Novel synthetic nucleotides of notifiable dengue (1–4), Japanese encephalitis, yellow fever and Zika flaviviruses

Aim: To produce synthetic nucleotides of notifiable dengue virus (1–4 types), Japanese encephalitis, yellow fever and Zika flaviviruses. These notifiable flaviviruses, particularly dengue and Zika, are problematic mosquito-borne infections in the Philippines, as well as in those countries with tropical and subtropical climates. Method: An algorithmic design formulation of overlap extension – polymerase chain reaction (OE-PCR) was performed to propagate 50–60 oligomer lengths of select notifiable flaviviral RNAs to DNA nucleotides via the two-step process of OE-PCR. Result: Algorithmic OE-PCR design formulation efficiently produced 253–256 bp of notifiable flaviviruses. Comparing the newly designed algorithmic OE-PCR with existing executable programs demonstrated it to be efficient and useful in generating accurate sequences of synthetic flaviviral nucleotides. Conclusion: The efficiently and accurately produced novel synthetic nucleotides of notifiable dengue virus 1–4, Japanese encephalitis, yellow fever and Zika flaviviruses using OE-PCR is useful in understanding the dynamics of flaviviral species and holds potential for the development of synthetic nucleotide-based immunogens.

Dengue and Zika fevers, including Japanese encephalitis (JEV), are particularly burdensome mosquito-borne infections in the Philippines and are also selectively reported in Japan [1][2][3][4]. The challenges these diseases pose and the need to efficiently convert these notable flaviviruses into larger DNA fragments are evident, considering that the performance of currently developed vaccines and DNA-based immunogens remain imperfect [5,6]. Molecularbased methodologies are presently available in the literature with varying degrees of precision and accuracy for PCR amplification, disease detection, genetic probing and DNA construction [7,8]. Many artificial genes are now commercially produced by several manufacturers. Moreover, the inherent risks, including the biosecurity concerns associated with handling and producing DNA fragments of pathogenic viruses, as well as some highly virulent bacteria, delimit its commercialized propagation [4,9,10]. Depending on the type of oligomer being used, the costeffectiveness of oligomer-size fragments varies. One of the promising modes for developing larger molecules of DNA is through the use of the overlap-extension polymer chain reaction (OE-PCR) method, which produces DNA fragments larger than 100 bp in size using synthetic oligomers [9,11,12]. The concerns that may have contributed to a rise in the price of oligomers have encouraged the development of novel model templates for PCR primers that can serve as a new application tool for OE-PCR. However, the oligomer design for OE-PCR may be problematic. This is because of homogeneity of the annealing temperature of the overlapping regions as well as the sense-antisense design of sequences [11,12]. As for positive controls for PCR detection, many DNA fragments may be produced; therefore, an algorithmic or automated design of oligomers for OE-PCR is indispensable [12]. Using an algorithmic OE-PCR design, this study was performed to efficiently propagate synthetic nucleotides of select flaviviruses [3,4]. Nucleotides of notifiable flaviviruses, namely dengue (1-4), JEV, yellow fever (YF) and Zika fevers, were efficiently and cost-effectively synthesized without the use of a DNA template, hence, generating synthetic select flaviviral DNAs useful for further viral studies and immunological explorations.

Materials & methods
The select list of notifiable flaviviral pathogens Table 1 & Box 1 show the profiles of the seven selected flaviviruses (Eurofins Genomics, Co. Limited, Ota-ku Tokyo, Japan) for amplification using OE-PCR. The OE-PCR in this experiment was performed via two processes: the first one is using the reference or original OE-PCR protocol [11,12] and the next one is the modified version of the OE-PCR. This was done to ensure optimization of deriving the desired amplified products.     Figure 1 is the principle and process of OE-PCR as applied in this experiment.
In the second PCR, the most outside oligomers work for PCR primers and amplified the whole size of target DNA.
An electrophoresis of OE-PCR products was done for PCR product-size prediction after amplification of both OE-PCR and pathogen-specific PCR. Single product was confirmed on 1.5% agarose gel electrophoresis with 1 × Tris/Borate/EDTA (TBE) buffer and UV-visualized with 0.7 micro-g/ml-ethidium bromide (Figure 2). The PCR product sizes were determined by comparison with DNA molecular weight marker whereby sizes of the products estimated are referred to the 100 bp-ladder (Dooh Chemical Co., Ltd, Sapporo, Japan).

Results & discussion
Stepwise performance of overlap extension-polymerase chain reaction The following notable flaviviruses, namely dengue (4 types), YF, JEV and Zika, were specifically processed for production of artificial DNAs. The algorithmic formulated OE-PCR was subsequently carried out in two-step cycles, with each cycle's DNA products depicted via UV-illuminated bands following gel electrophoresis (Figure 3). In the preliminary trials using this algorithmic OE-PCR, it was observed that a high success rate was derived when the number of oligomers was six or less compared with using an 8-oligomer-set or more. Thus, when OE-PCR product was used as a positive control, the ability to design PCR primers that produce about 100 bases in the product is required. This is possible at around 250 bp long and with algorithmic precision a well-synthesized 253-256 bp of DNA bands was yielded. DNA sequencing was carried out in similar steps as previously described [1,7] (Eurofins Genomics, Co. Ltd, Ota-ku Tokyo). The newly sequenced products were subsequently registered at DDBJ/NCBI Gene Bank (see Table 2).
Approaches to determine efficiency and cost-effectiveness of the current algorithmic OE-PCR tool versus the existing programs are presented in Table 3. These data delineate the utilized platform, the license, the program execution, the problems encountered in oligomer design and the methods of assembly [13][14][15][16][17][18].
It must be noted that the price of oligomers varies greatly depending on the length in base and according to the viral species involved. Owing to this, an algorithm was designed to achieve the maximum length within the lowest cost range in base size. Unfortunately, this is difficult to realize using the currently available reported design algorithms. In the stated design algorithms, the difficulty lies in how to control the length of the oligomer. This is because the setting of overlapping region of the oligomer has been designed first. With the current study, the basic length has been decided to begin with; coupled with a lowered priority on the thermodynamic stability of the overlapping region. This has resulted in fewer problems in the conduct of OE-PCR.

Conclusion
The ongoing dilemma of largely problematic and imperfectly developed flaviviral immunogens prompted us to responsibly contribute on the need to develop an efficient algorithmic OE-PCR program design for synthetic nucleotide production of select notifiable dengue (1-4), JEV, YF and Zika flaviviruses. To this end, we developed an OE-PCR program that can be utilized as reference tool in the furtherance of flaviviral research. It can be deduced that the program formulation was found to be demonstrably reproducible, cost-effective and efficient in yielding substantial nucleotides of select notifiable flaviviral DNAs, which can be sourced out at the databases of DDBJ/NCBI with the respective accession numbers of LC227563, LC227561, LC227562, and LC227568 (dengue 1-4); LC227560 (JEV); LC227567 (YF); and LC227589 (Zika). The OE-PCR is a reliable method that can be utilized when designed and accurately predicted using algorithmic manipulation. Henceforth, we finally conclude that the DNA primer design using algorithmic OE-PCR is a valuable tool in producing synthetic nucleotide products of pathogenic species of flaviviruses.

Future perspective
The novel nucleotide sequences generated from this study can be utilized for studies looking to further understand the genomic diversity of a variety of flaviviral strains, including dengue (1-4), YF, JEV and Zika. In addition, clinical trials involving initial utilization of whole nucleotide sequence followed by booster immuno-stimulation of antigenic protein may serve as a starting point for generating long-term immune responses for flaviviral infections such as dengue and Zika, where trials for DNA-based vaccines are ongoing, yet faced with challenging dosedependency concerns. Further experiments should be conducted to determine whether administration of synthetic nucleotides in vivo would result in pathological or immunological response.