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The Department of Emerging
and Re-emerging Infections,
Central Research Institute
of Epidemiology;
Moscow, Russia
2000-2004
Contacts: [email protected]
West Nile fever
Crimean-Congo hemorrhagic fever
Tick borne encephalitis
Omsk hemorrhagic fever
Japanese encephalitis
other flavivirus infections
hantaviral infection
Borreliosis
Rickettsiosis
Enteroviral infection
Meningococcal infection
Haemophilus influenzae type b
Pneumococcal infection
Russia: Annual sum of effective temperatures (t >= 10oC)
Moscow
200-500
1000-1500
2500-3000
500-1000
1500-2000
3000-3500
2000-2500
West Nile fever:
classical and
molecular epidemiology,
diagnosis,
pathogenesis, treatment
Molecular investigation of the simultaneous outbreaks
of West Nile fever in the USA and Russia in 1999.
(Bioterrorist's attack? No, the attack of nature)
The beginning – last week of July,
The peak of outbreak – first week of September
?
Genetic distance of West Nile virus isolates
based on complete nucleotide sequence
"New York group" – equine, flamingo,
human, and mosquito isolates in 1999,
as well as the USA strains from 2000-2002
and Israel strains from 1999-2001
Astrakhan strain, 1999
Italian strain, 1998
Kenyan strain, 1998
Mosquito isolate, Romania 1996
and human clinical isolate, Volgograd 1999,
(as well as the Volgograd strains from
humans, crows and C.pipiens, 1999-2002)
Eg-101
Kunjin strains
0.01
Genetic distance
The nearest relative of the Volgograd WN
isolate was the mosquito isolate from
Romania-1996. The strains differed from each
other in 46 nucleotide positions, 43 of them
were located in coding region. 35 mutations
were silent so the strains differed in 8 amino
acid only. So the homology of WN-Volgograd-4
and WN-Romania-1996M strains was 99.77% for
aa sequence and 99.58% for nt sequence.
Is the difference of 0.42% really small?
Do these strains belong to the same clone?
Problem:
the origin of "Volgograd" variant of
West Nile virus.
Is this variant endemic or are
several variants of West Nile virus
introduced in Volgograd region
every year by migrating birds?
WNF outbreak in 1999:
Volgograd - 38 deaths;
Astrakhan - 5 deaths;
Krasnodar - 3 deaths.
500
>500
400
Volgograd
region
300
200
100
0
>5
>35
32
15
14
0
1997 1998 1999 2000 2001 2002 2003
Volgograd
Astrakhan
Number of WNF cases
Krasnodar
Number of WNF cases
West Nile fever in Russia in 1999-2003
500
Astrakhan
region
400
300
200
95
100
0
?
?
24
49
33
12
1997 1998 1999 2000 2001 2002 2003
Genetic tree based on envelope gene fragment, 512 nt,
of WN virus isolates from Volgograd 1999-2002
Volgograd WN clone appear to be endemic in Volgograd
region because the same isolates were found in 1999-2002
patient-1999
patient-1999
C.pipiens
pool-2001
patient-1999
0.002 p-distance
0.001
(one substitution)
crow-2001
9
of
1999
two
patients
in 2000,
one in
2002
two
crows
in 2001
Selected publications and presentations:
Platonov AE. West Nile encephalitis in Russia 1999-2001: Were we
ready? Are we ready? In: West Nile virus: Detection, surveillance, and
control. D.J.White and D.L.Morse, eds. New York, Annals of the NYAS,
2001; V.951, pp.102-116.
Platonov A.E., Shipulin G.A., Shipulina O.Yu., et al. Outbreak of West
Nile infection - Volgograd region, Russia, 1999. Emer. Infect. Dis. 2001;
7: 128-132
Platonov A.E., Karan L.S., Yazyshina S.B., et al. Microheterogenicity of
the Volgograd clone of West Nile virus. International Conference on
Emerging Infectious Diseases. Atlanta, March 24-27, 2002, p. 112.
Platonov A.E., Zhuravlev V.I., Lazorenko V.V. The weather and the
mosquito-borne infections: What was wrong in 1999 in Southern
Russia? International Conference on Emerging Infectious Diseases.
Atlanta, February 29 - March 3, 2004, p.63-64.
Crimean-Congo
hemorrhagic fever:
early pathogen
detection,
viral load
measurement,
genotyping
Crimean hemorrhagic fever (CHF) was diagnosed in the
Russian Federation since 1944.
334 human cases were registered in the Rostov region
from 1963 to 1971 years, 51 cases (15%) were fatal.
CHF outbreaks have been reported also in the
Republics of Kalmykya and Dagestan, the Stavropol,
Astrakhan and Krasnodar regions (colored in red) of the
Southern Russia
Volgograd
Stavropol
After the period of
relative composure the
CHF epidemic situation
has become worse last
years.
In 2000-2003 more than 200 CHF cases
with 18 deaths were laboratory confirmed in
Russia. Both old endemic regions and new
region (Volgograd - colored in yellow)
were affected. In the latter region there were
18 CHF cases in 2000, 9 cases in 2001, 4
cases in 2002-2003; the Crimean-Congo
hemorrhagic fever virus (CCHFV) RNA was
found in the ticks.
The most affected region was Stavropol
region, where we have done our studies on
viral load at CCHF.
Crimean-Congo hemorrhagic fever
in Stavropol Region, population 2,655,000
number of CCHF cases
60
50
40
30
lethal
all
20
10
0
1998
1999
2000
2001
year
2002
2003
Laboratory diagnosis of Crimean-Congo hemorrhagic fever
IgG diagnosis is possible
IgM diagnosis is possible
positive samples, %
PCR diagnosis is possible
100
80
60
40
20
0
days 1-4
days 5-7
Critical time for treatment and prevention
week 2
week 3
week 4
week 5
days of disease
PCR
IgM
IgG-- diagnostic methods
Viral load, arbitrary units,
logarithmic scale
The decrease of viral load in patients
with Crimean-Congo hemorrhagic fever
100000
10000
1000
100
10
1
0
1 2 3 4 5 6 7 8 9 10 11 12 13 14
day of hospitalization
Viral load, arbitrary units,
logarithmic scale
Viral load correlates with the severity of Crimean-Congo
hemorrhagic fever (day 3 – day 5 of hospitalization)
1000
1000
100
100
10
10
1
1
0,1
0,1
mild
moderate
severe
without hemorrhagic
syndrome
with hemorrhagic
syndrome
Phylogenetic tree based on partial sequences
of the small S segment of CCHF isolates
0.05
Africa:
South Africa,
Senegal,
Nigeria,
Mauritania,
Burkina Faso,
C.A.R.
U.A.E.
U.A.E. United
0.05
Arab Emirates,
Pakistan,
Madagaskar
p-distance
South Europe:
Rostov,
Volgograd,
Stavropol,
Astrakhan,
Kosovo,
Albania
South Africa,
Uganda
Greece
China,
Kazakhstan
Senegal,
Maurinatia,
Iran
CCHF PCR-positive result in tick pools from Volgograd
H.marginatum
962 ticks
155 pools
13 CHFpositive
H.scupense
220 ticks
22 pools
2 CHFpositive
D.marginatus
17 ticks
2 pools
0 CHFpositive
R.rossicus
26 ticks
2 pools
0 CHFpositive
Selected publications and presentations.
Platonov A.E., Karan L.S., Yazyshina S.B., et al.
Molecular identification of Crimean-Congo hemorrhagic fever
virus in human clinical cases in Southern Russia.
International Conference on Emerging Infectious Diseases.
Atlanta, March 24-27, 2002, p. 83.
Karan L.S., Sannikova I.V., Platonov A.E., et al. Viral load at
Crimean-Congo hemorrhagic fever and its clinical significance.
International Conference on Emerging Infectious Diseases.
Atlanta, February 29 - March 3, 2004, p.125.
Karan L.S., Shipulin G.A., Platonov A.E. [PCR-based laboratory
diagnosis of Crimean-Congo hemorrhagic fever]. Clinical
Laboratory Diagnostics, 2003, No 10, p.50-54.
PCR-based assay for CCHF RNA detection is approved by the
State Institute for Biological Standards and Control
The advantages for
physicians and
epidomiologists:
the diagnostics of
unusual or
new pathogen
Birds mortality was observed in 1997-2001 in Southern
Europe. The WNF infection was suspected due to
concurrent West Nile fever equine enzootic
Genodiagnostics of infectious diseases (approach 2)
Possible
infectious
agents
non-specific probes
+
+
direct sequencing
of specific
fragment
…CTTGGAGCACGGT
ATCTAGAGTTTGAAG
CYYTGGGGTTC..
identification of pathogens:
both usual, unusual, or new pathogens
Phylogenetic tree
of flaviviruses
based on NS5
West Nile
fever
Denge
fever
Yellow
fever
Japanese
encephalitis
Tick-borne
encephalitis
Negishi, LI
Omsk hemorrhagic fever
Up to 100 flaviviruses may be identified using NS5 gene
Non-specific NS5-based assay for the detection of
genus Flavivirus RNA
Tick-borne encephalitis strains
К-
К-
Japanese encephalitis strains
К-
West Nile fever strains
К+
К+
Omsk hemorrhagic fever strains
К+К-
К+
Also positive results with Langat, Powassan, looping ill, Saint Louis
encephalitis viruses
Specific E gene-based assay for the detection of
Japanese encephalitis virus RNA
1 2 3 4 5 6 7 8 9 NC C- C+
1 2 3 4 5 6 7 8 9 1011121314151617 C-C+
Lines 1-17 – avian brain samples
C+ - positive control
10 11 12 13 14 15 16 17 18 ок к- к+
Lines 1-5, 10-15 – JE strains (positive)
Line 6 - SLE strains (negative)
Line 7-9 - TBE strains (negative)
Line 16 - Powassan strain (negative)
Line 17 – Langat strain (negative)
Line 18 – Looping ill strain (negative)
Genetic tree (E gene nucleotide sequences) of avian
JE isolates and reference strains of JEV, WNFV, SLEV
Japanese encephalitis
West Nile fever
Saint Louis encephalitis
0.05
JE-Tmer/s|AF501311|
25-JE-Italy2003-twotrace-need
JE-Tmus/p|AF501312|
JE-Svul/h|AF501313|
JE-Tphil/h|AF501314|
JE-Cliv/b|AF501315|
JE-NAKAYAMA/AF112298/
JE-NAKAYAMA-RFVL/S75726/
JE-Ling/L78128/
JE-YLG/AY243837/human brain-China
Kunjin-MRM61C/D00246/
WN-Eg101/AF260968/
AY033390 ISR99-GULL Israel-1999 Seagull
WN-VOLGOGRAD-1999
AF380670 Isr00-PigT Israel-2000 Pigeon
SLE-PV0-620/AF205492/
Birds mortality in 1997-2001 in Southern Europe Natural enzootic JE infection in Europe?
Карань Л.С.
Булгакова Т.А.
Венгеров Ю.Я.
Гаранина С.Б.
Малеев В.В.
Миронов К.О.
Платонов А.Е.
Платонова О.В.
Рудникова Н.А.
Федорова М.В.
Ceccherelli R.
Gubler D.
Lanciotti R.S.
Renzoni G.
Rossi G.
Tarantino C.
Антонов В.А.
Бочкова Н.Г.
Бутенко А.М.
Виноградова Е.Б.
Вышемирский О.И.
Галимзянов Х.М.
Говорухина М.В.
Громашевский В.И.
Ефременко В.И.
Еременко Е.И.
Жуков.А.Н.
Журавлев В.И.
Ковалев Н.Г.
Краснова Е.М.
Литовкина Н.А.
Лазоренко В.В.
Лопатина Ю.В.
Маленко Г.В.
Миронов К.О.
Обухов И.Л.
Погодина В.В.
Подколзин А.Т.
Родионова Е.Н.
Рыжков В.И.
Смирнова С.М.
Тялина Ю.Ю
Фролочкина Т.И
Швагер М.М.
Шипулин Г.А.
Шипулина О.Ю.
Якименко В.В.,
Яцышина С.Б.
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