# Complete Genome Sequence of a Rabies Virus Isolated from a Human in Central African Republic

Vianney Tricou, Nicolas Berthet, Emmanuel Nakouné, Mirdad Kazanji

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Vianney Tricou, Nicolas Berthet, Emmanuel Nakouné, Mirdad Kazanji. Complete Genome Sequence of a Rabies Virus Isolated from a Human in Central African Republic. Genome Announcements, 2014, 2 (3), pp.e00598-14. 10.1128/genomeA.00598-14. pasteur-03516030

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# Complete Genome Sequence of a Rabies Virus Isolated from a Human in Central African Republic

Vianney Tricou,ª Nicolas Berthet,ᵇ,ᶜ Emmanuel Nakouné,ª,ᵈ Mirdad Kazanjiaª

Department of Virology, Institut Pasteur de Bangui, Bangui, Central African Republicª; Epidemiology and Physiopathology of Oncogenic Viruses, Institut Pasteur, Paris, Franceᵇ; UMR3569, Centre National de la Recherche Scientifique, Paris, Franceᶜ; National Laboratory for Rabies, Institut Pasteur de Bangui, Bangui, Central African Republicᵈ

To validate the feasibility of using next-generation sequencing in an African context, the complete genome of a rabies virus isolated from a human patient was obtained by high-throughput sequencing after virus isolation in mice and random unbiased amplification. Phylogenetic analysis suggested that this virus belongs to the Africa II clade.

Received 26 May 2014 Accepted 29 May 2014 Published 19 June 2014

Citation Tricou V, Berthet N, Nakouné E, Kazanjii M. 2014. Complete genome sequence of a rabies virus isolated from a human in Central African Republic. Genome Announc. 2(3):e00598-14. doi:10.1128/genomeA.00598-14.

Copyright © 2014 Tricou et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to Vianney Tricou, vianney.tricou@gmail.com.

Although it is a fatal but preventable disease, rabies is still a widespread neglected zoonosis that represents an important public health threat in developing countries (1). Rabies virus (RABV) belongs to the genus *Lyssavirus* and family *Rhabdoviridae*. Humans get infected through close contact with secretions of rabid animals, mainly dogs. Rabies is almost always fatal once symptoms appear. Annually, 55,000 people die of rabies mostly in Asia and Africa (2). However, only a few complete genomes of African canine RABV are available (3, 4). Recent development of next-generation sequencing technologies allows virus whole-genome sequencing at relatively low cost. This might bring new insight into virus evolution, host-virus interactions, and pathogenicity (5). In September 2011, a man deeply bitten by a dog a few weeks before and suffering from mental confusion was treated at the anti-rabies dispensary in Bangui, Central African Republic, by 2 doses of vaccine according to the WHO-approved 2-1-1 regimen (6). Although required after severe exposures, rabies immunoglobulin was not administered as risk assessment was made difficult by incomplete anamnesis. He was supposed to come back for 2 more doses but never showed up again. Attempts to find out what happened remained unsuccessful. A sample of saliva was produced just before the first vaccine doses. Intra-cerebral inoculation of mice followed by direct immunofluorescence and PCR confirmed RABV presence in saliva. For the whole-genome sequencing, RNA extracted from inoculated mouse brain tissue using a QIAmp Viral RNA Minikit (Qiagen) was treated with TURBO DNAse (Life Technologies) to remove contaminating DNA and retro-transcribed using SuperScript III enzyme and random hexamers (Life Technologies). Amplification was done using Phi29 enzyme as described previously (7). High-throughput sequencing was performed by GATC Biotech (Konstanz, Germany) using a HiSeq 2000 system (Illumina). After removal of low-quality reads, 45.7 million of 100-bp single-reads were filtered using Bowtie 2 to discard murine sequences (8). Reads corresponding to RABV were selected by a similarity approach using BLASTn and BLASTx search tools with accession no. KC196743 as

a reference (3). Final assembly was made using Ray software (9). Each position was covered on average 7,800 times. Overall length was 11,923 nucleotides (nt). Coding sequence lengths were 1,353 nt for the nucleoprotein, 894 nt for the phosphoprotein, 609 nt for the matrix protein, 1,575 nt for the glycoprotein, and 6,384 nt for the polymerase genes. Only one similar complete genome (98% identity) was found in GenBank after a similarity search, corresponding to the DRV-NG11 virus isolated from a dog in Nigeria in 2011 (3). Sequence analysis of the N gene showed a close relationship with viruses found in Chad and Niger in 1987, 1990, 1996, and 2005–2006 (identity ≥99%). Phylogenetic analysis suggests that our isolate belongs to Africa II clade group e, which includes viruses from Chad, Niger, Cameroon, and Nigeria (10). To our knowledge, this is the first reported complete genome of a RABV isolated from a human in Africa and one of a few of all the hosts combined.

**Nucleotide sequence accession number.** The complete genome sequence is available in the DDBJ/EMBL/GenBank database under accession no. KF977826.

## ACKNOWLEDGMENTS

This study was financially supported by the Programme Transversal de Recherche (PTR) CEVACAR No. 385 funded by the Institut Pasteur (Paris, France).

All animal work has been approved by the local equivalent of the Institutional Review Board.

We gratefully thank Josiane Leal (Anti-Rabies Dispensary, Institut Pasteur de Bangui) and Xavier Konamna (National Laboratory for Rabies, Institut Pasteur de Bangui) for their technical help.

## REFERENCES

1. Bourhy H, Dautry-Varsat A, Hotez PJ, Salomon J. 2010. Rabies, still neglected after 125 years of vaccination. PLOS Negl. Trop. Dis. 4:e839. http://dx.doi.org/10.1371/journal.pntd.0000839.

2. Knobel DL, Cleaveland S, Coleman PG, Fèvre EM, Meltzer MI, Miranda ME, Shaw A, Zinsstag J, Meslin FX. 2005. Re-evaluating the burden of rabies in Africa and Asia. Bull. World Health Organ. 83: 360–368.
3. Zhou M, Zhou Z, Kia GS, Gnanadurai CW, Leyson CM, Umoh JU, Kwaga JP, Kazeem HM, Fu ZF. 2013. Complete genome sequence of a street rabies virus isolated from a dog in Nigeria. Genome Announc. 1(1): e00214-12. http://dx.doi.org/10.1128/genomeA.00214-12.

4. Marston DA, McElhinney LM, Ellis RJ, Horton DL, Wise EL, Leech SL, David D, de Lamballerie X, Fooks AR. 2013. Next generation sequencing of viral RNA genomes. BMC Genomics 14:444. http://dx.doi.org/10.1186/1471-2164-14-444.

5. Radford AD, Chapman D, Dixon L, Chantrey J, Darby AC, Hall N. 2012. Application of next-generation sequencing technologies in virology. J. Gen. Virol. 93:1853-1868. http://dx.doi.org/10.1099/vir.0.043182-0.

6. World Health Organization, WHO. 2013. Rabies. Fact sheet no. 99. Updated July 2013. World Health Organization, Geneva, Switzerland.

7. Berthet N, Reinhardt AK, Leclercq I, van Ooyen S, Batéjat C, Dickinson P, Stamboliyska R, Old IG, Kong KA, Dacheux L, Bourhy

H, Kennedy GC, Korfhage C, Cole ST, Manuguerra JC. 2008. Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR. BMC Mol. Biol. 9:77. http://dx.doi.org/10.1186/1471-2199-9-77.

8. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9:357-359. http://dx.doi.org/10.1038/nmeth.1923.

9. Boisvert S, Laviollette F, Corbeil J. 2010. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J. Comput. Biol. 17:1519-1533. http://dx.doi.org/10.1089/cmb.2009.0238.

10. Talbi C, Holmes EC, de Benedictis P, Faye O, Nakouné E, Gamatié D, Diarra A, Elmamy BO, Sow A, Adjogoua EV, Sangare O, Dundon WG, Capua I, Sall AA, Bourhy H. 2009. Evolutionary history and dynamics of dog rabies virus in western and central Africa. J. Gen. Virol. 90:783-791. http://dx.doi.org/10.1099/vir.0.007765-0.