WRLFMD Identification of a Ninth Foot-and-Mouth Disease Virus Type O Topotype and Evidence for a Recombination Event in its Evolution Nick J. Knowles,

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WRLFMD Identification of a Ninth Foot-and-Mouth Disease Virus Type O Topotype and Evidence for a Recombination Event in its Evolution Nick J. Knowles, Paul R. Davies, Rebecca J. Midgley and Jean-François Valarcher Institute for Animal Health, Pirbright Laboratory, Ash Road, Woking, Surrey, GU24 0NF, UK IAH

WRLFMD FMDV O in Africa IAH

Previous studies Few studies on the European FMDV serotypes in Africa: WRLFMD Previous studies Few studies on the European FMDV serotypes in Africa: Knowles et al., 1998 (type A) Samuel et al., 1999 (type O) Samuel & Knowles, 2001 (type O) Sangare et al., 2001 (type O) Sahle et al., 2004 (type O) Bronsvoort et al., 2004 (types O & A) Distinct genetic lineages of both FMDV-O and FMDV-A circulate in East and West Africa and viruses occurring in North Africa may be introduced from a variety of sources (Europe, South America, Middle East and West Africa). Outbreaks of FMD types O and A in southern Africa are very rare and are usually introduced from outside the continent. IAH

FMDV O Topotypes - 2001 IAH WRLFMD Samuel, A.R. & Knowles, N.J. 2001. Foot-and-mouth disease type O viruses exhibit genetically and geographically distinct evolutionary lineages (topotypes). J. Gen. Virol. 82: 609-621.

Position within the gene WRLFMD RT-PCR & Sequencing Capsid Non-structural proteins 5’ UTR L P1 P2 P3 3’ UTR IRES VPg AAAAAAAAAn Poly C VP4 VP2 VP3 VP1 2A 2B 2C 3A 3B 3C 3D O-1C244F O-1C272F O-1C283F NK61 Primers for RT-PCR an sequencing of FMDV O RNA. Designation Sequence (5' to 3') Genome location Gene Position within the gene O-1C244F GCAGCAAAACACATGTCAAACACCTT VP3 244-269 O-1C272F TBGCRGGNCTYGCCCAGTACTAC 272-294 O-1C283F GCCCAGTACTACACACAGTACAG 283-305 NK61 GACATGTCCTCCTGCATCTG 2B 58-77 NK72 GAAGGGCCCAGGGTTGGACTC 2A/2B 34-48; 1-6 O-1C499F TACGCGTACACCGCGTC 499-515 O-1C583F GACGGYGAYGCICTGGTCGT 583-602 IAH

WRLFMD VP1 (complete) IAH

WRLFMD VP1 (145-642) IAH

WRLFMD VP1 (478-642) IAH

Scanning analysis of VP1 WRLFMD Scanning analysis of VP1 IAH

Scanning analysis of VP1 WRLFMD Scanning analysis of VP1 IAH

Occurrence of FMDV O Topotypes in Africa WRLFMD Occurrence of FMDV O Topotypes in Africa IAH

Middle East-South Asia WRLFMD FMDV O Topotypes - 2004 East Africa 1 (EA-1) South-east Asia (SEA) West Africa (WA) O/ALG/1/99 O/CIV/8/99 O/UGA/5/96 O/TAI/4/99 O/KEN/2/95 O/KEN/83/79 O/GHA/5/93 O/CAM/2/98 O/TAW/81/97 O/VIT/7/97 Middle East-South Asia (ME-SA) O/PHI/7/96 Cathay O/IRQ/30/2000 O/HKN/14/82 O1/Manisa/TUR/69 O/A/CHA/58 O/ISA/8/83 O/BUN/7/2003 Indonesia-1 (ISA-1) O/KEN/5/2002 O/ISA/9/74 O/KEN/7/2002 East Africa 2 (EA-2) O/UGA/3/2002 O/KEN/3/2002 O/ISA/1/62 O/TAN/7/98 O/MAL/1/98 O/JAV/5/72 1% O/ISA/1/74 IAH Indonesia-2 (ISA-2) O3/VEN/51 O2/Brescia/ITL/47 Europe-South America (Euro-SA) O1/Kaufbeuren/FRG/66

Future work We are completing the complete capsid sequencing of 9 African FMDV O isolates including representatives of all indigenous topotypes We have an on-going study of FMDV O in Africa We have completed a study of FMDV A in Africa (~80 VP1 sequences) IAH

WRLFMD Conclusions Two previously unrecognised genetic lineages of FMDV O were identified in East Africa, each having a distinct geographic distribution. Recombination near the 3’ end of VP1 may have played a role in the evolution of the EA-2 topotype. Alternatively, it may be that all the African lineages evolved after the introduction of Asian FMD viruses into Africa and more mutations have subsequently accumulated in certain parts of the capsid-coding region while other parts may have remained more conserved. IAH

WRLFMD Recommendations Future phylogenetic analyses for molecular epidemiological purposes should be based on complete VP1 sequences. More extensive molecular epidemiological studies of the European FMDV serotypes in Africa should be undertaken (this is in progress in our laboratory for serotypes O and A). More extensive genome analyses need to be performed to access the role of recombination in the natural evolution of FMD viruses. IAH

Acknowledgements Nigel Ferris & Geoff Hutchings WRLFMD Acknowledgements Nigel Ferris & Geoff Hutchings for viruses Rahana Dwarka & Wilna Vosloo for sequences IAH