(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT)
`
`(19) World Intellectual Property Organization
`International Bureau
`
`9 December 2010 (09.12.2010) (10) International Publication Number
`
`(43) International Publication Date
`
`WO 2010/141433 A3
`
`
`(51)
`
`International Patent Classification:
`C12Q 1/68 (2006.01)
`C40B 40/06 (2006.01)
`CIZQ 1/70 (2006.01)
`
`(74)
`
`Agents: EINHORN. Gregory, P. et al.; Gavrilovich,
`Dodd & Lindsey LLP, 4660 La Jolla Village Drive, Suite
`750, San Diego, CA 92122 (US).
`
`(21)
`
`International Application Number:
`PCT/USZOlO/036849
`
`(81)
`
`(22)
`
`International Filing Date:
`
`(25)
`
`(26)
`
`(30)
`
`(71)
`
`(72)
`(75)
`
`Filing Language:
`
`Publication Language:
`
`1 June 2010 (01.06.2010)
`
`English
`
`English
`
`Priority Data:
`61/183,377
`61/286,742
`
`2 June 2009 (02.06.2009)
`15 December 2009 (15.12.2009)
`
`US
`US
`
`Applicant (for all designated States except US): THE
`REGENTS OF THE UNIVERSITY OF CALIFOR-
`NIA [US/US]; 1111 Franklin Street, 5th Floor, Oakland,
`CA 94607-5200 (US).
`
`Inventors; and
`Inventors/Applicants $01” US only): DING, Shou-Wei
`[US/US]; 8797 Barnwood Lane, Riverside, CA 92508
`(US). WU, Qingfa [CN/US]; 1177 Linden Street, Apt.
`19, Riverside, CA 92507 (US).
`
`(84)
`
`Designated States (unless otherwise indicated, for every
`kind ofnational protection available): AE, AG, AL, AM,
`AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ,
`CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO,
`DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT,
`HN, HR, HU, ID, IL, 1N, lS, JP, KE, KG, KM, KN, KP,
`KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD,
`ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI,
`NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD,
`SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR,
`TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
`
`Designated States (unless otherwise indicated, for every
`kind of regional protection available): ARIPO (BW, GH,
`GM, KE, LR, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG,
`ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ,
`TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK,
`EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU,
`LV, MC, MK, MT, NL, NO, PL, PT, R0, SE, SI, SK,
`SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ,
`GW, ML, MR, NE, SN, TD, TG).
`
`(54) Title: VIRUS DISCOVERY BY SEQUENCING AND ASSEMBLY OF VIRUS-DERIVED SIRNAS, MIRNAS, PIRNAS
`
`[Continued on nextpage]
`
`FlGURE 2
`
`
`
`
`
`
`
`
`(57) Abstract: In one embodiment, the
`disclosure provides methods and sys-
`tems for identifying viral nucleic acids
`in a sample. In another embodiment the
`invention provides methods
`for viral
`genome assembly and viral discovery
`using small inhibitory RNAS, or "small
`silencing," RNAS
`(siRNAS), micro—
`RNAS (miRNAs) and/or P1WI-interacl-
`ing RNAS (piRNAs), including siRNAS,
`miRNAs and/or piRNAs isolated or se-
`quenced from invertebrate organisms
`such as insects (Anthropoda), nematodes
`(Nemapoda), Mollusca, Porifera, and
`other invertebrates, and/or plants, fungi
`or algae, Cyanobacteria and the like.
`
`EGQS nt
`
`9211““
`
`{1‘va
`
`EEV
`
`£3 mTRv
`
`
`
`W02010/141433A3|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
`
`

`

`WO 2010/141433 A3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
`
`Published:
`— Wlth international 3&1le report (Art. 218))
`— before the expiration of the time limitfor amending the
`claims and to be republished in the event of receipt of
`amendments (Rule 48.2(h))
`
`— with sequence listing part nfdescription (Rule 5.2(a))
`(88) Date of publication of the international search report:
`21 April 2011
`
`

`

`INTERNATIONAL SEARCH REPORT
`
`International application NO.
`PCT/USZOlO/036849
`
`A.
`
`CLASSIFICATION OF SUBJECT MATTER
`
`CIZQ I/68(2006.01)i, CIZQ I/70(2006.01)i, C403 40/06(2006.01)i
`
`
`According to International Patent Classification (IPC) or to both national classification and IPC
`B.
`FIELDS SEARCHED
`
`Minimum documentation searched (classification system followed by classification symbols)
`C12Q 1/68
`
`Documentation searched other than minimum documentation to the extent that such documents are included in the fields searched
`
`Korean utility Inodels and applications for utility Inodels
`Japanese utility models and applications for utility models
`
`Electronic data base consulted during the international search (name of data base and, Where practicable, search terms used)
`eKOMPASS(KIPO internal),Google & PubMed
`
`
`C. DOCUMENTS CONSIDERED TO BE RELEVANT
`
`Categ01y*
`
`Citation of document, with indication, where appropriate, of the relevant passages
`
`Relevant to claim No.
`
`KREUZE J.F. et al. ”Complete viral genome sequence and discovery of novel vi
`ruses by deep sequencing of small RNAsZ a generic method for diagnosis, disc
`every and sequencing of viruses" Virology, 25 May 2009, Vol. 388, No. 1, pp
`1 177
`
`Sec Abstract
`
`; Figures 1-3; Pages 3; Column 1; Table 1
`
`for mapping b
`LI Z. et al. ”Improved rapid amplification of cDNA ends (RACE)
`eth the 5‘ and 3'
`terminal sequences of paramyxevirus genomes" J. Virel Meth
`eds, December 2005, Vol. 130, No. 1-2, pp. 154-156
`See Abstract; Figures 1, 2
`
`ZERBINO DR. et al. "Velvet; algorithms for de novo short read assembly usin
`g de Bruijn graphs" Genome Res., May 2008, Vol. 18, No. 5, pp.821’829
`Sec Abstract; Figure 1; Pages 821; Column 1
`
`WU Q. et al. "Virus discovery by deep sequencing and assembly of virus-deriv
`ed small silencing RNAs" Prec Natl Acacl Sci U S A., 26 January 2010, Vol. 10
`7, No. 4, pp.1606-1611
`See Abstract; Figures 1-4
`
`1—11;13;14
`
`12,15-17
`
`12,15—17
`
`
`
`*
`"A"
`
`"E"
`
`"L"
`
`
`
`|:| Further documents are listed in the continuation ofBox C.
`Special categories 0f cited documents:
`document defining the general state of the art which is not considered
`to be ofparticular relevance
`earlier application or 1331011t but PU—bliSth on 01‘ after the international
`filing date
`document which may throw doubts on priority claim(s) or which is
`cited to establish the publication date 0f citation 0T other
`special reason (as specified)
`document referring 10 an oral disclosure, use, exhibition or other
`means
`document published prior to the international filing date but later
`than the priority date claimed
`
`"T"
`
`E SOC patent family annex.
`later document published after the international filing date or priority
`date and not in conflict with the application but cited to understand
`the principle or theory underlying the invention
`" 7" document of particular relevance; the claimed invention cannot be
`considered novel or cannot be considered to involve an inventive
`step when the document is taken alone
`document of particular relevance; the claimed invention cannot be
`considered to involve an inventive step When the document
`is
`combined with one or more other such documents,such combination
`being obvious to a person skilled in the art
`"&" document member of the same patent family
`
`Date of the actual completion ofthe international search
`
`Date of mailing of the international search report
`
`28 JANUARY 2011 (28.01.2011)
`Name and mailing address of the ISA/KR
`Korean Intellectual Propelty Office
`Government Complex-Daejeon, 139 Seonsa-ro, Seo-
`gu, Daejeon 302-701, Republic of Korea
`Facs1mile No. 82-42-472-7140
`
`Form PCT/ISA/210 (second sheet) (July 2009)
`
`21 FEBRUARY 2011 (21.02.2011)
`Authorized officer
`
`Park, Jung Min
`
`Telephone No.
`
`82—42—481—8291
`
`

`

`INTERNATIONAL SEARCH REPORT
`
`International application No.
`
`PCT/US2010/036849
`
`Box No. I Nucleotide and/or amino acid sequence(s) (Continuation of item1.b of the first sheet)
`
`1. With regard to any nucleotide and/or amino acid sequence disclosed in the international application,
`carried out on the basis of :
`
`the international search was
`
`a. a sequence listing filed or furnished
`
`D on paper
`IZI in electronic form
`
`b.
`
`time of filing or furnishing
`
`|:| contained in the international application as filed
`filed together with the international application in electronic form
`
`|:| furnished subsequently to this Authority for the purposes of search
`
`3. Additional comments:
`
`In addition, in the case that more than one version or copy of a sequence listing has been filed or furnished, the required
`statements that the information in the subsequent or additional copies is identical to that in the application as filed or does
`not go bcyond thc application as filcd, as appropriatc, wcrc furnishcd.
`
`Form PCT/ISA/ZIO (continuation of first sheet (1))
`
`(July 2009)
`
`

`

`International application No. Information on patent family members
`
`INTERNATIONAL SEARCH REPORT
`
`PCT/U52010/036849
`
`Patent document
`cited in search report
`
`Publication
`datc
`
`Patent family
`mcmbcr(s)
`
`Publication
`datc
`
`None
`
`
`
`Form PCT/ISA/210 (patent family annex) (July 2009)
`
`