flaviviruses in biological specimens and for subsequent sequence analysis.

Restriction enzyme analysis of American region dengue viruses

Restriction fragment heterogeneity of Hae III digestion products of cDNA to virion RNA was used to map the distribution of dengue virus topotypes found in the American region. By comparing the electrophoretic patterns of fragments produced, dengue virus isolates were placed in groups that agreed with those previously determined by oligonucleotide fingerprinting. Dengue-1 and dengue-4 viruses occur throughout the western hemisphere as single genetic types, with most of the isolates sharing at least 70% of their Hae III restriction enzyme fragments. Dengue-2 virus exists as two topotypes in the region with apparently non-overlapping distributions. The Puerto Rico topotype, which has been in the Caribbean for at least 40 years, is genetically diverse, while the Jamaica topotype, first isolated in 1981, is more homogeneous and has expanded its range from the original Caribbean focus to South America.

Genetic and biological differentiation of dengue 3 isolates obtained from clinical cases in Java, Indonesia, 1976-1978

Previous epidemiological, virological and clinical studies have documented a series of outbreaks of dengue fever and dengue haemorrhagic fever/dengue shock syndrome which occurred in Java, Indonesia in 1976-1978. In the current study we compare growth characteristics in cell culture, and nucleotide sequence data for the viral prM and E genes, of five low passage DEN-3 isolates obtained during these epidemics from clinically defined cases. All isolates had the same passage history: human sera were passed twice in mosquitoes and three times in a mosquito cell line (Aedes albopictus, C 6/36 cells). Growth differences were observed between individual isolates in Vero cells; growth differences were not observed in C 6/36 cells. Nucleotide sequencing of the prM and E gene region indicated that no two isolates were identical (sequence divergence ranged from 0.4 to 1.6% in pairwise comparisons) but that they were closely enough related to present a single genetic type. There were one or two differences in deduced amino acid sequence in E between isolates. Differences were at residues 65, 187, 298 or 443. One isolate differed from all others at residue 16 in the M protein. No relationship was apparent between the amino acid sequence of M or E and the nature of the disease profile, the year of isolation or the geographic region of isolation. The isolates showed 3.5 to 4.4% nucleotide sequence divergence from the highly-adapted H 87 prototype, isolated in the Philippines in 1956. The isolates showed a total of twelve common amino acid differences in prM and E proteins from H 87. Ten of these twelve residues were at positions which differed between the four dengue serotypes. Two differences (at residues 37 in M and 293 in E) were at positions which are conserved in sequence between the four dengue serotypes. The data are discussed in relation to the dengue outbreaks in Java in the period 1976-1978.

Use of NS3 consensus primers for the polymerase chain reaction amplification and sequencing of dengue viruses and other flaviviruses

Consensus primers for the polymerase chain reaction were designed based on conserved motifs within the serine protease and RNA helicase domains encoded by the NS 3 genes of dengue and other flaviviruses. Target fragments of 470 bp were amplified on cDNA templates synthesized from RNAs of dengue types 1, 2, 3, and 4, Japanese encephalitis, Kunjin, and yellow fever viruses using random or specific downstream primers. PCR of oligo(dT)-primed cDNAs from Japanese encephalitis and Kunjin viral RNAs did not yield target bands. As few as 10(3) copies of dengue viral RNA could be detected. Direct DNA sequencing of PCR products of reference strains of dengue 2 (NGC), Kunjin (MRM 61C) and yellow fever (17 D) viruses demonstrated complete concurrence with published data. However, 2 nucleotide differences were observed between our data for dengue 3 H87 strain and the published sequence, resulting in a single amino acid disparity. Differences at 21, 16, and 11 nucleotide positions were noted between dengue 1 Hawaii and S 275/90; dengue 4 H 241 and 814669; Japanese encephalitis Nakayama and JaOArS 982 viral strains, culminating in only 4, 1 and 1 amino acid residue differences, respectively. These amino acid disparities occurred outside putative active sites of the enzymatic domains, emphasizing the important role of the NS3 protein in flaviviral replication. This RNA-PCR consensus primer strategy coupled with DNA sequencing represents a valuable tool for the molecular diagnosis and epidemiology of dengue and other flaviviral infections.

Direct sequencing of genomic cDNA fragments amplified by the polymerase chain reaction for molecular epidemiology of dengue-2 viruses

A nucleotide fragment encoding amino acids 29 to 94 in the E-protein of 28 dengue-2 isolates of diverse geographic and host origins was examined by direct sequencing of a polymerase chain reaction (PCR)-amplified product, and compared to six previously published sequences. Nucleotide divergence ranged from 0 to 19.8% corresponding to a maximum of 9% divergence in the amino acid sequence. Taking a divergence of 6% between the nucleotide sequence as a cut off for genotype classification, six groups have been established. Southeast Asian and the Jamaican 1983 genotypes show a high rate of similarity (> 95.2%). Our results suggest that virus of this group is now circulating as the dominant topotype in Brazil (1990) and in French Guyana (1986-1991). African strains fall into two groups, one endemic group (1970-1990) and one epidemic group (1986-1987). The three other groups correspond to viruses from Sri Lanka (1982) and the Seychelles (1977), from Puerto Rico (1973) and from Tahiti (1975). Our approach appears to be valuable characterizing dengue isolates, easily and rapidly.

Geographical clusters of dengue virus type 2 isolates based on analysis of infected cell RNA by the chemical cleavage at mismatch method

Genetic variation in 12 strains of dengue virus type 2, isolated from several epidemic areas in different years, was studied by chemical cleavage at mismatched cytosine in DNA:RNA heteroduplexes. End-labelled cDNA probes derived from the E and NS2A genes of the New Guinea C strain were hybridized to total RNA extracted from cells infected by individual isolates. Following modification of mismatched cytosine by hydroxylamine and nucleic acid strand cleavage by piperidine, the resulting fragments of radiolabelled probe were analysed by electrophoresis and autoradiography. The patterns of bands generated corresponded to the geographical groupings of the isolates. Thus this method is suitable in epidemiological studies for rapidly surveying a large number of isolates for genetic variation in a particular gene of interest.

Direct sequencing of large flavivirus PCR products for analysis of genome variation and molecular epidemiological investigations

The polymerase chain reaction (PCR) was used to amplify viral cDNAs from selected regions of dengue genomic RNA by using appropriate 'consensus' primers. DNA amplicons containing the structural genes from all 4 dengue serotypes were prepared and directly sequenced using dengue-virus-specific primers. This method can characterize reliably flavivirus field isolates at the molecular level without extensive virus propagation and molecular cloning, and will be a valuable tool for molecular epidemiological studies.

Direct sequence analysis of amplified dengue virus genomic RNA from cultured cells, mosquitoes and mouse brain

A method is described for direct sequence analysis of selected regions of dengue virus genomic RNA in infected tissues. Using specific primers, total high-molecular-weight infected-cell RNA is reverse transcribed to single-stranded (ss) complementary DNA, amplified using the polymerase chain reaction (PCR) and sequenced using ssDNA obtained after lambda exonuclease digestion of one strand of the PCR product (R.G. Higuchi and H. Ochman, Nucleic Acids Research, 17, 5865, 1989). Sequence data for the envelope protein gene of two dengue-3 virus isolates were obtained using RNA from small numbers (10(5)) of cultured mosquito or monkey kidney cells, from one mg of infected mouse brain and from 1/300th of an infected Toxorhynchites amboinensis mosquito. Independent determinations showed that errors occurring during reverse transcription or PCR were not represented to a significant degree in the sequence of the amplified DNA. The method does not depend on extensive passaging of virus or large-scale growth to generate material for sequencing and therefore provides a means of obtaining sequence data for unadapted dengue virus isolates.

Full-length cDNA sequence of dengue type 1 virus (Singapore strain S275/90)

The complete nucleotide sequence and the deduced amino acid sequence of the genome of dengue virus type 1 (Singapore strain S275/90) were determined from cDNA clones. The single-stranded, positive-sense RNA is 10,718 nucleotides in length and contains a single long open reading frame of 10,188 nucleotides encoding a polyprotein of 3396 amino acids. The genomic size and organization were found to be similar to that of other dengue virus serotypes. Both the nucleotide and deduced amino acid sequences were compared with the partial sequence of DEN1 (Nauru Island) and complete sequences of DNE2 (Jamaica), DEN3 (H87), and DEN4 (Dominica) virus genomes.

Molecular variants of human papillomavirus type 16 from four continents suggest ancient pandemic spread of the virus and its coevolution with humankind

We have amplified by the polymerase chain reaction, cloned, and sequenced genomic segments of 118 human papillomavirus type 16 (HPV-16) isolates from 76 cervical biopsy, 14 cervical smear, 3 vulval biopsy, 2 penile biopsy, 2 anal biopsy, and 1 vaginal biopsy sample and two cell lines. The specimens were taken from patients in four countries--Singapore, Brazil, Tanzania, and Germany. The sequence of a 364-bp fragment of the long control region of the virus revealed 38 variants, most of which differed by one or several point mutations. Phylogenetic trees were constructed by distance matrix methods and a transformation series approach. The trees based on the long control region were supported by another set based on the complete E5 protein-coding region. Both sets had two main branches. Nearly all of the variants from Tanzania were assigned to one (African) branch, and all of the German and most of the Singaporean variants were assigned to the other (Eurasian) branch. While some German and Singaporean variants were identical, each group also contained variants that formed unique branches. In contrast to the group-internal homogeneity of the Singaporean, German, and Tanzanian variants, the Brazilian variants were clearly divided between the two branches. Exceptions to this were the seven Singaporean isolates with mutational patterns typical of the Tanzanian isolates. The data suggest that HPV-16 evolved separately for a long period in Africa and Eurasia. Representatives of both branches may have been transferred to Brazil via past colonial immigration. The comparable efficiencies of transfer of the African and the Eurasian variants to the New World suggest pandemic spread of HPV-16 in past centuries. Representatives of the African branch were possibly transferred to the Far East along old Arab and Indonesian sailing routes. Our data also support the view that HPV-16 is a well-defined virus type, since the variants show only a maximal genomic divergence of about 5%. The small amount of divergence in any one geographic location and the lack of marked divergence between the Tanzanian and Brazilian African genome variants two centuries after their likely introduction into the New World suggest a very slow rate of viral evolution. The phylogenetic tree therefore probably represents a minimum of several centuries of evolution, if not an age equal to that of the respective human races.

Direct nucleotide sequencing using total cellular RNA from dengue-virus-infected mosquito cells

In recent years, a large amount of nucleotide sequence data for dengue viruses has been published. Most of it was derived by sequencing cDNA synthesized from highly purified genomic viral RNA. This paper presents a simple and rapid method for the isolation of total RNA from mosquito cells infected with dengue viruses. This RNA can be used for direct nucleotide sequencing with specific primers without the need for further purification.

Sequence variants of human papillomavirus type 16 in clinical samples permit verification and extension of epidemiological studies and construction of a phylogenetic tree

Genomic variability between different viral isolates provides a powerful epidemiological tool for verifying ultrasensitive diagnostic procedures, understanding infectious pathways in individuals and human populations, and studying viral evolution. The potential of this approach has not yet been exploited for the diagnosis of human papillomaviruses (HPVs) like HPV type 16 (HPV-16), which are involved in genital cancer. Toward this end, we amplified by polymerase chain reaction, cloned, and sequenced a 364-bp noncoding segment of the HPV-16 genome from cell lines, cervical biopsy specimens, and cervical smears. The HPV-16 genomes in the cell lines SiHa and CaSki showed an identical point mutation, and in the SiHa cell line it had an additional 38-bp deletion. Only 4 of 22 cervical lesions biopsied from patients at several hospitals in Singapore contained HPV-16 DNA with the prototype sequence, while the DNAs of the other 18 cervical lesions differed by 1 to 10 mutations. This excludes contaminations with cloned HPV-16 DNA as the source of this DNA. To test whether this diversity was a geographic idiosyncrasy, we analyzed 25 cervical biopsy specimens from Brazil. Eight of these contained the prototype sequence, while 17 were mutated. Altogether, 11 genomic variants were found in the Singaporean samples and 12 genomic variants were found in the Brazilian samples, and only 5 of these occurred identically in both cohorts. All variants could be connected to form a phylogenetic tree, with some branches being specific for each cohort. This suggests that the variants did not originate over a short period in the individual patient but, rather, evolved consecutively while spreading throughout humankind.(ABSTRACT TRUNCATED AT 250 WORDS)

NS 1 gene sequences from eight dengue-2 viruses and their evolutionary relationships with other dengue-2 viruses

The nucleotide sequences of the NS 1 genes from five Thai and three Sri Lankan dengue-2 viruses were determined by sequencing the viral RNA using synthetic oligonucleotide primers. The results were shown to be similar to four published dengue-2 NS 1 sequences and the classification of these genes was compared with the one obtained for the envelope genes of the same viruses. The classification was similar and showed that the Thai isolates could be divided into two separate groups and that the Sri Lankan isolates were distinct. We found no correlation between disease severity, serological response (1 degree or 2 degrees), or year of isolation and various aspects of NS 1 protein sequence variation; and no particular amino acid changes were correlated with virulence. The sequences were combined with those published and classified elsewhere to provide a comprehensive E/NS 1 gene taxonomy of dengue-2 virus isolates.

New viruses and new disease: mutation, evolution and ecology

Given the extraordinarily high mutation rate of viruses, particularly those with RNA genomes, it is not surprising that new viruses are continually evolving. However, the symptomatology of old viral diseases has remained stable for centuries. The combination of genetic and ecological factors that constrain as well as facilitate the emergence of new viruses is analyzed.

Molecular evolution of eastern equine encephalomyelitis virus in North America

We examined the rate and spatial pattern of eastern equine encephalomyelitis virus (EEEV) evolution in North America using primer-extension sequencing of viral RNA. Nucleotide sequences of the entire 26 S structural gene region of four EEEV strains revealed remarkable conservation between 1933 and 1985, with an estimated 0.7% divergence or 1.4 x 10(-4) nucleotide substitutions per site per year. Sequences from smaller 26 S regions of nine additional strains suggested that EEEV evolves in North America in a single lineage, with genetic exchange regularly occurring among enzootic transmission foci. In these limited 26 S genome regions, only synonymous nucleotide substitutions became fixed between 1933 and 1988, implying a high degree of conservation in protein structure. Short nucleotide sequences from a Panamanian, South American variety isolate revealed a relatively distant relationship to North American serotype viruses. This suggested genetic divergence between antigenic varieties, and independent evolution of EEEV in North and South America. Factors related to replication and epidemiology of EEEV, which may constrain its evolution in nature, are discussed. Possible mechanisms of genetic exchange among enzootic foci are also considered.

Identification of dengue sequences by genomic amplification: rapid diagnosis of dengue virus serotypes in peripheral blood

Polymerase chain reaction (PCR) was developed for the in vitro amplification of dengue virus RNA via cDNA. A fraction of the N-terminus gene of the envelope protein in the four dengue serotypes was amplified using synthetic oligonucleotide primer pairs. Amplified products were cloned and used as dengue type-specific probes in gel electrophoresis and dot-blot hybridization. We detected and characterized dengue virus serotypes in blood samples by the three-step procedure DNA-PAH consisting in cDNA priming (P), DNA amplification (A) and hybridization (H) using specific non-radiolabelled probes. Our findings showed that DNA-PAH was more rapid and sensitive in the identification of the infecting serotype than the mosquito cell cultures. Moreover, the failure of cultures to detect virus particles in sera containing few copies of viral genome or anti-dengue antibodies justified the approach of DNA-PAH to the dengue identification in clinical specimens.

The dengue viruses

Dengue, a major public health problem throughout subtropical and tropical regions, is an acute infectious disease characterized by biphasic fever, headache, pain in various parts of the body, prostration, rash, lymphadenopathy, and leukopenia. In more severe or complicated dengue, patients present with a severe febrile illness characterized by abnormalities of hemostasis and increased vascular permeability, which in some instances results in a hypovolemic shock. Four distinct serotypes of the dengue virus (dengue-1, dengue-2, dengue-3, and dengue-4) exist, with numerous virus strains found worldwide. Molecular cloning methods have led to a greater understanding of the structure of the RNA genome and definition of virus-specific structural and nonstructural proteins. Progress towards producing safe, effective dengue virus vaccines, a goal for over 45 years, has been made.