Table A1

Molecular Epidemiology of Rift Valley Fever Virus

Antoinette A. Grobbelaar, Jacqueline Weyer, Patricia A. Leman, Alan Kemp, Janusz T. Paweska, and Robert Swanepoel

Author affiliations: National Institute for Communicable Diseases of the National Health Service, Sandringham, South Africa (A.A. Grobbelaar, J. Weyer, P.A Leman, A. Kemp, J.T. Paweska, R. Swanepoel); University of Pretoria, Pretoria, South Africa (R. Swanepoel)

Main Article

Virus isolates used for molecular epidemiologic analysis of Rift Valley fever virus*

Isolate	Year	Country	Source	Passage	Donor†	Lineage	GenBank accession no.
MgH824	1979	Madagascar	Human	mic6, tc4	1	A	HM587040‡
MgAr811	1979	Madagascar	Aedes spp. mosquito	NA	1	A	HM587041‡
ZH 501	1977	Egypt	Human	mic2, tc3	GenBank	A	M33072‡
94EG Tambul	1994	Egypt	Ovine	NA	2	A	HM587042‡
94EG Bahr	1994	Egypt	Bovine	NA	2	A	Seq as above
ZS6365	1979	Egypt	Ovine	mic2, tc2	GenBank	A	DQ 380205‡
ZH548	1977	Egypt	Human	mic2, tc2	GenBank	A	M33075‡
ZH1776	1978	Egypt	Human	mic2, tc2	GenBank	A	DQ 380203‡
ZM657	1978	Egypt	Culex pipiens mosquito	mic2, tc2	GenBank	A	DQ380204
ZC3349	1978	Egypt	Bovine	mic2, tc2	GenBank	A	DQ380206
93EG Abeer	1993	Egypt	Human	mic1, tc2	2	A	HM587043‡
93EG Buffalo	1993	Egypt	Asian buffalo	mic1, tc1	2	A	Seq as above
MP12§	1977	Egypt	RVF isolate ZH548	NA	GenBank	A	DQ380208‡
VRL2250/74	1974	Zimbabwe	Bovine	mic3, tc2	GenBank	A	DQ 380209‡
VRL1516/78	1978	Zimbabwe	Ovine	mic2	3	A	HM587044‡
VRL1750/78	1978	Zimbabwe	Ovine	mic2	3	A	Seq as above
VRL1842/78	1978	Zimbabwe	Ovine	mic2	3	A	Seq as above
S35	1972	Kenya	Ovine	NA	4	B	HM587045‡
SPU52/99/1	1999	South Africa	African buffalo	mic2	5	C	HM587046‡
SPU52/99/5	1999	South Africa	African buffalo	mic2	5	C	HM587047‡
SPU52/99/2	1999	South Africa	African buffalo	mic2	5	C	HM587048‡
SPU52/99/3	1999	South Africa	African buffalo	mic2	5	C	HM587049‡
SPU52/99/4	1999	South Africa	African buffalo	mic2	5	C	Seq as above
SPU52/99/6	1999	South Africa	African buffalo	mic2	5	C	Seq as above
SPU50/99/1	1999	South Africa	Waterbuck	mic2	5	C	Seq as above
An278	2000	Saudi Arabia	Ovine	0	5	C	HM587050‡
Ar21218	2000	Saudi Arabia	Ae. vexans arabiensis mosquito	0	5	C	Seq as above
Ar21219	2000	Saudi Arabia	Ae. vexans arabiensis mosquito	0	5	C	Seq as above
Ar21220	2000	Saudi Arabia	Cx. tritaeniorhynus mosquito	0	5	C	Seq as above
Ar21229	2000	Saudi Arabia	Ae. vexans arabiensis mosquito	0	5	C	Seq as above
Ar21233	2000	Saudi Arabia	Ae. vexans arabiensis mosquito	0	5	C	Seq as above
Ar21236	2000	Saudi Arabia	Ae. vexans arabiensis mosquito	0	5	C	Seq as above
10911	2000	Saudi Arabia	Human	tc1	GenBank	C	DQ 380197
SA01–1322	2001	Saudi Arabia	Ae. vexans arabiensis mosquito	tc2	GenBank	C	AF393745‡
SPU12/99/21	1998	Somalia	Goat	0	5	C	HM587051‡
SPU65/98/1598	1998	Tanzania	Human	0	5	C	Seq as above
SPU65/98/1380	1998	Tanzania	Human	0	5	C	Seq as above
SPU384/97/1	1997	Kenya	Human	0	5	C	HM587052‡
SPU384/97/5	1997	Kenya	Human	0	5	C	Seq as above
SPU384/97/20	1997	Kenya	Human	0	5	C	Seq as above
SPU384/97/24	1997	Kenya	Human	0	5	C	Seq as above
SPU2/98/1	1998	Kenya	Human	0	5	C	HM587053‡
SPU2/98/3	1998	Somalia	Human	0	5	C	Seq as above
SPU12/98/2	1998	Somalia	Goat	0	5	C	Seq as above
VRL2241/98	1998	Zimbabwe	Bovine	mic2	3	C	Seq as above
VRL2181/98	1998	Zimbabwe	Bovine	mic2	3	C	Seq as above
VRL2104/98	1998	Zimbabwe	Ovine	mic1	3	C	Seq as above
VRL2215/98	1998	Zimbabwe	Ovine	mic2	3	C	Seq as above
VRL2413/98	1998	Zimbabwe	Bovine	mic1	3	C	HM587054‡
SPU2/98/9	1998	Kenya	Goat	0	5	C	HM587055‡
00523	1998	Kenya	Human	tc2	GenBank	C	DQ 380196‡
VRL1187/79	1979	Zimbabwe	Bovine	mic3	3	C	HM587056‡
MgAn1002	1991	Madagascar	Bovine	NA	1	C	HM587057‡
VRL1548/78	1978	Zimbabwe	Bovine	mic2	3	C	HM587059‡
VRL2142/78	1978	Zimbabwe	Ovine	mic2	3	C	Seq as above
VRL2354/78	1978	Zimbabwe	Bovine	mic2	3	C	HM587058‡
MgAn991	1991	Madagascar	Bovine	NA	1	C	HM587060‡
MgAn990	1991	Madagascar	Bovine	NA	1	C	HM587061‡
SPU22/07/118	2007	Kenya	Human	0	5	C	HM587062‡
SPU22/07/125	2007	Kenya	Human	0	5	C	HM587063‡
SPU22/07129	2007	Kenya	Human	0	5	C	HM587064‡
SPU103/07/1	2007	Kenya	Human	0	5	C	Seq as above
SPU103/07/2	2007	Kenya	Human	0	5	C	Seq as above
SPU103/07/14	2007	Kenya	Human	0	5	C	Seq as above
SPU103/07/35	2007	Kenya	Human	0	5	C	Seq as above
H1MAU03	2003	Mauritania	Human	0	GenBank	C	EF160116‡
SPU86/09	2009	South Africa	Human	0	5	C	HM587065‡
SPU89/09	2009	South Africa	Human	0	5	C	Seq as above
SA72/09	2009	South Africa	Human	0	5	C	Seq as above
SA77/09	2009	South Africa	Human	0	5	C	Seq as above
SA152/08	2008	South Africa	Human	0	5	C	HM587066‡
M84/08	2008	South Africa	Bovine	0	5	C	Seq as above
M48	2008	Madagascar	Bovine	NA	GenBank	C	HQ009512‡
H2MAU03	2003	Mauritania	Human	0	GenBank	C	EF160115‡
M37/08	2008	South Africa	African buffalo	0	6	C	HM587067‡
SPU22/07/4	2007	Kenya	Human	0	5	C	HM587068‡
SPU22/07/126	2007	Kenya	Human	0	5	C	Seq as above
SPU22/07/120	2007	Kenya	Human	0	5	C	Seq as above
SPU22/07/121a	2007	Kenya	Human	0	5	C	Seq as above
SPU22/07/121b	2007	Kenya	Human	0	5	C	Seq as above
SA52/08	2008	South Africa	Human	0	5	C	HM587069‡
J40/6	2008	South Africa	African buffalo	0	6	C	Seq as above
J48/6	2008	South Africa	African buffalo	0	6	C	Seq as above
N2131	2008	South Africa	African buffalo	0	6	C	Seq as above
SPU204/85	1985	Angola	Human	mic2	5	C	HM587076‡
B309	1977	Kenya	Bovine	NA	4	C	HM587070‡
VRL825/79	1979	Zimbabwe	Bovine	mic3	3	C	HM587071‡
VRL1217/78	1978	Zimbabwe	Ovine	mic2	3	C	HM587073‡
VRL845/78	1978	Zimbabwe	Bovine	mic2	3	C	Seq as above
VRL2129/78	1978	Zimbabwe	Bovine	mic2	3	C	Seq as above
VRL688/78	1978	Zimbabwe	Bovine	mic1	3	C	Seq as above
VRL2051/76	1976	Zimbabwe	Human	mic3	3	C	HM587072‡
21445	1983	Kenya	Ae. mcintoshi mosquito	ha1, tc1	7	C	HM587074‡
B1143	1977	Kenya	Bovine	NA	4	C	HM587075‡
VRL1290/78	1978	Zimbabwe	Bovine	mic2	3	C	HM587077‡
VRL1508/78	1978	Zimbabwe	Bovine	mic2	3	C	Seq as above
73HB1230	1973	CAR	Human	mic6, tc4	GenBank	D	DQ 380221‡
VRL2140A/75	1975	Zimbabwe	Bovine	mic2	3	E	HM587078‡
SPU44/85	1985	Zambia	Human	mic1, tc3	5	E	HM587079‡
SPU45/85	1985	Zambia	Human	mic1, tc3	5	E	Seq as above
VRL1887/78	1978	Zimbabwe	Bovine	mic2	3	E	HM587080‡
VRL1905/78	1978	Zimbabwe	Bovine	mic2	3	E	Seq as above
VRL3108/78	1978	Zimbabwe	Bovine	mic2	3	E	Seq as above
VRL2230/78	1978	Zimbabwe	Bovine	mic2	3	E	Seq as above
VRL1260/78	1978	Zimbabwe	Bovine	mic2	3	E	HM587081‡
74HB59	1974	CAR	Human	mic6, tc3	7	E	HM587082‡
73HB1449	1973	CAR	Human	mic5, tc1	GenBank	E	DQ 380211‡
Ar20364	1981	South Africa	Cx. zombaensis mosquito	mic4	5	F	HM587101‡
Ar20368	1981	South Africa	Cx. zombaensis mosquito	mic3	5	F	Seq as above
ArB1976 (Zinga)	1969	CAR	Mansonia africana mosquito	mic5, tc3	7	G	HM587083‡
AnK6087	1984	Guinea	Micropteropus pusillus bat	NA	GenBank	G	AF134502‡
AnK3837	1981	Guinea	Hipposideros caffer bat	mic7, tc1	7	G	HM587084‡
ArD104769	1993	Senegal	Ae. vexans arabiensis mosquito	NA	GenBank	G	AF134499‡
VRL1032/78	1978	Zimbabwe	Bovine	mic2	3	G	HM587085‡
VRL1853/78	1978	Zimbabwe	Bovine	mic2	3	G
HvB375	1985	CAR	Human	mic4, tc4	GenBank	G	DQ 380218‡
CAR R1662	1985	CAR	Human	mic4, tc3	7	G	HM587086‡
CAR R1752	1986	CAR	Human	mic4, tc3	7	G	HM587087‡
SA71/10	2010	South Africa	Human	0	5	H	HM587088‡
SA482/10	2010	South Africa	Human	0	5	H	HM587089‡
SA1221/10	2010	South Africa	Human	0	5	H	HM587090‡
SA59/10	2010	South Africa	Human	0	5	H	HM587091‡
SA54/10	2010	South Africa	Human	0	5	H	HM587092‡
SA79/10	2010	South Africa	Human	0	5	H	Seq as above
SA122/10	2010	South Africa	Human	0	5	H	Seq as above
SA197/10	2010	South Africa	Human	0	5	H	Seq as above
SA226/10	2010	South Africa	Human	0	5	H	Seq as above
SA227/10	2010	South Africa	Human	0	5	H	Seq as above
SA257/10	2010	South Africa	Human	0	5	H	Seq as above
SA360/10	2010	South Africa	Human	0	5	H	Seq as above
SA377/10	2010	South Africa	Human	0	5	H	Seq as above
SA420/10	2010	South Africa	Human	0	5	H	Seq as above
SA486/10	2010	South Africa	Human	0	5	H	Seq as above
SA509/10	2010	South Africa	Human	0	5	H	Seq as above
SA533/10	2010	South Africa	Human	0	5	H	Seq as above
SA578/10	2010	South Africa	Human	0	5	H	Seq as above
SA591/10	2010	South Africa	Human	0	5	H	Seq as above
SA611/10	2010	South Africa	Human	0	5	H	Seq as above
SA663/10	2010	South Africa	Human	0	5	H	Seq as above
SA1143/10	2010	South Africa	Human	0	5	H	Seq as above
SA1147/10	2010	South Africa	Human	0	5	H	Seq as above
SA1171/10	2010	South Africa	Human	0	5	H	Seq as above
SA1325/10	2010	South Africa	Human	0	5	H	Seq as above
SA276/10	2010	South Africa	Human	0	5	H	HM587093‡
SA106/10	2010	South Africa	Human	0	5	H	HM587094‡
SA100/10	2010	South Africa	Human	0	5	H	Seq as above
SA195/10	2010	South Africa	Human	0	5	H	Seq as above
SA225/10	2010	South Africa	Human	0	5	H	Seq as above
SA325/10	2010	South Africa	Human	0	5	H	Seq as above
SA328/10	2010	South Africa	Human	0	5	H	Seq as above
SA492/10	2010	South Africa	Human	0	5	H	Seq as above
SA423/10	2010	South Africa	Human	0	5	H	HM587095‡
SA404/10	2009	South Africa	Human	0	5	H	HM587096‡
SA373/10	2010	South Africa	Human	0	5	H	HM587097‡
SA85/10	2010	South Africa	Human	0	5	H	HM587098‡
SPU68/10	2010	South Africa	Human	0	5	H	Seq as above
SA95/10	2010	South Africa	Human	0	5	H	Seq as above
SA206/10	2010	South Africa	Human	0	5	H	Seq as above
SA317/10	2010	South Africa	Human	0	5	H	Seq as above
SA394/10	2010	South Africa	Human	0	5	H	Seq as above
SA395/10	2010	South Africa	Human	0	5	H	Seq as above
SA414/10	2010	South Africa	Human	0	5	H	Seq as above
SA1108/10	2010	South Africa	Human	0	5	H	Seq as above
SA1224/10	2010	South Africa	Human	0	5	H	HM587099‡
SPU77/04	2004	Namibia	Human	0	5	H	HM587100‡
An1830	1956	South Africa	Ovine	mic5	5	I	HM587108‡
Ar74	1955	South Africa	Ae. circumluteolus mosquito	mic7	5	I	HM587109‡
VRL2269/74	1974	Zimbabwe	Bovine	mic2	GenBank	J	DQ 380222‡
SNS¶	1944	Uganda	Eretmapodites spp. bat	mic103, tc2	8	K	HM587102‡
SNS 105/2010#	1944	Uganda	Eretmapodites spp. bat	mic103, tc5	8	K	Seq as above
95EG vaccine**	1944	Uganda	RVF strain SNS	NA	2	K	HM587103‡
KEN57 Rintoul	1951	Kenya	Ovine	mic31, tc1	7	K	HM587104‡
Entebbe/KCS††	1944	Uganda	Eretmapodites spp. bat	mip184, tc2	GenBank	K	DQ380191‡
B314	1963	Kenya	Bovine	NA	4	K	HM587105‡
B674	1962	Kenya	Bovine	NA	4	K	HM587106‡
SA184/10	2010	South Africa	Human	0	5	K	HM587107‡
VRL2373/74	1974	Zimbabwe	Bovine	mic3	3	K	HM587121‡
H1739	1975	South Africa	Human	NA	5	L	HM587110‡
VRL763/70	1970	Zimbabwe	Bovine	mic2	3	L	HM587111‡
Ar12568	1971	South Africa	Er. quinquivittatus bat	mic3	5	L	HM587112‡
Ar11186	1969	Zimbabwe	Ae. lineatopennis mosquito	mic5	5	L	HM587113‡
H1825	1975	South Africa	Human	NA	5	L	HM587114‡
35/74	1975	South Africa	Bovine	NA	GenBank	L	JF784387‡
95EG Cow-2509	1995	Egypt	Bovine	NA	2	L	HM587115‡
KEN56/B2653/IB8	1963	Kenya	Bovine	ha1, mic8, tc27	4	L	HM587117‡
Kitale 1840	1964	Kenya	Bovine	NA	4	L	HM587116‡
SA75	1975	South Africa	Human	tc3	GenBank	L	DQ380189‡
Lunyo	1955	Uganda	Aedes spp. mosquito	mic3	5	M	HM587119‡
Ar118	1955	South Africa	Ae. circumluteolus mosquito	mic7	5	M	HM587120‡
OS-4	1988	Mauritania	Human	tc2	7	N	HM587122‡
OS-1	1987	Mauritania	Human	tc2	GenBank	N	DQ380186
OS-3	1987	Mauritania	Human	tc2	GenBank	N	DQ380184
OS-8	1987	Mauritania	Human	tc2	GenBank	N	DQ380185
OS-9	1987	Mauritania	Human	tc2	GenBank	N	DQ380183
HD47502	1987	Mauritania	Human	NA	GenBank	N	AF134494‡
HD47311	1987	Mauritania	Human	NA	GenBank	N	AF134495‡
ArD38388	1983	Burkina Faso	Ae. cuminsi mosquito	tc5	GenBank	N	DQ380187‡
ArD38457	1984	Burkina Faso	Ae. furcifer mosquito	NA	GenBank	N	AF134497‡
HD47408	1987	Mauritania	Human	NA	GenBank	N	AF134496‡
HD21955	1975	Senegal	Human	mic5	7	N	HM587123‡
ArD38661	1983	Senegal	Ae. dalzieli mosquito	NA	7	N	HM587124‡
AnD106417	1993	Senegal	Bovine	NA	GenBank	N	AF134500‡
SA51 van Wyk	1951	South Africa	Ovine	ov3, mic2	5	O	HM587125‡

*mic, mouse intracranial; tc, tissue culture; NA, not available; seq, sequence; RVF, Rift Valley fever; ha, hamster; CAR, Central African Republic; SNS, Smithburn neurotropic strain; mip, mouse intraperitoneal; ov, ovine. Isolates are listed in order of appearance in phylogenetic groups in the tree in Figure A1. Ninety-five isolates displaying unique sequences are indicated in boldface. Isolates in standard text have identical sequences to isolates indicated in boldface directly above.
†1, Institut Pasteur, Antananarivo, Madagascar; 2, US Naval Medical Research Unit 3, Cairo, Egypt; 3, Central Veterinary Research Laboratory, Harare, Zimbabwe; 4, Central Veterinary Research Laboratory, Nairobi, Kenya; 5, National Institute for Communicable Diseases, Johannesburg, South Africa; 6, Agricultural Research Council–Onderstepoort Veterinary Institute, Pretoria, South Africa; 7, US Army Medical Research Institute for Infectious Diseases, Frederick, MD, USA; 8, Onderstepoort Biologic Products, Pretoria, South Africa.
‡Sequences selected for analysis and inclusion in the tree (see Materials and Methods).
§Candidate vaccine strain derived by culturing isolate ZH548 from Egypt with the mutagen 5-fluorouracil.
¶SNS master seed stock derived from a 1944 mosquito isolate from Uganda by serial intracranial passage of infected brain suspension in mice and used to produce live animal vaccine in BHK cell cultures.
#Batch of live SNS animal vaccine from South Africa issued in 2010.
**Animal vaccine from Egypt derived from SNS vaccine from South Africa.
††Hepatotropic strain derived from the same 1944 mosquito isolate from Uganda used to produce the SNS strain, but produced by serial intraperitoneal passage of infected liver suspension in mice; referred to as the Entebbe strain in some publications.

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Page created: December 01, 2011

Page updated: December 01, 2011

Page reviewed: December 01, 2011

The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.