LSD symposium - A. Van Schalkwyk - Evolutionary changes between LSDV strains from South Africa

1. Evolutionary changes
between LSDV strains
from South Africa
Antoinette van Schalkwyk
Agricultural Research Council – Onderstepoort Veterinary Institute

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• Northern Rhodesia (Zambia), December 1929 to March
1930 in the (Kafue) Lusaka and Mazabuka districts
• Ngamiland, October 1943
• Groot Marico, Dec 1944
• Salisbury, March 1945
Spread in Africa
Lumpy skin disease in southern Africa
Lumpy Skin Disease symposium, Rome, March 2023

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• Groot Marico, Dec 1944
• Onderstepoort Veterinary Institute.
• Transmission (March 1945):
- Spread to stables Anaplasma centrale (200 yards; 43 / 83 cattle)
- 80,000 doses vaccine to the FreeState
- Blood transmission is possible
- Predominantly spread with the roads / railways
- June of 1946: LSD in all 4 provinces
South Africa: 1944 - 1946
Lumpy skin disease in South Africa
Lumpy Skin Disease symposium, Rome, March 2023

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• Sporadic outbreaks, except 1953-54 and 1957
• Virus isolation
• Lumpy skin disease virus is a poxvirus (Alexander et al., 1957)
o Group 1: Orphan virus (Bezuidenhoudt)
o Group 2: BHV-2 (Allerton)
o Group 3: LSDV (Neethling)
- Western Cape 1957
- Attenuated: Embryonated eggs (van Rooyen et al., 1959)
- Vaccine: Neethling-LW1959
- Vaccine: 1960: 10, 000 doses per week
South Africa: 1953 - 1960
Lumpy skin disease in South Africa
Lumpy Skin Disease symposium, Rome, March 2023

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• Oldest isolate: Haden / 1954 (van Schalkwyk et al., 2021)
• Prototype: Neethling-WC / 1957(van Schalkwyk et al., 2022)
• Vaccine: Neethling-LW1959 (Kara et al., 2003)
• Vaccine: OBP, Herbivac, SIS-Lumpyvax (Mathijs et al., 2016;
Douglass et al., 2019)
▪ Wild type field isolates: South Africa
▪ 1950’s, 1970’s and 1990’s (van Schalkwyk et al., 2020 and 2022)
▪ Virulent isolates belonging to Cluster 1.1 have only
been identified in South Africa.
▪ 43 years (1954 to 1997)
Cluster 1.1 (Biswas et al., 2019)
Phylogenetics of Neethling virus
Lumpy Skin Disease symposium, Rome, March 2023

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• ± 12 SNPs between Neethling-WC/1957 and wild
type virus from 1970’s
• ± 60 SNPs between Neethling-WC/1957 and wild
type virus from 1990’s
• 18: IGR
• 5: Alter the reading frame
• 21: (13+8) (20 ORFs) Synonymous SNPs
• 16: (9+7) (14 ORFs) Non-synonymous SNPs
Cluster 1.1
Phylogenetics of Neethling virus
Lumpy Skin Disease symposium, Rome, March 2023

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• Seven SNPs between Neethling-WC/1957 isolate and Neethling-
LW1959 vaccine
• Non-synonymous SNPs:
o LW028 T135A
o LW083: K663N
o LW098: G553S
o LW098: I625T
• Reading frame:
o LW086: Termination (210 aa vs. 213 aa)
o LW131: Termination (108aa vs. 161 aa)
o LW134: Termination (2026 aa vs. 721 aa + 1253 aa)
Neethling: isolate and vaccine
Lumpy Skin Disease in South Africa
Lumpy Skin Disease symposium, Rome, March 2023

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• Isolate: 2490/Kenya/1958 (Tulman et al., 2000)
• Isolate from South Africa in 2000
(Warmbaths/RSA/2000) (Kara et al., 2003)
• Vaccine: KSGPO-240/1959 (Vandenbussche et al., 2016)
- Kenya vaccine stain (KS1) detected in outbreaks in
Bangladesh, India, Nepal and Pakistan since 2019
• Isolates from Middle East, Europe and Asia 2012 – 2016
• Isolates from southern Africa 2000 – 2022
Cluster 1.2 (Biswas et al., 2019)
Phylogenetics of Kenyan virus
Lumpy Skin Disease symposium, Rome, March 2023

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• ± 169 – 230 SNPs between Kenya/1959 and wild type
viruses from southern Africa and Northern hemisphere
• 185 SNPs (29 ORFs) between Ni-2490/Kenya/1958 and
Warmbaths/RSA/2000
• ± 40 – 70 SNPs between Warmbaths/RSA/2000 and
Isolates from Middle East, Europe and Asia 2012 – 2016
• Cluster 1.2 is currently the only LSDV observed in South
Africa.
Cluster 1.2
Phylogenetics of Kenyan virus
Lumpy Skin Disease symposium, Rome, March 2023

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• ± 2,200 SNPs between cluster 1.1 and 1.2
• ± 1860 SNPs in 114 ORFs
- 57% Synonymous
- 26% Non-Synonymous
- ± 330 (15%) IGR
• TMRCA: ± 500 years
• LSDVs representing sequences from both clusters
were circulating in Africa in the 1950’s.
• Majority of the DIVA assays are based on
differentiation between cluster 1.1 and 1.2.
Clusters 1.1 and 1.2
Phylogenetics of LSDV
Lumpy Skin Disease symposium, Rome, March 2023

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• 7.4 × 10−6 substitutions / site / year under field
conditions
• Significant Indels: 4
- Cluster 1.1: 60 SNPs / 43 years (Only South Africa)
- Cluster 1.2: ~48 SNPs / 22 years (Only South Africa)
- Cluster 1.2: ~230 SNPs / 64 years (Africa, Middle East,
Europe, Russia)
Genetic drift
Evolution of LSDV
MW656252 LSDV Haden RSA 1954
OM793606 LSDV Potter RSA 1958
OM793608 LSDV Neethling-WC RSA 1957
OM793605 LSDV Hoffmeyer RSA 1958
OM793607 LSDV Fourie-FS RSA 1959
MN636839 LSDV 103-GP RSA 1991
MN636843 LSDV 148-GP RSA 1997
MN636838 LSDV 58-LP RSA 1993
MN636840 LSDV 248-NW RSA 1993
MN636841 LSDV 220-1-NW RSA 1993
MN636842 LSDV 220-2-NW RSA 1993
OM793604 LSDV 33-KZN RSA 1977
AF325528 LSDV NI-2490 Kenya 1958
MT007951 LSDV Neethling 10F Namibia 2016
MT007950 LSDV Neethling 9F Namibia 2016
MW656253 LSDV 280-KZN RSA 2018
AF409137 LSDV Warmbaths-LW RSA 2000
LSDV MN-KZN RSA 2013
LSDV GP1-3 RSA 2019
KY702007 LSDV Bujanovac Serbia 2016
MT643825 LSDV 210-249 Bulgaria 2016
MH893760 LSDV Neethling Russia 2015
KY829023 LSDV Evros Greece 2015
KX894508 LSDV Neethling 155920 Israel 2012
MN995838 LSDV Pendik Turkey 2014
MN642592 LSDV Kubash Kazakhstan 2016
100
100
97
99
61
93
100
100
65
100
91
99
80
0.0010
Lumpy Skin Disease symposium, Rome, March 2023

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• Novel recombinants since 2017:
• Parental sequences are both vaccines:
- Neethling-LW1959 (Cluster 1.1)
- KSGPO-240 (Cluster 1.2)
Recombination
Evolution of LSDV
LSDV Cluster 1.1
MH646674 LSDV Saratov Russia 2017
OM530217 LSDV Saratov Russia 2019
LSDV Recombinant
LSDV Recombinant
OL542833 LSDV Tyumen Russia 2019
MZ577076 20L81 Bang-Thanh VietNam 2020
OL752713 LSDV KM Taiwan 2020
MZ577073 20L42 Quyet-Thang VietNam 2020
MZ577075 20L70 Dinh-To VietNam 2020
MZ577074 20L43 Ly-Quoc VietNam 2020
OM793602 LSDV Russia Tomsk 2020
OM793603 LSDV Russia Khabarovsk 2020
MW355944 GD01 China 2020
MW732649 LSDV Hongkong 2020
LSDV Recombinant
LSDV Recombinant
MT134042 LSDV Udmurtya Russia 2018
LSDV Recombinant
MT992618 LSDV Kostanay Kazakhstan 2018
LSDV Cluster 1.2
Goatpox virus
Sheeppox virus
100
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100
96
100
100
100
64
100
100
100
34
82
99
65
15
13
70
Lumpy Skin Disease symposium, Rome, March 2023

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• Possible recombinantion?
Recombination
Evolution of LSDV
• Multiple ORFs in Cluster 1.1 produced incongruent
phylogenetic trees (cluster 1.1 / SPPV and GTPV)
- When was cluster 1.2 introduced into South Africa?
- Is cluster 1.1 still circulating in South Africa?
Lumpy Skin Disease symposium, Rome, March 2023

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• Organizers and sponsors of the workshop
• Department of Agriculture, Land Reform and Rural
Development in South Africa
• Gauteng Department of Agriculture and Rural
Development
ARC-OVI: University of Pretoria:
- Livio Heath - Estelle Venter
- Pravesh Kara - Karen Ebersohn
- David Wallace - Henry Annandale
- Arshad Mather
ARC - Onderstepoort Veterinary Institute
Thank you
Lumpy Skin Disease symposium, Rome, March 2023

15. Protecting people, animals, and the environment every day
Drawings: FAO/Chiara Caproni