A PCR-restriction enzyme technique for determining dengue virus subgroups within serotypes

Genetic polymorphisms rs1800871 and rs1800872 of IL-10 gene are associated with dengue infection, especially with serotype 1 and DwoWS in Mexican population

INTRODUCTION

Dengue infection is generated by a complex interaction between DENV (Dengue Virus) and the host's immune response. Interleukin-10 is an immunoregulatory cytokine during DENV infection. The objective of this study was to investigate whether genetic variants in IL-10 could be useful as a predictive and susceptibility marker in the prognosis of DENV infection, particularly with serotype 1, and in participants with dengue without warning signs.

MATERIAL AND METHODS

A study of cases (n = 365) and controls (n = 364) was carried out. Genotyping was performed by real-time PCR using TaqMan probes. Sample size power was calculated using Quanto software RESULTS: This is the first report showing the independent association of the T allele of rs1800871 (P = 0.023) and the A allele of rs1800872 (P = 0.010) with the risk of dengue infection. Statistical analysis established the genotypic association of IL-10 SNPs with DENV infection under different inheritance models. Our results also showed the association of the CC, TC, and CA haplotypes (P = 0.0064, P = 0.0032, and P = 0.0010 respectively) with infection. Furthermore, both polymorphic sites were associated with the risk of DwoWS and serotype 1 (Den-1) under different inheritance models. Finally, under the dominant model, we identified a positive correlation between IL-10 levels vs. IFN-γ and IL-8.

CONCLUSION

Our results show the first independent association of the T and A alleles of the polymorphic sites rs1800871 and rs1800872, with dengue infection, particularly with Den-1, and in participants with DwoWs.

Gene Polymorphisms and Serum Levels of Pro- and Anti-Inflammatory Markers in Dengue Viral Infections

Pro- and anti-inflammatory markers (tumor necrosis factor [TNF]-α, TNF-β, interferon [IFN]-γ, interleukin [IL]-6, IL-8, IL-10, and C-reactive protein [CRP]) were investigated in 80 patients infected with dengue viruses, 100 patients presenting with febrile illness but negative for dengue, and 99 healthy subjects. Immunoenzyme methods were used for quantitative assays in the plasma. Polymorphisms of TNF-α, TNF-β, IL-6, IL-8, and IL-10 genes were assessed by polymerase chain reaction (PCR)-restriction fragment length polymorphism and allele-specific oligonucleotide (ASO)-PCR for the IFN-γ. The highest mean serum levels of TNF-α, IFN-γ, IL-8, and CRP were observed in dengue-positive individuals. TNF-β, IL-6, and IL-10 levels were significantly higher in the dengue-negative individuals. No cytokine expression pattern was evidenced according to virus serotype. Genotypic frequency distributions were statistically significant for the polymorphisms of TNF-α and IFN-γ among positive, negative, and control dengue groups and IFN-γ among groups DENV-1, DENV-2, DENV-3, and controls. Modulation of cytokine expression and polymorphisms is a complex matter and needs further explanation considering the ethnic origins of the Brazilian population.

Simple, specific molecular typing of dengue virus isolates using one-step RT-PCR and restriction fragment length polymorphism

A one-step RT-PCR and one-enzyme RFLP was used to detect and distinguish among flaviviruses, including the four serotypes of dengue and the St. Louis Encephalitis, West Nile and Yellow Fever viruses in cultured virus samples or acute-phase human serum. Using a previously described RT-PCR, but novel RFLP procedure, results are obtained in 24 h with basic PCR and electrophoresis equipment. There is 95% agreement between RT-PCR/RFLP results and those achieved by indirect immunofluorescence assays, and 100% agreement between RT-PCR/RFLP results and gene sequencing. This method is more rapid than tests of cytopathic effect based on virus isolation in tissue culture, and simpler than real-time PCR. It does not require specialized equipment, radioisotopes or computer analysis and is a method that can be applied widely in the developing world. It allows for prompt determination of whether a flavivirus is the cause of illness in a febrile patient, rapid identification of dengue serotypes in circulation, and improved patient management in cases where prior dengue exposure make dengue hemorrhagic fever or dengue shock syndrome a risk.

Endurance, refuge, and reemergence of dengue virus type 2, Puerto Rico, 1986-2007

To study the evolution of dengue virus (DENV) serotype 2 in Puerto Rico, we examined the genetic composition and diversity of 160 DENV-2 genomes obtained through 22 consecutive years of sampling. A clade replacement took place in 1994-1997 during a period of high incidence of autochthonous DENV-2 and frequent, short-lived reintroductions of foreign DENV-2. This unique clade replacement was complete just before DENV-3 emerged. By temporally and geographically defining DENV-2 lineages, we describe a refuge of this virus through 4 years of low genome diversity. Our analyses may explain the long-term endurance of DENV-2 despite great epidemiologic changes in disease incidence and serotype distribution.

Genetic diversity of the E protein of dengue type 3 virus

Background

Dengue is the most important arbovirus disease in tropical and subtropical countries. The viral envelope (E) protein is responsible for cell receptor binding and is the main target of neutralizing antibodies. The aim of this study was to analyze the diversity of the E protein gene of DENV-3. E protein gene sequences of 20 new viruses isolated in Ribeirao Preto, Brazil, and 427 sequences retrieved from GenBank were aligned for diversity and phylogenetic analysis.

Results

Comparison of the E protein gene sequences revealed the presence of 47 variable sites distributed in the protein; most of those amino acids changes are located on the viral surface. The phylogenetic analysis showed the distribution of DENV-3 in four genotypes. Genotypes I, II and III revealed internal groups that we have called lineages and sub-lineages. All amino acids that characterize a group (genotype, lineage, or sub-lineage) are located in the 47 variable sites of the E protein.

Conclusion

Our results provide information about the most frequent amino acid changes and diversity of the E protein of DENV-3.

Characterization of dengue virus serotype 1 in epidemics in Porto Velho, Rondônia, in 2001-2003

The first dengue fever epidemic in the State of Rondônia (western region of Brazil) was recorded in 1997, without laboratory confirmation. Following this, there was an epidemic in Manaus, in the neighboring State of Amazon, in 1998, in which DENV-1 and DENV-2 viruses were isolated from patients. In the present paper, the serotype characterization of the dengue virus isolated from patients with clinically suspected dengue in Porto Velho, Rondônia, between 2001 and 2003 is described. One hundred and fifty blood samples were collected between the first and fifth days of symptoms. Seventy samples of virus isolates were subjected to dengue identification by means of RT-PCR using universal primers for the NS1 gene of DENV, which amplifies a 419 bp fragment. The amplicons obtained were subjected to enzymatic digestion to characterize the viral serotypes. All the samples analyzed were DENV-1. A nucleotide sequence randomly selected from one amplicon, which was also DENV-1, presented 98% similarity to sequences from Southeast Asia that were obtained from GenBank.

Effect of dengue-1 antibodies on American dengue-2 viral infection and dengue haemorrhagic fever

In Iquitos, Peru, no cases of dengue haemorrhagic fever have been recorded in individuals infected with dengue-1 virus followed by American genotype dengue-2 (American dengue-2) virus. We assayed serum samples collected in Iquitos that tested positive for antibodies of monotype dengue-1 and monotype dengue-2 using a plaque reduction neutralisation test to determine their ability to neutralise the infectivity of two dengue-1 viruses, two American dengue-2 viruses, and two Asian dengue-2 viruses. Sera positive for the dengue-1 antibody neutralised dengue-1 viruses and American dengue-2 viruses much more effectively than Asian dengue-2 viruses. Neutralisation of American dengue-2 virus by sera positive for dengue-1 antibodies may account for the absence of dengue haemorrhagic fever in individuals infected with dengue-1 in 1990-91 followed by American dengue-2 virus in 1995 in Iquitos, Peru.

The use of reverse transcription-polymerase chain reaction (RT-PCR) for the rapid detection and identification of dengue virus in an endemic region: a validation study

Dengue is the most important arboviral disease worldwide. Dengue diagnosis is usually made by serology, but serological techniques do not identify the infecting strain, and are only useful late in the course of infection. Several reverse transcription-polymerase chain reaction (RT-PCR) protocols have been described for dengue diagnosis but none of them has been used on a regular basis. We conducted a validation study of PCR-based diagnosis in an area (in Brazil) where dengue-1 virus has been circulating at a low incidence rate. Viral detection by RT-PCR was evaluated using the sera of 253 patients with clinical diagnosis of dengue, and the results were compared to those obtained by IgM capture enzyme-linked immunosorbent assay (MAC-ELISA) and virus isolation. Out of 75 IgM-positive samples, 17 were RT-PCR positive, and only 2 were positive for virus isolation. Through enzymatic digestion of PCR amplicons, we were able to differentiate the 2 dengue serotypes circulating in Brazil (dengue-1 and dengue-2), and to determine that dengue-1 was the virus responsible for the infections. We show with this study that RT-PCR is more sensitive than virus isolation on clinical samples and allows for a rapid detection of dengue infections and for a straightforward identification of the circulating serotype.

Detection and identification of dengue-1 virus in clinical samples by a nested-PCR followed by restriction enzyme digestion of amplicons

Dengue viruses cause a disease with clinical findings ranging from asymptomatic infections to severe manifestations, characterised by haemorrhage and shock and known as dengue haemorrhagic fever/dengue shock syndrome. Since this fever and syndrome usually results from sequential infections by distinct dengue serotypes, rapid detection and identification of dengue viruses circulating in endemic areas are important to implement control measures, and ultimately to avoid secondary infections that could result in dengue haemorrhagic fever/dengue shock syndrome. A nested-PCR was developed followed by restriction enzyme (Kpn I) digestion of the amplicons to differentiate dengue-1 from dengue-2. Seventy-five IgM-containing samples collected from 2 to 17 days after the beginning of the symptoms were examined. These samples were submitted to nested-PCR amplification, the amplicons were digested with Kpn I, and the results compared to virus isolation in C6/36 cells and to results obtained by the standard PCR. Out of 75 tested samples, virus was isolated from 2 (2.6%), 17 (22.7%) were positive by the regular PCR protocol, and 58 (77.3%) were positive by nested-PCR. All of the amplicons digested by Kpn I identified dengue-1 virus as the infecting strain. These results indicate that the nested-PCR provided a high yield of dengue genome amplification even in the presence of IgM antibodies, and restriction enzyme digestion defined rapidly the circulating serotype. Therefore, the combination of these techniques may be useful to rapidly identify dengue viruses in countries where dengue-1 and dengue-2 circulates, and this approach can also be applied to the other two serotypes.

Rapid subtyping of dengue virus serotypes 1 and 4 by restriction site-specific PCR

We previously reported a simple subtyping method, restriction site-specific PCR (RSS-PCR), for dengue virus serotypes 2 and 3; here we describe its application for subtyping dengue virus serotypes 1 and 4. Three major RSS-PCR types were observed for dengue virus serotype 1 and two types were observed for dengue virus serotype 4, in agreement with previous strain classifications based on sequence analysis. Because of its simplicity, this method is amenable to rapid subtyping and application to epidemiological studies of dengue in countries where dengue is endemic.

Short communication: dengue serotype 2 subtype III ('Jamaica') epidemic in Santa Cruz, Bolivia

BACKGROUND

During the past decade, dengue and dengue haemorrhagic fever (DHF) have become a public health problem in various Latin American countries. Indications of increased dengue cases in the city of Santa Cruz, Bolivia, early in 1997 were promptly investigated.

METHODS

We conducted a sample sero-survey in one district of the city. Levels of antidengue IgM were determined and genetic analysis was performed on virus isolates.

RESULTS

IgM antibodies were detected in 6.5% (95% CI: 3.4%-9.6%) of adults (over 15 years old) and 5.1% (2.0%-8.2%) of children (5-7 years old). Dengue virus serotype 2 subtype III ('Jamaica') was isolated.

CONCLUSIONS

The estimated attack rates are compatible with a dengue epidemic in Santa Cruz. Isolation of dengue-2 'Jamaica' virus documents the further spread of this subtype from the Caribbean via Brazil into South America. Increased DHF preparedness seems mandatory.

Coupled PCR-restriction enzyme analysis for rapid identification of structural gene relationships among strains of eastern equine encephalitis virus

We have used restriction endonuclease digestion analysis of polymerase chain reaction (PCR)-amplified gene regions to rapidly examine individual structural gene relationships among field isolates of eastern equine encephalitis (EEE) virus. The E1+ (E1 gene plus 292 nucleotides 3' of the coding region), E2, and C gene regions from North American (NA) variety viruses and the E1 and C gene regions of South American (SA) variety viruses were successfully amplified by RT-PCR using a single primer set for each locus. The products were then digested with a panel of restriction endonucleases and the resulting DNA fragments electrophoretically compared. Our findings revealed marked similarity among the E1+ and the E2 gene restriction patterns, respectively, of most NA strains. In contrast, the restriction patterns exhibited by the E1+ gene of SA strains differed substantially from those of NA strains and also appeared more heterogeneous. The digestion patterns of the C gene were generally similar for all strains of the virus examined. These results thus demonstrate that EEE viral E1+ and C structural gene sequences can be amplified from an assortment of both NA and SA varieties of the virus by RT-PCR using a single primer set per locus, and that both varietal and individual isolate distinctions can be identified by comparison of subsequent restriction digestion patterns. This technique should prove useful as an epidemiological tool for rapid identification of EEE isolates from clinical and field specimens, and as a rapid screen for alterations within structural gene regions.

A strain-type clustering of potato virus Y based on the genetic distance between isolates calculated by RFLP analysis of the amplified coat protein gene

Potato virus Y (PVY) isolates have been classified into genetic strains by a host-independent criterion using a molecular typing method. The method used extracts from infected tissue, and included immunocapture-RT-PCR-RFLP analysis using 5 different restriction endonucleases (Dde I, Eco RV, Hinf I, Rsa I and Taq I). Genetic distances between the different PVY "restrictotypes" were calculated and used to define the PVY genetic strains. Three main clusters were found: PVYO, PVYN, and non-potato PVY (PVYNP), in good agreement with classical PVY strain definitions that combine different biological criteria. Our approach was incomparably quicker and more reliable and reproducible than biotyping. The potential of this approach for very quick, simple and automatable molecular epidemiological studies is discussed.