PMC

Phylogenetic tree generated by Bayesian analysis of partial non-structural five gene sequences of flavivirus. The virus strain, GenBank accession number, host, collection country and year are noted. The flavivirus sequences obtained in this study are marked in red. Bootstrap values (1,000 replicates, not shown for less than 75%) of maximum likelihood; Bayesian analyses and neighbor-joining are shown above the main lineages. The bar indicates 0.1 substitutions per site. Sequences shaded sky blue represent tick-borne flavivirus, those shaded aquamarine represent no-known vector flavivirus, those shaded khaki represent infect specific flavivirus, those shaded rose-brown represent mosquito-borne flavivirus. AAFV, Anopheles associated flavivirus; AeFV, Aedes flavivirus; CFAV, cell fusing agent virus; CTFV, Culex theileri flavivirus; CxFV, Culex flavivirus; DGV, Donggang virus; HANKV, Hanko virus; JEV, Japanese encephalitis virus; KRV, Kamiti River virus; LTNV, La Tina virus; MMLV, Montana myotis leukoencephalitis virus; MODV, Modoc virus; NAKV, Nakiwogo virus; PAFV, Phlebotomus associated flavivirus; QBV, Quang Binh flavivirus; OcFV, Ochlerotatus caspius flavivirus; SLEV, Santa Louis encephalitis virus; TBEV, tick-borne encephalitis virus; WNV, West Nile virus; YDFV, Yamadai flavivirus; YNCxFV, Yunnan Culex flavivirus.

Molecular phylogeny of the 30 insect-specific flavivirus (ISFV) strains from Shanghai and other ISFVs based on partial NS5 gene (261 base pairs) sequences. The maximum likelihood tree was constructed by the GTR + I + R model. Sequences referable to the same host-genus are shown with the same colours in the tree. Bootstrap values (1000 replicates, not shown for less than 60%) of maximum likelihood, neighbour-joining, and Bayesian analyses are shown above the main lineages. The bar indicates 0.05 substitutions per site. AEFV, Aedes flavivirus; CFAV, cell fusing agent virus; CTFV, Culex theileri flavivirus; CxFV, Culex flavivirus; HANKV, Hanko virus; KRV, Kamiti River virus; NAKV, Nakiwogo virus; QBV, Quang Binh virus; OcFV, Ochlerotatua flavivirus; SCxFV, Spanish Culex flavivirus; YDFV, Yamadai flavivirus; YNCxFV, Yunnan Culex flavivirus. See Table for information on the sequences of the Shanghai strains of ISFVs

Phylogenetic tree generated by Bayesian analysis of flavivirus partial non-structural 5 gene. The GenBank accession number, virus name, origin, collection country and year are noted. The JEV and ISFV sequences obtained in this study are marked in red. The numbers above each branch represent the bootstrap support for the Bayesian analyses, maximum likelihood, and neighbor-joining, respectively, based on 1000 replicates. The scale-bar indicates 0.1 substitutions per site. AAFV Anopheles-associated flavivirus, AeFV Aedes flavivirus, AnFV Anopheles flavivirus, CFAV cell fusing agent virus, CHAOV Chaoyang virus, CTFV Culex theileri flavivirus, CxFV Culex flavivirus, DGV Donggang virus, HANKV Hanko virus, JEV Japanese encephalitis virus, KRV Kamiti River virus, LAMV Lammi virus, LTNV La Tina virus, MMLV Montana myotis leukoencephalitis virus, MMV Marisma mosquito virus, MODV Modoc virus, NAKV Nakiwogo virus, PAFV Phlebotomus associated flavivirus, QBV Quang Binh flavivirus, OcFV Ochlerotatus caspius flavivirus, SLEV Santa Louis encephalitis virus, TBEV tick-borne encephalitis virus, WNV West Nile virus, YDFV Yamadai flavivirus, YNCxFV Yunnan Culex flavivirus

Pairwise amino acid analyses comparing unclassified Ae. notoscriptus flavivirus isolates with 161 known flaviviruses. Major flavivirus groups are shown, namely classical insect-specific flavivirus (cISF), dual-host associated insect-specific flavivirus (dISF), mosquito-borne flavivirus (MBFV), tick-borne flavivirus (TBFV), and no known vector flavivirus (NKVF). (A) Radar plot of per cent amino acid pairwise distances of complete flavivirus ORF sequences compared to Ae. notoscriptus flavivirus (AenoFV) 207218 (derived from the near-complete genome nucleotide sequence, GenBank accession number MZ358856) with number of sequences (if >1) used in the analysis included in parentheses. Average per cent (_AV) pairwise values for each virus group are shown in bold. The cISFs, HANKV, OCFV, and PaRV sharing the highest per cent pairwise amino acid identities with AenoFVs 207218 (MZ358856) and 207252 (MZ358857) are also highlighted. (B) Sliding-window analysis using Simple Sequence Editor software () comparing mean pairwise amino acid identities across the complete flavivirus ORF. Virus groupings and abbreviations as per