Objective To identify the pathogen that caused an outbreak of viral encephalitis in Henan area in 2011.Phylogenic analysis was carried out on Coxsackie-virus B5 (CVB5) which was isolated during this outbreak.Methods Five throat swab,21 stool and 14 cerebrospinal fluid (CSF) specimens were collected from 29 inpatients during this outbreak.Viral isolation and real time RT-PCR were then performed for all specimens.Viral nucleic acid of enterovirus 71 (EV71),coxsackievirus A 16 (CA16) and pan-enterovirus (PE)were detected by real time RT-PCR.Phylogenetic tree based on entire VP1 sequences was constructed among CVB5 isolates from 2 stool and 3 CSF specimens of 5 inpatients and others published data retrieved from GenBank.Results The real time RT-PCR results showed that the PE nucleic acid positive rates of throat swab,stool and CSF specimens were 60.0％ (3/5),61.9％ (13/21) and 85.7％ (12/14) respectively.All of these specimens were negative for EV71 and CA16.The isolation rates of throat swab,stool and CSF specimens were 20.0％ (1/5),25.0％ (5/21) and 29.0％ (4/14),respectively.BLAST with both VP1 and 5′-UTR sequences and molecular typing indicated that CVB5 was the main pathogen.Analysis among the 5 positve isolates based on the complete VP1 sequences showed 97.9％-99.5％ homology.Data from homologous comparisons indicated that these isolates had the highest nucleotide acid identity with the Changchun CVB5 CC10/10/Changchun strain (97.1％-98.1％) which caused hand,foot,and mouth disease (HFMD) outbreak in Changchun in 2010,and lower identity (89.0％-89.6％ and 91.8％-92.5％) with the COXB5/Henan/2010 and 03001N strain isolated from Pingdingshan,Henan in 2010 and 2012,respectively.Phylogenetic tree in VP1 region showed that isolates of this outbreak belonged to genotype D,the same clade with Changchun strain.Conclusion CVB5 was the major etiological agent correlated with this outbreak.The shift of predominant genotype might serve as one of the causes that associated with this outbreaks.