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Volume 17, Number 12—December 2011

Research

Molecular Epidemiology of Rift Valley Fever Virus

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

Table A1

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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