Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 15, Number 2—February 2009

Enteroviruses in Patients with Acute Encephalitis, Uttar Pradesh, India

Article Metrics
citations of this article
EID Journal Metrics on Scopus
Gajanan N. Sapkal, Vijay P. Bondre, Pradip V. Fulmali, Pooja Patil, Vipul Dadhania, Vijay M. Ayachit, Daya Gangale, K.P. Kushwaha, A.K. Rathi, Shobha D. Chitambar, Akhilesh Chandra Mishra, Milind M. GoreComments to Author , and Gopalkrishna
Author affiliations: National Institute of Virology, Pune, India (G.N. Sapkal, V.P. Bondre, P.V. Fulmali, P. Patil, V. Gopalkrishna, V. Dadhania, V.M. Ayachit, D. Gangale, S.D. Chitambar, A.C. Mishra, M.M. Gore); Baba Raghav Das Medical College, Gorakhpur, India (K.P Kushwaha, A.K. Rathi)

Cite This Article


An outbreak of viral encephalitis occurred in northern India in 2006. Attempts to identify an etiologic agent in cerebrospinal fluid by using reverse transcription–PCR showed positivity to enterovirus (EV) in 66 (21.6%) of 306 patients. Sequencing and phylogenetic analyses of PCR products from 59 (89.3%) of 66 specimens showed similarity with EV-89 and EV-76 sequences.

Acute viral encephalitis is caused by a wide range of viruses and can occur either in sporadic episodes or in outbreaks. Viral etiologic agents that have been identified as causing encephalitis include herpesvirus, enterovirus, alphavirus, influenza A virus, rabies virus, HIV, flavivirus, and Chandipura (CHP) virus (1,2). An outbreak of viral encephalitis was reported from April through October 2006 from predominantly Gorakhpur and 5 adjoining districts of eastern Uttar Pradesh (Maharajganj, Kushinagar, Sant Kabir Nagar, Siddharthnagar, and Deoria) and 2 adjoining districts of Bihar (Gopalganj and West Champaran), locations where Japanese encephalitis (JE) is known to be endemic in India. According to state government health services records, 1,912 cases of viral encephalitis occurred in these areas, and 411 (21.5%) patients died. From August through September 2006, we investigated 306 patients admitted with encephalitis to Baba Raghav Das Medical College in Gorakhpur, Uttar Pradesh. The patients represented all 8 districts of eastern Uttar Pradesh. ELISA and reverse transcription–PCR (RT-PCR) performed on the patients’ cerebrospinal fluid (CSF) samples identified 40 (13.1%) of 306 specimens as positive for JE virus (3). Laboratory tests were negative for alphavirus and CHP virus, and the etiologic agent in a large number of cases was unidentified.

Enteroviruses (EVs) cause a wide variety of diseases that range from nonspecific viral illness to mild infections of herpangina and hand, foot, and mouth disease to potentially serious diseases such as myopericarditis, meningitis, myelitis, and neonatal sepsis. EVs are also etiologic agents of encephalitis outbreaks in humans (4). These viruses comprise more than 90 serotypes, and most are known to cause human infections. We focused on the detection, isolation, and molecular characterization of EVs in 306 patients from eastern Uttar Pradesh.

The Study

A total of 850 specimens collected from 306 patients who had encephalitis included 306 CSF specimens, 304 blood samples, 120 throat swabs, and 120 rectal swabs. All samples were stored at –20oC before being transported for analysis and thereafter were stored at –70oC at the National Institute of Virology in Pune, India. Laboratory tests conducted by state government health services of Uttar Pradesh were negative for bacteria and malaria. According to standard protocol (2), virus isolation was attempted in human rhabdosarcoma (RD) and in baby hamster kidney (BHK) cell lines.

Separate aliquots were processed in 2 laboratories to maintain quality control and monitor possible contamination during PCR processing. Viral nucleic acids were extracted by using viral RNA mini kits (QIAamp, Qiagen, Hilden, Germany). RT-PCR was performed for EV by using 5′ noncoding region (NCR)–specific primers, as has been described (5,6). Genotyping was conducted by using RT-PCR of virion protein (VP) 1/2A and VP1 regions and sequencing (7,8). Table 1 describes the locations and sequences of the primers used in the assays.

PCR products were purified by using a Gel Extraction Kit (QIAquick, Qiagen). Both strands were sequenced by using BigDye Terminator Cycle Sequencing Ready Reaction Kit (Applied Biosystems, Carlsbad, CA, USA) in ABI PRISM 3130 XL Genetic Analyser (Applied Biosystems). MEGA 3.1 software generated the phylogenetic tree by using the neighbor-joining algorithm and Kimura 2–parameter distance model and applying a bootstrap test that used 1,000 bootstrap replications (9).

Patient age ranged from <1 month to 15 years. Clinical histories available for 253 of the 306 patients showed fever and altered sensorium in 100.0%, hepatomegaly in 70 (27.8%), splenomegaly in 49 (19.4%), and meningeal signs in 35 (13.9%) of the 253 patients.

Specimens available in sufficient quantity were inoculated into RD and BHK cell lines. Specimens that were adequate for isolation included 85 of 306 CSF specimens, 18 of 304 serum samples, 19 of 120 rectal swabs, and 19 of 120 throat swabs. Cytopathic effect was observed in cell cultures inoculated with 4 CSF specimens, 2 rectal swabs, 2 throat swabs, and 1 serum sample. Electron microscopic examination of cultures infected with 2 CSF samples showed picornavirus-like particles 25–27 nm in diameter. Attempts to detect EV RNA in the isolates and clinical specimens used nested RT-PCR in 5′ NCR. Eight of 9 cultures showed amplicons of 407 bp. Sequences of amplicons from 3 CSF specimens and 2 rectal swabs showed 97.2%–98.9% homology with EV-89 (i.e., the strain named BANoo-10359, GenBank accession no. AY697459) and 95.7%–96.9% homology with EV-76 (FRA91-10369, GenBank accession no. AY697458). Sequences from 1 isolate from a CSF specimen and 1 isolate from a rectal swab showed 100.0% homology with coxsackie virus B3 (CV-B3) strain 20. One isolate from serum showed 98.3% homology with coxsackie virus B1 (CV-B1) strain SAMP2.17.

Figure 1

Thumbnail of Phylogenetic tree based on partial 5’ noncoding region sequences of enterovirus (EV) genome detected in cerebrospinal fluid samples from encephalitis patients. Specimens are identified by repository serial numbers obtained from the National Institute of Virology (NIV), Pune, India. GenBank accession nos. EU672893–EU762967 indicate the nucleotide sequences of EV strains of the present study. Scale bar indicates nucleotide substitutions per site. EV, enterovirus; CSF, cerebrospinal fl

Figure 1. Phylogenetic tree based on partial 5’ noncoding region sequences of enterovirus (EV) genome detected in cerebrospinal fluid samples from encephalitis patients. Specimens are identified by repository serial numbers obtained from the...

Sixty-six (21.5%) of 306 CSF specimens, 7 (6.4%) of 110 rectal swabs, 4 (3.7%) of 110 throat swabs, and 1 (5.5%) of 18 serum samples showed amplification in 5′ NCR of the EV genome. Sequences of 64 of 78 (82.0%) PCR products (59 from CSF specimens, 4 from rectal swabs, and 1 from a throat swab) showed 97.2%–98.9% and 95.7%–96.9% homology with EV-89 and EV-76, respectively. Ten (12.8%) products (7 from CSF, 2 from rectal swabs, and 1 from serum) showed 99.3%–100.0% homology with CV-B3 (Figure 1). Three PCR products, each derived from a throat swab, showed 93.3%–96.6% homology with coxsackie virus A (CV-A), echovirus 11, and echovirus 30, respectively. PCR products from a rectal swab showed 96.3% homology with CV-B1. Multiple specimen positivity was noted in 6 patients who tested positive for EV RNA.

Figure 2

Thumbnail of Phylogenetic tree based on partial virion protein 1 (VP1) sequences (2602–2977) detected in enterovirus (EV) isolates and clinical specimens from encephalitis patients. GenBank accession nos. indicate the nucleotide sequences of EV strains of the present study. Scale bar indicates nucleotide substitutions per site. EV, enterovirus; CV-A, coxsackie virus A; CV-B, coxsackie virus B; HEV, human enterovirus; NIV, National Institute of Virology, Pune, India.

Figure 2. Phylogenetic tree based on partial virion protein 1 (VP1) sequences (2602–2977) detected in enterovirus (EV) isolates and clinical specimens from encephalitis patients. GenBank accession nos. indicate the nucleotide sequences of EV...

Isolates from 2 of 5 cell cultures, 2 of 59 CSF specimens, and 1 of 4 rectal swabs contained EV-76. Two of 4 rectal swabs were characterized as EV-89 on the basis of partial VP1/2A (2917–3374) or VP1 (2602–2977) gene sequences. Phylogenetic analysis revealed 92.7%–97.7% homology with Bangladesh EV-76 strains (GenBank accession nos. AY697463, AY697464, AY697471, AY697469, AY697462, and AY697468) and 93.6%–94.5% homology with EV-89 strain (GenBank accession no. AY697459) (Figure 2). Within EV-76 and EV-89 strains of the study, homology ranged from 81.2% to 91.3%. Attempts to amplify VP1/2A or VP1 regions of EV RNA detected in most clinical specimens failed despite the use of sensitive primer pairs that have been discussed recently (10).

Table 2 describes details of clinical findings in the subsets of EV-positive and EV-negative specimens of the patients for whom clinical histories were available. Further, hepatomegaly and splenomegaly appeared to be proportionately higher in patients with enteroviral infections than in patients whose specimens were negative for EV and JE virus.


The viral RNA detected in CSF samples from patients hospitalized with encephalitis in Uttar Pradesh showed close identity with the EV-89 and EV-76 that recently were reported as an unusual group classified genetically as group A EV (EV-A) (10). Presence of the virus was also confirmed by its isolation and typing. Human EV-76 was detected in isolates in 1 rectal swab and 2 CSF specimens, and human EV-89 was detected in 2 rectal swabs by using amplification of VP1/2A or VP1 regions. Sequence analysis showed nt homology of 92.7%–97.7% with Bangladesh EV-76 and EV-89 strains recovered from patients with acute flaccid paralysis (AFP). The failure of amplification of typing regions in most specimens may be due to a low viral load.

EVs are known to cause severe neurologic diseases ranging from AFP to encephalitis (11). In recent years, Southeast Asian countries have reported outbreaks of encephalitis caused by EV-71 (12,13). During AFP surveillance activities, Bangladesh strains were isolated from stool specimens (14). AFP patients infected with echoviruses and coxsackie B viruses also have been detected in India (15). Isolation of EV from clinical specimens collected from children with encephalitis in the present study indicates viable virus. Detection of EV-89/76 RNA in the CSF of ≈20% of the patients suggests the association of these viruses with encephalitis. Also, in 10 (3.3%) of 306 patients, co-infections of JE virus and EV were detected. Further studies are needed to understand the relative contributions of these viruses in causing sporadic and outbreak infections of encephalitis.

Accumulation of water in a saucer-shaped landscape (terai) and extensive rice cultivation in eastern Uttar Pradesh and adjoining regions favor the growth of vector mosquito populations and waterborne pathogens. Though the source of infection in the present study is unclear, the data warrant active surveillance of encephalitis cases. Inadequate hygiene and the unsanitary conditions that prevail in the study region may encourage the spread of EV infections in the community. Studies conducted on environmental samples may provide clues related to the dynamics of EV infections in humans.

Mr Sapkal is a research scientist working in the Japanese encephalitis group at the National Institute of Virology, Pune, India. His research interests include diagnostic virology of Japanese encephalitis and West Nile viruses, molecular pathogenesis, and emerging viral infections. He has worked on isolation of Japanese encephalitis, dengue, and Chandipura viruses in various epidemics using peripheral blood mononuclear cells coculture systems.



We thank the Directorate of Health Services, Government of Uttar Pradesh, India, for help and cooperation; M. Steven Oberste for useful discussion, manuscript review, and provision of enterovirus typing primers; V. Shankaraman, S. Mahamuni, M. Joshi, H. Verma, M. Biswas, M. Shejwalkar, P. Chabra, R. Arora, V. Tatte, S. Ransingh, R. Gangwar, and F. Ahsan for their technical support; P. Pant and R. Dviwedi for the clinical history analysis of patients; A. Basu for expertise in electron microscopic analysis of the isolates; and A. Shendrikar for manuscript typing.

Funds were provided by the Indian Council of Medical Research, Ministry of Health and Family Welfare, Government of India.



  1. Kennedy  PG. Viral encephalitis: causes, differential diagnosis, and management. J Neurol Neurosurg Psychiatry. 2004;75(Suppl 1):i105. DOIPubMedGoogle Scholar
  2. Rao  BL, Basu  A, Wairagkar  NS, Gore  MM, Arankalle  VA, Thakare  JP, A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh, India, in 2003, associated with Chandipura virus. Lancet. 2004;364:86974. DOIPubMedGoogle Scholar
  3. Sapkal  GN, Wairagkar  NS, Ayachit  VM, Bondre  VP, Gore  MM. Detection and isolation of Japanese encephalitis virus from blood clots collected during the acute phase of infection. Am J Trop Med Hyg. 2007;77:113945.PubMedGoogle Scholar
  4. Pallansch  MA, Roos  RP. Enteroviruses: polioviruses, coxsackieviruses, echoviruses, and newer enteroviruses. In: Fields virology, 5th ed. Knipe DM, Howley PM, Griffin DE, Lamb RA, Martin MA, Roizman B, et al., editors. Philadelphia: Lippincott Williams & Wilkins; 2006. p. 839–94.
  5. Zoll  GJ, Melchers  WJ, Kopecka  H, Jambroes  G, van der Poel  HJ, Galama  JM. General primer-mediated polymerase chain reaction for detection of enteroviruses: application for diagnostic routine and persistent infections. J Clin Microbiol. 1992;30:1605.PubMedGoogle Scholar
  6. Puig  M, Jofre  J, Lucena  F, Allard  A, Wadell  G, Girones  R. Detection of adenoviruses and enteroviruses in polluted waters by nested PCR amplification. Appl Environ Microbiol. 1994;60:296370.PubMedGoogle Scholar
  7. Oberste  MS, Maher  K. Kilpatrick. DR, Flemister MR, Brown BA, Pallansch MA. Typing of human enteroviruses by partial sequencing of VP1. J Clin Microbiol. 1999;37:128893.PubMedGoogle Scholar
  8. Nix  WA, Oberste  MS, Pallansch  MA. Sensitive, seminested PCR amplification of VP1 sequences for direct identification of all enterovirus serotypes from original clinical specimens. J Clin Microbiol. 2006;44:2698704. DOIPubMedGoogle Scholar
  9. Kumar  S, Tamura  K, Jakobsen  IB, Nei  M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics. 2001;17:12445. DOIPubMedGoogle Scholar
  10. Oberste  MS, Maher  K, Michele  SM, Bellot  G, Uddin  M, Pallansch  MA. Enteroviruses 76, 89, 90 and 91 represent a novel group within the species Human enterovirus A. J Gen Virol. 2005;86:44551. DOIPubMedGoogle Scholar
  11. Wildin  S, Chonmaitree  T. The importance of the virology laboratory in the diagnosis and management of viral meningitis. Am J Dis Child. 1987;141:4547.PubMedGoogle Scholar
  12. Hayward  JC, Gillespie  SM, Kaplan  KM, Packer  R, Pallansch  M, Plotkin  S, Outbreak of poliomyelitis-like paralysis associated with enterovirus 71. Pediatr Infect Dis J. 1989;8:6116. DOIPubMedGoogle Scholar
  13. Kehle  J, Roth  B, Metzger  C, Pfitzner  A, Enders  G. Molecular characterization of an enterovirus 71 causing neurological disease in Germany. J Neurovirol. 2003;9:1268. DOIPubMedGoogle Scholar
  14. Oberste  MS, Penaranda  S, Maher  K, Pallansch  MA. Complete genome sequences of all members of the species Human enterovirus A. J Gen Virol. 2004;85:1597607. DOIPubMedGoogle Scholar
  15. Kapoor  A, Ayyagari  A, Dhole  TN. Non-polio enteroviruses in acute flaccid paralysis. Indian J Pediatr. 2001;68:9279. DOIPubMedGoogle Scholar




Cite This Article

DOI: 10.3201/eid1502.080865

Table of Contents – Volume 15, Number 2—February 2009

EID Search Options
presentation_01 Advanced Article Search – Search articles by author and/or keyword.
presentation_01 Articles by Country Search – Search articles by the topic country.
presentation_01 Article Type Search – Search articles by article type and issue.



Please use the form below to submit correspondence to the authors or contact them at the following address:

Milind M. Gore, National Institute of Virology, Sus Rd Campus, Pashan, Pune 411 021, India;

Send To

10000 character(s) remaining.


Page created: December 08, 2010
Page updated: December 08, 2010
Page reviewed: December 08, 2010
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.