Metagenomic Analysis of Fever, Thrombocytopenia and Leukopenia Syndrome (FTLS) in Henan Province, China: Discovery of a New Bunyavirus

English version České info

Since 2007, many cases of fever, thrombocytopenia and leukopenia syndrome (FTLS) have emerged in Henan Province, China. Patient reports of tick bites suggested that infection could contribute to FTLS. Many tick-transmitted microbial pathogens were tested for by PCR/RT-PCR and/or indirect immunofluorescence assay (IFA). However, only 8% (24/285) of samples collected from 2007 to 2010 tested positive for human granulocytic anaplasmosis (HGA), suggesting that other pathogens could be involved. Here, we used an unbiased metagenomic approach to screen and survey for microbes possibly associated with FTLS. BLASTx analysis of deduced protein sequences revealed that a novel bunyavirus (36% identity to Tehran virus, accession: HQ412604) was present only in sera from FTLS patients. A phylogenetic analysis further showed that, although closely related to Uukuniemi virus of the Phlebovirus genus, this virus was distinct. The candidate virus was examined for association with FTLS among samples collected from Henan province during 2007–2010. RT-PCR, viral cultures, and a seroepidemiologic survey were undertaken. RT-PCR results showed that 223 of 285 (78.24%) acute-phase serum samples contained viral RNA. Of 95 patients for whom paired acute and convalescent sera were available, 73 had serologic evidence of infection, with 52 seroconversions and 21 exhibiting a 4-fold increase in antibody titer to the virus. The new virus was isolated from patient acute-phase serum samples and named Henan Fever Virus (HNF virus). Whole-genome sequencing confirmed that the virus was a novel bunyavirus with genetic similarity to known bunyaviruses, and was most closely related to the Uukuniemi virus (34%, 24%, and 29% of maximum identity, respectively, for segment L, M, S at maximum query coverage). After the release of the GenBank sequences of SFTSV, we found that they were nearly identical (>99% identity). These results show that the novel bunyavirus (HNF virus) is strongly correlated with FTLS.

Vyšlo v časopise: Metagenomic Analysis of Fever, Thrombocytopenia and Leukopenia Syndrome (FTLS) in Henan Province, China: Discovery of a New Bunyavirus. PLoS Pathog 7(11): e32767. doi:10.1371/journal.ppat.1002369
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1002369

Souhrn

Zdroje

1. HeJGChengZXWuJBYangXXLiQ 2006 The Epidemiological Investigation on a human to human anaplasmosis infection in South Anhui Province in 2006. World J Infect 5 343 347

2. XuBLChenHMZhuQZhangJXiaSL 2006 The Epidemiological Investigation on the First Outbreak of Tsutsugamushi Disease in Henan Province. Henan J Prev Med 17 3

3. WenBJianRZhangYChenR 2002 Simultaneous Detection of Anaplasma marginale and a New Ehrlichia Species Closely Related to Ehrlichia chaffeensis by Sequence Analyses of 16S Ribosomal DNA in Boophilus microplus Ticks from Tibet. J Clin Microbiol 40 3286 3290

4. DuP 1982 Medical experimental virology. Shanghai Shanghai Association of Microbiology 211 212

5. DumlerJSChoiKSGarcia-GarciaJCBaratNSScorpioDG 2005 Human granulocytic anaplasmosis and Anaplasma phagocytophilum. Emerg Infect Dis 11 1828 1834

6. EngTRHarkessJRFishbeinDBDawsonJEGreeneCN 1990 Epidemiologic, clinical, and laboratory findings of human ehrlichiosis in the United States, 1988. JAMA 264 2251 2258

7. MOH of the people's republic of China 2008 Guide for Human granulocytic anaplasmosis control. http://www.moh.gov.cn/publicfiles/business/htmlfiles/mohbgt/pw10805/200804/31429.htm

8. PaulSDianaS 2001 Dictionary of Microbiology and Molecular Biology. Chichester John Wiley & Sons, Ltd 1 4 3rd edition.

9. MeiyuFHuoshengCCuihuaCXiaodongTLianhuaJ 1997 Detection of flaviviruses by reverse transcriptase polymerase chain reaction with the universal primer set. Microbiol Immunol 41 209 213

10. BaiZLiuLTuZYaoLLiuJ 2008 Real-time PCR for detecting circulating dengue virus in the Guangdong Province of China in 2006. J Med Microbiol 57 1547 1552

11. XieRHXuFZhuHPChengYKFuGM 2009 Development and evaluation of TaqMan-based one-step reverse transcription-polymerase chain reaction assay for the detection of Japanese encephalitis virus. Zhonghua Liu Xing Bing Xue Za Zhi 30 277 280

12. SanthoshSRParidaMMDashPKPateriyaAPattnaikB 2007 Development and evaluation of SYBR Green I-based one-step real-time RT-PCR assay for detection and quantification of Chikungunya virus. J Clin Virol 39 188 193

13. KangXLiYLiuHLinFCaiX 2010 A duplex real-time reverse transcriptase polymerase chain reaction assay for the detection of Western Equine Encephalitis virus and Eastern Equine Encephalitis virus. Virol J 7 284

14. ChinikarSGoyaMMShirzadiMRGhiasiSMMirahmadiR 2008 Surveillance and laboratory detection system of Crimean-Congo haemorrhagic fever in Iran. Transbound Emerg Dis 55 200 204

15. SuzukiABisordiILevisSGarciaJPereiraLE 2004 Identifying rodent hantavirus reservoirs, Brazil. Emerg Infect Dis 10 2127 2134

16. GarciaSCranceJMBillecocqAPeinnequinAJouanA 2001 Quantitative Real-Time PCR detection of Rift Valley Fever virus and its application to evaluation of antiviral compounds. J Clin Microbiol 39 4456 4461

17. JinQ 2001 Medical Molecular Virology. Beijing Science Press 1st edition. 659

18. PeirisJSMLaiSTPoonLLGuanYYamLY 2003 Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet 361 1319 1325

19. FranchiniGCollaltiEAryaSKFenyöEMBiberfeldG 1987 Genetic analysis of a new subgroup of human and simian T-lymphotropic retroviruses: HTLV-IV, LAV-2, SBL-6669, and STLV-IIIAGM. AIDS Res Hum Retroviruses 3 11 17

20. Cox-FosterDLConlanSHolmesECPalaciosGEvansJD 2007 A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder. Science 318 283

21. FinkbeinerSRAllredAFTarrPIKleinEJKirkwoodCD 2008 Finkbeiner Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery. PLoS Pathog 4 e1000011

22. PalaciosGDruceJDuLTranTBirchC 2008 A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases. N Engl J Med 358 991 998

23. Woods Lt ColJB 2005 USAMRIID's Medical Management of Biological Casualties Handbook. Fort Detrick, Maryland U.S. Army Medical Institute of Infectious Diseases 143 144 6th edition.

24. LiRLiYKarstenKWangJ 2008 Sequence analysis SOAP: short oligonucleotide alignment program. BIOINFORMATICS 24 713 714

25. BohlanderSKEspinosaR3rdLe BeauMMRowleyJDDíazMO 1992 A method for the rapid sequence-independent amplification of microdissected chromosomal material. Genomics 13 1322 1324

26. AltschulSFMaddenTLSchäfferAAZhangJZhangZ 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25 3389 3402

27. LiWGodzikA 2006 Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22 1658 1659

28. HuangXMadanA 1999 CAP3: a DNA sequence assembly program. Genome Res 9 868 877

29. SlootsTPMcErleanPSpeicherDJArdenKENissenMD 2006 Evidence of human coronavirus HKU1 and human bocavirus in Australian children. J Clin Virol 35 99 102

30. BishopDHCalisherCHCasalsJChumakovMPGaidamovichSY 1980 Bunyaviridae. Intervirology 14 125 143

31. JinQ 2001 Medical Molecular Virology. Beijing Science Press 1st edition. 528

32. EwingBHillierLWendlMCGreenP 1998 Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8 175 185

33. SwoffordDL 1998 PAUP*.Phylogenetic Analysis Using Parsimony (*and Other Methods). Sunderland, Massachusettes Sinauer Associates

34. WoottonSCKimDSKondohYChenELeeJS 2011 Viral infection in acute exacerbation of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 183 1698 1702

35. GreeneCEAddieDD 2006 Feline parvovirus infections. In: Greene CE (ed). Infectious Diseases of the Dog and Cat. St. Louis: Saunders Elsevier 78-88

36. MayoMA 2002 Virus taxonomy-Houston 2002. Arch Virol 147 1071 1076

37. YuXJLiangMFZhangSYLiuYLiJD 2011 Fever with Thrombocytopenia Associated with a Novel Bunyavirus in China. N Engl J Med 364 1523 1532