phylogenetic relationships amongst hev strains

Phylogenetic relationships amongst HEV strains

Participants:•Agnes Zotter•Lambert Motilal•Maria Montalvo•Marissa Moses•Robin Antoine

Hepatitis E Virus• Hepeviridae, Hepevirus genus• Unenveloped RNA virus, 27-34nm in diameter• +ve stranded RNA genome, 7.2 kb in size• Very labile and sensitive

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

Most outbreaks associated with faeceally contaminated drinking water.

Large epidemics have occurred in the Indian subcontinent, USSR, China, Africa and Mexico.

In the United States and other non-endemic areas, where there are no documented outbreaks of hepatitis E, a low prevalence of anti-HEV (<2%) has been found in healthy populations. The source of infection for these persons is unknown.

Minimal person-to-person transmission.

Hepatitis E - Epidemiologic

Features

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

Incubation period: Average 40 days

Range 15-60 days Case-fatality rate: Overall, 1%-3%

Pregnant women, 15%-25%

Illness severity: Increased with age

Chronic sequelae: None identified

Hepatitis E - Clinical Features

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

HEV isolates have been grouped into four genotypes (1 to 4)

•Genotype 1 groups isolates found mainly in Asia and Africa

•Genotype 2 contains an isolate from an outbreak in Mexico and Africa

•Genotype 3 groups isolates found in the US & Europe

•Genotype 4 groups isolates found in China, Taiwan and Japan

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

Hepatitis E Virus Genome

Research question

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

To determine the genotype identity of isolates found in Cuba

Possible ways of managing the disease

Methods:

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

Sequences from RNA polymerase in GenBanK (NCBI)

13 hits

CUB9-1999 isolate chosen (241 bp linear RNA)Blastn: 30 entries chosen/E-value

Length +/- 10 nucleotides alignment

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

Blastp Protein ID from initial selected isolate

ClustalX2 multiple alignmentAnalysis in Phylogenetic software

>gb|ACD39863.1| RNA-dependent RNA polymerase [Hepatitis E virus] Length=116

Score = 133 bits (334), Expect = 6e-37, Method: Compositional matrix adjust. Identities = 61/79 (77%), Positives = 69/79 (87%), Gaps = 0/79 (0%)

Query 1 CALFGPWFRAIEKAILALLPQGVFYGDAFDDTVFSATVAAAKASMVFENDFSEFDSTQNN 60 CALFGPWFRAIEK ILALLP +FYGDA++++VFSA ++ A +SMVFENDFSE ST NN Sbjct 9 CALFGPWFRAIEKE ILALLPPN IFYGDAYEES VFSAAISGAGSSMVFENDFSEDXSTLNN 68

Query 61 FSLGLECAIMEECGMPQWL 79 FSLGLEC IMEECGMPQWL Sbjct 69 FSLGLECVIMEECGMPQWL 87

Protein alignment (MSA):

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

Results:

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

R

Nucleic Acids Research 2005 33(Web Server Issue):W553-W556; doi:10.1093/nar/gki494 . C-Y Lin*, F-K Lin, CH Lin, L-W Lai, H-J Hsu, S-H Chen and CA Hsiung

http://power.nhri.org.tw/

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

Genotype 1

Genotype 3

Genotype 4

Genotype 2

DNA data

NJ analysis

Phylogenetic tree:

Protein Seq.data

NJ analysis

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

Phylogenetic tree

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

Phylogenetic tree: Phylip with DNA data JAP291

Cub25_08 Mex017

Fin969Fin973

Ind LonInd097

Mor494 Chn001

Chn363

Ind103

Chn457Hyder Cub19_99

Cub9_99NindCub2_05

Cub27_99Cub10_99

Fin971Fin967

US2SKor476

US1SKor466Fr757

Fr719Fr767

Fr787Fr785

Phylogenetic tree: Phylip/protein data

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

DNA Alignment without Cub25-2008

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

Phylogenetic tree:

MEGA4/DNA data

Genotype 1

Genotype 2

Genotype 3

Genotype 4

Phylogenetic tree: MEGA/protein data

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

Genotype 1

Genotype 2

Genotype 3

Genotype 4

HEV from human in Cuba were clustered in at least two genotypes.

Conclusion

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

Genotype 1 with Asian and African isolates

Genotype 3 with American and European isolates from swine and human

A take-home message…

Avoid drinking water (and beverages with ice) of unknown purity, uncooked shellfish, and uncooked fruit/vegetables not peeled or prepared by traveler.

IG prepared from donors in Western countries does not prevent infection.

Unknown efficacy of IG prepared from donors in endemic areas.

Vaccine?

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

Thank you for your attention!

UWI, St. Augustine, Trinidad & Tobago, 29.01.2010.

Special thanks for the great teachers, who were very patient and helpful, who helped us to make this presentation better…

Dr. Urmila Kulkarni-Kale Dr. Jessica Kissinger Dr. Dinesh Gupta Dr. Arnab Pain

Dr. Vrijesh Tripathi