family currently comprises over 70 viruses, including mosquito-borne West Nile virus (WNV) and Kunjin virus (a subtype of WNV endemic to Oceania), yellow fever virus and dengue virus (DV), and tick-borne Japanese encephalitis virus (JEV). The Flavivirus
genus viruses are responsible for significant human disease and mortality. The WHO estimates that there are multimillion annual cases of DV type 1–4 (DV1–4), 200,000 annual cases of yellow fever virus and 50,000 annual cases of JEV worldwide. WNV was first isolated in 1937 in the West Nile district of Uganda. Since 1999, when the virus was identified in the USA, the virus has spread rapidly throughout the country [1
]. WNV has been detected in 46 states of the USA. According to the US CDC, the virus has already infected 30,000 people and has been the cause of approximately 1150 deaths (1999–2008). WNV may cause serious CNS damage unless specific treatment is administered [2
]. There is a significant level of probability that the number of flaviviral infections will grow and that their geographical incidence will spread as the continued warming of the planet will provide a more extensive and benign environment for the flavivirus-carrying mosquito. To date, there is no specific and effective therapy available for any flavivirus infection.
Following infection of the host, the flavivirus positive strand 11-kb RNA genome is transcribed into a negative-strand RNA. The daughter genomic RNA is then synthesized using a negative-strand RNA template. Reports of sequence analysis of several flavivirus RNAs, including the yellow fever virus genome [4
], DV4 [5
], DV2 [7
], Kunjin virus [11
] and WNV [12
], firmly established that flavivirus genomes share similar genomic organization (). Naturally, the respective individual flaviviral proteins are also homologous across the family (). As a result, the fundamental structural and regulatory parameters of the individual flaviviral proteins are also similar but not identical.
Figure 1 Organization of the capsid–membrane–envelope–NS1–NS2A–NS2B–NS3–NS4A–NS4B–NS5 polyprotein precursor, showing cleavage sites by the viral NS2B–NS3pro (gray arrows) and host (more ...)
NS3 sequences of the flaviviruses
The genomes of flaviviruses are translated into polyproteins, which then undergo proteolytic processing. This proteolytic processing takes place both cotranslationally and post-translationally, and it involves both the host and viral proteases. As a result of this extensive proteolytic processing, the polyprotein precursor is transformed into mature viral proteins [13
]. The genomic flaviviral RNA encodes a polyprotein precursor that consists of three structural proteins (capsid, membrane and envelope) and seven nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5) arranged in the order capsid protein–membrane protein–envelope protein–NS1–NS2A–NS2B–NS3–NS4A–NS4B–NS5 (). Crawford et al
. provided the early experimental evidence that flavivirus polyproteins are synthesized as a large precursor polyprotein, which are subsequently processed into mature polypeptides [15
]. The precursor is inserted into the endoplasmic reticulum membrane and processed by the host cell and viral proteases to transform the precursor into individual, functionally potent proteins.
During evolution, viruses usurped multiple host cell components to maintain infectivity. Thus, flaviviruses employ human proteases (furin and secretase), in addition to the viral NS3 protease (NS3pro), to transform the polyprotein precursor into mature viral proteins [16
]. It is also likely that flaviviruses efficiently use human miRNAs to regulate the genomic RNA translation and to maintain the required balance between the number of the early viral proteins, such as the capsid, membrane and envelope proteins, and the late proteins, including the NS5 RNA polymerase. If the balance between the early and the late genes is improperly maintained, the virus propagation would not be as efficient as it is.