Molecular characterization of Chikungunya virus during an outbreak in South India.
BACKGROUND
Re-emergence of Chikungunya is a major public health problem in the southern states of India.


OBJECTIVE
This study was undertaken to investigate an outbreak of Chikungunya, in June-August 2008 using PCR and determine the prevalent genotypes of Chikungunya virus (CHIKV) associated with the outbreak.


METHODS
Samples of blood were collected (in heparinized vacutainer tubes) from suspected patients of CHIKV infection from both Government Taluk Hospital in Kerala and a tertiary care hospital in Chennai, Tamil Nadu. A one-step RT-PCR was carried out on a block thermo-cycler targeting the E2 gene that codes for the viral envelope protein. The amplicons were verified for 305 bp size by standard agarose gel electrophoresis. The PCR products were purified, sequenced, and compared with other CHIKV strains reported from different geographical regions. A phylogenetic tree was constructed using MEGA 4.


RESULTS
Altogether 118 samples were collected from patients who presented with sudden onset of fever and/or joint pain, myalgia, and headache. CHIKV infection was confirmed by RT-PCR in 14 patients and all these cases were from Kerala. The positivity correlated with the early stage of the disease as all these patients had fever of less than seven days duration. The study isolates have been allotted the GenBank accession nos. GQ272368-GQ272381. Phylogenetic analysis of recent CHIKV isolates by partial sequencing of E2 region shows that isolates are closely related to strains from neighboring states and the African type.


CONCLUSIONS
RT-PCR is a useful technique for the early detection of CHIKV infection during outbreaks. Molecular characterization of the strains indicates that majority of the strains have originated from the Central/East African strains of CHIKV.
Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Chennai, Tamil Nadu, India. srikanth_padma@rediffmail.com
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P
Srikanth
G
G
Sarangan
K
K
Mallilankaraman
S A
SA
Nayar
R
R
Barani
T
T
Mattew
G F
GF
Selvaraj
K A
KA
Sheriff
G
G
Palani
K
K
Muthumani
D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D018354:Alphavirus Infections / Q000453:epidemiology* / Q000821:virology*; D002646:Chikungunya virus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D002648:Child; D004196:Disease Outbreaks; D005838:Genotype; D006801:Humans; D007194:India / Q000453:epidemiology; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny; D015995:Prevalence; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D014759:Viral Envelope Proteins / Q000235:genetics; D055815:Young Adult
D014759:Viral Envelope Proteins