Table 2.

Listed are the lineages of JEV, MVEV, WNV and USUV with a few representative strains, their geographical distribution and disease incidences.

Virus Lineage	Alternative Name/Included Strains	Accession Numbers	Geographical Distribution	Disease Prevalence	References
JEV
Genotype I	KV1899	AY316157	Asia including Korea, China, Japan, Cambodia, Vietnam, Thailand	Epidemics in temperate regions, predominant in humans	[8,9,29]
	Ishikawa	AB051292
	HEN0701	FJ495189
Genotype II	FU	AF217620	Asia, Australia, Korea	Endemic disease in tropical regions	[8,9,29]
Genotype III	p3 SA14-14-2 Vellore P20778	U47032 AF315119 AF080251	Asia including India, China, Japan, Korea (Temperate zones)	Epidemics in temperate regions, endemic activity, predominant in humans	[8,9,29]
Genotype IV	JKT6468	AY184212	Indonesia and Australia	Endemic disease in tropical regions	[8,9,29]
Genotype V	Muar strain XZ0934	HM596272 JF915894	Asia including Malaysia, China and Korea	Re-emerged strain, Human encephalitis	[8,9,29,30]
MVEV
Genotype 1	MVE-1-51 K49077 08-154300	AF161266 EF015056 JN119766	Australia	Epidemics, sporadic cases	[31]
Genotype 2	OR156 K6454	EF015074 EF015070	Australia	Human encephalitis	[32]
Genotype 3	NG156	EF015076	Papua New Guinea	Human encephalitis	[10,33,34]
Genotype 4	MK6684	EF015075	Papua New Guinea	-	[31]
WNV
Lineage I	HNY1999 VLG4 LEIV-Vlg99-27889 Eg101 Kunjin MRM61C	AF202541 AF317203 AY277252 AF260968 D00246	Europe, Russia, North Africa, Israel, United States, Middle-east, Australia and India	Outbreaks in humans	[12,35,36,37]
Lineage II	Sarafend Ug37	AY688948 NC_001563	Sub-saharan Africa including South Africa, Madagascar; Europe including Greece, Russia	Zoonotic outbreaks in South Africa, avian and human outbreaks in Europe	[12,35,37,38]
Lineage III	Rabensburg virus (RABV/97-103)	AY765264	Europe	-	[35,36,39]
Lineage IV	LEIV-Krnd88-190	AY277251	Russia	-	[36]
Lineage V	804994 G16146	DQ256376 GQ851605	India	Outbreaks in humans	[12]
Lineage VI	HU2925/06	GU047875	Spain	-	[40]
Lineage VII	Koutango virus ArD96655	KY703855	Africa, Malaysia, Senegal	Sporadic outbreaks in Africa	[37]
Lineage VIII	ArD94343	KY703856	Senegal	Sporadic outbreaks in Africa	[37]
Lineage XI	WNV-Uu-LN-AT-2013	KJ831223	Austria	-	[37,40]
USUV
Africa 1	Central African Republic 1969 (CAR 1969)	KC754958	Africa	-	[13,41,42]
Africa 2	South Africa1959 (SAAR 1776) Spain 2006	AY453412 KF573410	Africa Europe	-	[13,41,42]
Africa 3	Central African Republic (CAR 1981) Senegal 2007 Netherlands 2016	KC754955 KC754957 KY128482	Africa Europe	Human illness	[41,43]
Europe 1	Austria 2001 (Vienna 2001) Hungary 2005	AY453411 EF206350	Europe	Human meningo-encephalitis	[13]
Europe 2	Italy 2009 Austria 2016 Hungary 2016	HM569263 MF063042 MF063043	Europe	Human meningo-encephalitis, meningitis, asymptomatic blood donors	[42,44,45]
Europe 3	Germany 2011 Belgium 2016 France 2016	KJ438769 KX977447 KY128481	Europe	Asymptomatic blood donors	[13,42]
Europe 4	Italy 2009 Italy 2010	HM138711 JF834562	Europe	Asymptomatic blood donors	[13,42]
Europe 5	Germany 2016 France 2016	KY113091 LT854220	Europe	Atypical human illness	[13,14]