This evaluation is not exhaustive and was performed using the genomic sequence from the first StMartin isolates.
The authors will be grateful to receive additional contributions regarding either published
detection systems or commercial kits.
Please contact:
Xavier.de-lamballerie@univ-amu.fr
Systems successfully tested on St-Martin CHIKV samples:
1. J Virol Methods. 2005 Mar;124(1-2):65-71.
Development of a TaqMan RT-PCR assay without RNA extraction step for the detection and
quantification of African Chikungunya viruses.
Pastorino B, Bessaud M, Grandadam M, Murri S, Tolou HJ, Peyrefitte CN.
Primers and Probe were used in a one-step RT-PCR assay
Name
R-CHIK
F-CHIK
P-CHIK
5′ → 3′ sequence Genome position (a)
CCAAATTGTCCYGGTCTTCCT 10554–10574
AAGCTYCGCGTCCTTTACCAAG 10366–10387
bCCAATGTCYTCMGCCTGGACACCTTTc 10465–10490
(a) According to the CHIKV Ross strain sequence.
2. ALTONA RealStar kit for detection of CHIKV
Probe-based RT-PCR systems tested in silico
A. no mismatch in primers and probe
1. J Virol Methods. 2005 Mar;124(1-2):65-71.
Development of a TaqMan RT-PCR assay without RNA extraction step for the detection and
quantification of African Chikungunya viruses.
Pastorino B, Bessaud M, Grandadam M, Murri S, Tolou HJ, Peyrefitte CN.
Name
R-CHIK
F-CHIK
P-CHIK
5′ → 3′ sequence Genome position (a)
CCAAATTGTCCYGGTCTTCCT 10554–10574
AAGCTYCGCGTCCTTTACCAAG 10366–10387
bCCAATGTCYTCMGCCTGGACACCTTTc 10465–10490
(a) According to the CHIKV Ross strain sequence.
2. PLoS Negl Trop Dis. 2013 Jul 25;7(7):e2339.
Dried-blood spots: a cost-effective field method for the detection of Chikungunya virus circulation
in remote areas.
Andriamandimby SF, Heraud JM, Randrianasolo L, Rafisandratantsoa JT, Andriamamonjy S, Richard V.
3. J Virol Methods. 2009 Dec;162(1-2):1-7.
Simultaneous detection and quantitation of Chikungunya, dengue and West Nile viruses by multiplex
RT-PCR assays and dengue virus typing using high resolution melting.
Naze F, Le Roux K, Schuffenecker I, Zeller H, Staikowsky F, Grivard P, Michault A, Laurent P.
ChikF1
ChikR1
ChikProb
AAGCTCCGCGTCCTTTACCAAG
CCAAATTGTCCTGGTCTTCCT
CCAATGTCTTCAGCCTGGACACCTTT
10387–10407 Laurent et al. (2007)
10575–10595 Laurent et al. (2007)
10486–10511 Laurent et al. (2007)
1
4. Clin Chem. 2007 Aug;53(8):1408-14.
Development of a sensitive real-time reverse transcriptase PCR assay with an internal control to
detect and quantify chikungunya virus.
Laurent P, Le Roux K, Grivard P, Bertil G, Naze F, Picard M, Staikowsky F, Barau G, Schuffenecker I,
Michault A.
Designation
Primers
ChikF1
ChikR1
ChikProb
a
Sequence (5’ to 3’)
Position (a)
AAGCTCCGCGTCCTTTACCAAG
CCAAATTGTCCTGGTCTTCCT
CCAATGTCTTCAGCCTGGACACCTTT
10387-10407
10575-10595
10486-10511
Position refers to the CHIKV complete genome (African prototype strain S27, GenBank AF369024).
Cf 3.
5. Am J Trop Med Hyg. 2009 Oct;81(4):679-84.
Development of field-based real-time reverse transcription-polymerase chain reaction assays for
detection of Chikungunya and O'nyong-nyong viruses in mosquitoes.
Smith DR, Lee JS, Jahrling J, Kulesh DA, Turell MJ, Groebner JL, O'Guinn ML.
In the table, primers CHIK 2F, CHIK 2R and probe CHIK 2P (NSP1 gene) can be used.
6. Emerg Infect Dis. 2008 Mar;14(3):416-22.
Chikungunya fever in travelers returning to Europe from the Indian Ocean region, 2006.
Panning M, Grywna K, van Esbroeck M, Emmerich P, Drosten C.
Remark:
general system: no mismatch
Indian ocean adapted system: one mismatch in the ChikAsII Reverse primer (probably minor impact)
name
Purpose*
Sequence and label (5'-3')
ChikSI Forward primer,
ChikSII Forward primer,
ChikAsI Reverse primer,
ChikAsII Reverse primer,
ChikP Detection probe,
general CHIKV assay
TGATCCCGACTCAACCATCCT
adapted assay (Indian Ocean) CCGACTCAACCATCCTGGAT
general CHIKV assay
GGCAAACGCAGTGGTACTTCCT
adapted assay (Indian Ocean) GGCAGACGCAGTGGTACTTCCT
FAM-TCCGACATCATCCTCCTTGCTGGC-BHQ1
Position (GenBank accession no.)
241–261 (AF369024)
246–265 (DQ443544)
323–302 (AF369024)
323–302 (DQ443544)
300–277 (AF369024)
2
B. systems with in silico mismatches
1. Asian Pacific Journal of Tropical Medicine
Multiplex real-time RT-PCR for detecting chikungunya virus and dengue virus
Piyathida Pongsiri, Kesmanee Praianantathavorn, Apiradee Theamboonlers, Sunchai
Payungporn, Yong Poovorawan1
Virus Probe/primer Sequence (5’-3’)
ChikF10378-10398
GCATCAGCTAAGCTCCGGGTC
ChikR10487-10508
CAATGTCTTCAGCCTGGACACC
ChikP10443-10456 Cy5-ATGCAAACGGCGACCATGCCGTCA--BBQ
Region, position*
E1,
10378-10398
E1,
10487-10508
E1,
10433-10456
2. Am J Trop Med Hyg. 2007 Sep;77(3):521-4.
Rapid detection and quantification of Chikungunya virus by a one-step reverse transcription
polymerase chain reaction real-time assay.
Carletti F, Bordi L, Chiappini R, Ippolito G, Sciarrone MR, Capobianchi MR, Di Caro A, Castilletti
C.
CHK142f (5′-CCC GAG AGA CTC GCC AAT TA-3′),
CHK142r (5′-TGT GTA AGC AGA ATG TTG GCG T-3′),
CHK probe1 (5′-CCT GGA CAG AAA CAT CTC TGG AAA GAT CGG-3′-fluorescein),
and CHK probe2 (Red 610-5′-ACT TAC AAG CAG TAA TGG CCG TGC CAG AC-3′).
3. Journal of Clinical Virology 39 (2007) 271–275
Molecular diagnosis and analysis of Chikungunya virus
Carolyn J. Edwards ∗, Stephen R. Welch, John Chamberlain, Roger Hewson,
Howard Tolley, Patricia A. Cane, Graham Lloyd
Real-time RT-PCR
CHIK
E1
F
CHIK
E1
R
CHIK
E1
P
TCGACGCGCCCTCTTTAA
ATCGAATGCACCGCACACT
ACCAGCCTGCACCCATTCCTCAGAC
10,865–10,882b
10,973–10,991b
10,902–10,926b
Sybr Green based RT-PCR systems tested in silico
A. no mismatch in primers
1. Virol J. 2010 Jan 21;7:13.
Establishment of one-step SYBR green-based real time-PCR assay for rapid detection and
quantification of chikungunya virus infection.
Ho PS, Ng MM, Chu JJ.
2. J Clin Virol. 2007 Jul;39(3):188-93.
3
Development and evaluation of SYBR Green I-based one-step real-time RT-PCR assay for detection and
quantification of Chikungunya virus.
Santhosh SR, Parida MM, Dash PK, Pateriya A, Pattnaik B, Pradhan HK, Tripathi NK, Ambuj S, Gupta N,
Saxena P, Lakshmana Rao PV.
B. systems with in silico mismatches
1. Journal of Virological Methods, Volume 193, Issue 2, November 2013, Pages 419–425
Application of real-time RT-PCR in vector surveillance and assessment of replication kinetics of an
emerging novel ECSA genotype of Chikungunya virus in Aedes aegypti
Ankita Agarwala, Anil K. Singhb, Shashi Sharmaa, Manisha Sonia, Ashish K. Thakura, N. Gopalanb, M.M.
Paridaa, P.V.L. Raoa, Paban K. Dasha
SYBR Green I based one step real time quantitative RT-PCR:
forward primer: CHIK1: 5′-ACGCAGTTGAGCGAAGCAC-3′
reverse primer: CHIK2: 5′-CTGAAGACATTGGCCCCAC-3′
targeting a highly conserved region of E1 gene of CHIKV (Dash et al., 2008)
2. Trop Biomed. 2010 Dec;27(3):611-23.
Development and evaluation of a one-step SYBR-Green I-based real-time RT-PCR assay for the detection
and quantification of Chikungunya virus in human, monkey and mosquito samples.
Ummul Haninah A, Vasan SS, Ravindran T, Chandru A, Lee HL, Shamala Devi S.
4