Discovery of new viruses has been boosted by novel deep sequencing technologies. Currently, many viruses can be identified by sequencing without knowledge of the pathogenicity of the virus. However, attributing the presence of a virus in patient material to a disease in the patient can be a challenge. One approach to meet this challenge is identification of viral sequences based on enrichment by autologous patient antibody capture. This method facilitates identification of viruses that have provoked an immune response within the patient and may increase the sensitivity of the current virus discovery techniques. To demonstrate the utility of this method, virus discovery deep sequencing (VIDISCA-454) was performed on clinical samples from 19 patients: 13 with a known respiratory viral infection and 6 with a known gastrointestinal viral infection. Patient sera was collected from one to several months after the acute infection phase. Input and antibody capture material was sequenced and enrichment was assessed. In 18 of the 19 patients, viral reads from immunogenic viruses were enriched by antibody capture (ranging between 1.5x to 343x in respiratory material, and 1.4x to 53x in stool). Enriched reads were also determined in an identity independent manner by using a novel algorithm Xcompare. In 16 of the 19 patients, 21% to 100% of the enriched reads were derived from infecting viruses. In conclusion, the technique provides a novel approach to specifically identify immunogenic viral sequences among the bulk of sequences which are usually encountered during virus discovery metagenomics.
References
[1]
Assiri A, McGeer A, Perl TM, Price CS, Al Rabeeah AA, et al. (2013) Hospital outbreak of Middle East respiratory syndrome coronavirus. N Engl J Med 369: 407–416 10.1056/NEJMoa1306742 [doi].
[2]
Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, et al. (2003) Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300: 1394–1399 10.1126/science.1085952 [doi];1085952 [pii].
[3]
Zaki AM, van BS, Bestebroer TM, Osterhaus AD, Fouchier RA (2012) Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med 367: 1814–1820 10.1056/NEJMoa1211721 [doi].
[4]
Cotten M, Lam TT, Watson SJ, Palser AL, Petrova V, et al. (2013) Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus. Emerg Infect Dis 19: 736–42B 10.3201/eid1905.130057 [doi].
[5]
de Vries M, Deijs M, Canuti M, van Schaik BD, Faria NR, et al. (2011) A sensitive assay for virus discovery in respiratory clinical samples. PLoS One 6: e16118 10.1371/journal.pone.0016118 [doi].
[6]
Pyrc K, Berkhout B, van der Hoek L (2007) Identification of new human coronaviruses. Expert Rev Anti Infect Ther 5: 245–253 10.1586/14787210.5.2.245 [doi].
[7]
van der Hoek L, Pollakis G, Lukashov VV, Jebbink MF, Jeeninga RE, et al. (2007) Characterization of an HIV-1 group M variant that is distinct from the known subtypes. AIDS Res Hum Retroviruses 23: 466–470 10.1089/aid.2006.0184 [doi].
[8]
Canuti M, Eis-Huebinger AM, Deijs M, de Vries M, Drexler JF, et al. (2011) Two novel parvoviruses in frugivorous New and Old World bats. PLoS One 6: e29140 10.1371/journal.pone.0029140 [doi];PONE-D-11-19925 [pii].
[9]
Jazaeri Farsani SM, Oude Munnink BB, Deijs M, Canuti M, van der Hoek L (2013) Metagenomics in virus discovery. VOXS 8: 193–194.
Sauvage V, Cheval J, Foulongne V, Gouilh MA, Pariente K, et al. (2011) Identification of the first human gyrovirus, a virus related to chicken anemia virus. J Virol 85: 7948–7950 JVI.00639-11 [pii];10.1128/JVI.00639-11 [doi].
[12]
Tan le V, van Doorn HR, Nghia HD, Chau TT, Tu le TP, et al. (2013) Identification of a new cyclovirus in cerebrospinal fluid of patients with acute central nervous system infections. MBio 4 . mBio.00231-13 [pii];10.1128/mBio.00231-13 [doi].
[13]
Nishizawa T, Okamoto H, Konishi K, Yoshizawa H, Miyakawa Y, et al. (1997) A novel DNA virus (TTV) associated with elevated transaminase levels in posttransfusion hepatitis of unknown etiology. Biochem Biophys Res Commun 241: 92–97 S0006-291X(97)97765-2 [pii];10.1006/bbrc.1997.7765 [doi].
[14]
Boom R, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM, et al. (1990) Rapid and simple method for purification of nucleic acids. J Clin Microbiol 28: 495–503.
[15]
Endoh D, Mizutani T, Kirisawa R, Maki Y, Saito H, et al. (2005) Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription. Nucleic Acids Res 33: e65 33/6/e65 [pii];10.1093/nar/gni064 [doi].
[16]
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2010) GenBank. Nucleic Acids Res 38: D46–D51 gkp1024 [pii];10.1093/nar/gkp1024 [doi].
[17]
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410 10.1016/S0022-2836(05)80360-2 [doi];S0022-2836(05)80360-2 [pii].
[18]
Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC (2011) Integrative analysis of environmental sequences using MEGAN4. Genome Res 21: 1552–1560 gr.120618.111 [pii];10.1101/gr.120618.111 [doi].
[19]
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421 1471-2105-10-421 [pii];10.1186/1471-2105-10-421 [doi].
[20]
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792–1797 10.1093/nar/gkh340 [doi];32/5/1792 [pii].
[21]
Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113 10.1186/1471-2105-5-113 [doi];1471-2105-5-113 [pii].
[22]
Dijkman R, Jebbink MF, El Idrissi NB, Pyrc K, Muller MA, et al. (2008) Human coronavirus NL63 and 229E seroconversion in children. J Clin Microbiol 46: 2368–2373.
[23]
Dijkman R, Jebbink MF, Gaunt E, Rossen JW, Templeton KE, et al. (2012) The dominance of human coronavirus OC43 and NL63 infections in infants. J Clin Virol 53: 135–139 S1386-6532(11)00473-2 [pii];10.1016/j.jcv.2011.11.011 [doi].
[24]
Simhon A, Mata L (1985) Fecal rotaviruses, adenoviruses, coronavirus-like particles, and small round viruses in a cohort of rural Costa Rican children. Am J Trop Med Hyg 34: 931–936.
[25]
Gouandjika-Vasilache I, Akoua-Koffi C, Begaud E, Dosseh A (2005) No evidence of prolonged enterovirus excretion in HIV-seropositive patients. Trop Med Int Health 10: 743–747 TMI1454 [pii];10.1111/j.1365-3156.2005.01454.x [doi].
[26]
Smith CB, Purcell RH, Bellanti JA, Chanock RM, Laine P (1966) Protective Effect of Antibody to Parainfluenza Type 1 Virus. N Engl J Med 275: 1145–1152 doi: 10.1056/NEJM196611242752101.
[27]
Schomacker H, Schaap-Nutt A, Collins PL, Schmidt AC (2012) Pathogenesis of acute respiratory illness caused by human parainfluenza viruses. Curr Opin Virol 2: 294–299 S1879-6257(12)00028-4 [pii];10.1016/j.coviro.2012.02.001 [doi].
