US 2023/0174953 A1 · DEFECTIVE INTERFERING VIRAL GENOMES · patentgrep

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Abstract

Method for producing a defective interfering viral genome (DVG), defective interfering particles comprising the DVG, and methods and uses thereof.

Claims51

Dependent claims

A method for producing a defective interfering viral genome (DVG), the method comprising:

providing a first set of at least three replicate in vitro cell cultures, comprising a solid support and cells infected with a reference infectious virus at a high multiplicity of infection (MOI);
providing a second set of at least three replicate in vitro cell cultures, comprising a solid support and cells infected with the reference infectious virus at a low multiplicity of infection (MOI);
culturing the first and second sets of replicate in vitro cell cultures for at least 5 passages under mutagenic conditions;
collecting a plurality of DVG candidates from the medium of the first and second sets of in vitro replicate cell cultures;
deep sequencing the collected DVG candidates;
and
selecting a DVG from the plurality of DVG candidates.

4 more elements

A DVG comprising or consisting of a nucleotide sequence selected from the group consisting of:

SEQ ID NO:
1 (DG1 :
EV71 DVG 293-390), SEQ ID NO:
2 (DG2 :
EV71 DVG 294-404), SEQ ID NO:
3 (DG3 :
EV71 DVG 1746-2895), SEQ ID NO:
4 (DG4 :
EV71 DVG 1752-2894), SEQ ID NO:
5 (DG5 :
EV71 DVG 1752-2896), SEQ ID NO:
6 (DG6 :
EV71 DVG 1880-6487), SEQ ID NO:
7 (DG7 :
EV71 DVG 1880-6488), SEQ ID NO:
8 (DG8 :
EV71 DVG 3513-6516), SEQ ID NO:
9 (DG9 :
EV71 DVG 5475-5634), SEQ ID NO:
10 (DG10:
EV71 DVG 5610-6876), SEQ ID NO:
11 (DG11 :
EV71 DVG 5610-6877), SEQ ID NO:
12 (DG12:
EV71 DVG 5746-5821), SEQ ID NO:
13 (DG13 :
EV71 DVG 6322-6356), SEQ ID NO:
14 (DG14:
EV71 DVG 6322-6358), SEQ ID NO:
15 (DG15:
EV71 DVG 6728-6779), SEQ ID NO:
16 (DG16:
EV71 DVG 6966-7012), SEQ ID NO:
17 (DG17:
EV71 DVG 6966-7014), SEQ ID NO:
18 (DG18:
EV71 DVG 7098-7122), SEQ ID NO:
19 (DG19:
EV71 DVG 7165-7200), SEQ ID NO:
20 (DG20:
EV71 DVG 7165-7201), SEQ ID NO:
21 (DG21:
EV71 DVG 7238-7292), SEQ ID NO:
22 (ZIKV DVG-A), SEQ ID NO:
23 (ZIKV DVG-B), SEQ ID NO:
24 (ZIKV DVG-C), SEQ ID NO:
25 (ZIKV DVG-D), SEQ ID NO:
26 (ZIKV DVG-E), SEQ ID NO:
27 (ZIKV DVG-F), SEQ ID NO:
28 (ZIKV DVG-G), SEQ ID NO:
29 (ZIKV DVG-H), SEQ ID NO:
30 (ZIKV DVG-I), SEQ ID NO:
31 (ZIKV DVG-J), SEQ ID NO:
32 (ZIKV DVG-K), SEQ ID NO:
33 (ZIKV DVG-L), SEQ ID NO:
34 (CHIKV DVG-IV1), SEQ ID NO:
35 (CHIKV DVG-IV2), SEQ ID NO:
36 (CHIKV DVG-IV3), SEQ ID NO:
37 (CHIKV DVG-IV4), SEQ ID NO:
38 (CHIKV DVG-IH1), SEQ ID NO:
39 (CHIKV DVG-IU1), SEQ ID NO:
40 (CHIKV DVG-CV1), SEQ ID NO:
41 (CHIKV DVG-CV2), SEQ ID NO:
42 (CHIKV DVG-CV3), SEQ ID NO:
43 (CHIKV DVG-CV4), SEQ ID NO:
44 (CHIKV DVG-CH1), SEQ ID NO:
45 (CHIKV DVG-CH2), SEQ ID NO:
46 (CHIKV DVG-CH3), SEQ ID NO:
47 (CHIKV DVG-CM1), SEQ ID NO:
48 (CHIKV DVG-CU1), SEQ ID NO:
49 (CHIKV DVG-CU2), SEQ ID NO:
50 (CHIKV DVG-CA1), SEQ ID NO:
51 (CHIKV DVG-CA2), SEQ ID NO:
52 (CHIKV DVG-CA3), SEQ ID NO:
53 (CHIKV DVG-CA4), SEQ ID NO:
55 (RV DVG A01a-TIP-01), SEQ ID NO:
56 (RV DVG A01a-TIP-02), SEQ ID NO:
57 (RVDVG A01a-TIP-03), SEQ ID NO:
58 (RV DVG A01a-TIP-04), SEQ ID NO:
59 (RVDVG A01a-TIP-05), SEQ ID NO:
60 (RV DVG A01a-TIP-06), SEQ ID NO:
62 (RVDVG A16-TIP-01), SEQ ID NO:
63 (RV DVG A16-TIP-02), SEQ ID NO:
64 (RV DVG A16-TIP-03), SEQ ID NO:
65 (RV DVG A16-TIP-04), SEQ ID NO:
66 (RV DVG A16-TIP-05), SEQ ID NO:
89 (RV DVG C15-TIP-01), SEQ ID NO:
90 (RV DVG C15-TIP-02), SEQ ID NO:
91 (RV DVG C15-TIP-03), SEQ ID NO:
92 (RV DVG C15-TIP-04), SEQ ID NO:
68 (RV DVG B14-TIP-01), SEQ ID NO:
69 (RV DVG B14-TIP-02), SEQ ID NO:
70 (RV DVG B14-TIP-03), SEQ ID NO:
71 (RV DVG B14-TIP-04), SEQ ID NO:
72 (RV DVG B14-TIP-05), SEQ ID NO:
73 (RV DVG B14-TIP-06), SEQ ID NO:
74 (RV DVG B14-TIP-07), SEQ ID NO:
75 (RV DVG B14-TIP-08), SEQ ID NO:
76 (RV DVG B14-TIP-09), SEQ ID NO:
77 (RV DVG B14-TIP-10), SEQ ID NO:
78 (RV DVG B14-TIP-11), SEQ ID NO:
79 (RV DVG B14-TIP-12), SEQ ID NO:
80 (RV DVG B14-TIP-13), SEQ ID NO:
81 (RV DVG B14-TIP-14), SEQ ID NO:
82 (RV DVG B14-TIP-15), SEQ ID NO:
83 (RV DVG B14-TIP-16), SEQ ID NO:
84 (RV DVG B14-TIP-17), SEQ ID NO:
85 (RV DVG B14-TIP-18), SEQ ID NO:
86 (RV DVG B14-TIP-19), SEQ ID NO:
87 (RV DVG B14-TIP-20), SEQ ID NO:93 (YFV DVG-A), SEQ ID NO:
94 (YFV DVG-B), SEQ ID NO:
95 (YFV DVG-C), SEQ ID NO:
96 (YFV DVG-D), SEQ ID NO:
97 (YFV DVG-E), SEQ ID NO:
98 (YFV DVG-F), SEQ ID NO:
99 (YFV DVG-G), SEQ ID NO:
100 (YFV DVG-H), SEQ ID NO:
101 (YFV DVG-I), SEQ ID NO:
102 (YFV DVG-J), SEQ ID NO:
103 (YFV DVG-K), SEQ ID NO:
104 (YFV DVG-L), SEQ ID NO:105 (WNV DVG-1), SEQ ID NO:
106 (WNV DVG-2), SEQ ID NO:
107 (WNV DVG-3), SEQ ID NO:
108 (WNV DVG-4), SEQ ID NO:
109 (WNV DVG-5), SEQ ID NO:
110 (WNV DVG-6), SEQ ID NO:
111 (SARS-CoV-2 DVG-1), SEQ ID NO:
112 (SARS-CoV-2 DVG_2) and SEQ ID NO:
113 (SARS-CoV-2 DVG_3), or a nucleotide sequence having at least 70% identity, more preferably at least 80% identity ;
more preferably at least 90% identity, more preferably at least 91% identity, more preferably at least 92% identity, more preferably at least 93% identity, more preferably at least 94% identity, more preferably at least 95% identity, more preferably at least 96% identity, more preferably at least 97% identity, more preferably at least 98% identity, or more preferably at least 99% identity with one of these sequences.

127 more elements

A polynucleotide comprising or consisting of a nucleotide sequence selected from the group consisting of:

SEQ ID NO:
1 (DG1 :
EV71 DVG 293-390), SEQ ID NO:
2 (DG2 :
EV71 DVG 294-404), SEQ ID NO:
3 (DG3 :
EV71 DVG 1746-2895), SEQ ID NO:
4 (DG4 :
EV71 DVG 1752-2894), SEQ ID NO:
5 (DG5 :
EV71 DVG 1752-2896), SEQ ID NO:
6 (DG6 :
EV71 DVG 1880-6487), SEQ ID NO:
7 (DG7 :
EV71 DVG 1880-6488), SEQ ID NO:
8 (DG8 :
EV71 DVG 3513-6516), SEQ ID NO:
9 (DG9 :
EV71 DVG 5475-5634), SEQ ID NO:
10 (DG10:
EV71 DVG 5610-6876), SEQ ID NO:
11 (DG11 :
EV71 DVG 5610-6877), SEQ ID NO:
12 (DG12:
EV71 DVG 5746-5821), SEQ ID NO:
13 (DG13 :
EV71 DVG 6322-6356), SEQ ID NO:
14 (DG14:
EV71 DVG 6322-6358), SEQ ID NO:
15 (DG15:
EV71 DVG 6728-6779), SEQ ID NO:
16 (DG16:
EV71 DVG 6966-7012), SEQ ID NO:
17 (DG17:
EV71 DVG 6966-7014), SEQ ID NO:
18 (DG18:
EV71 DVG 7098-7122), SEQ ID NO:
19 (DG19:
EV71 DVG 7165-7200), SEQ ID NO:
20 (DG20:
EV71 DVG 7165-7201), SEQ ID NO:
21 (DG21:
EV71 DVG 7238-7292), SEQ ID NO:
22 (ZIKV DVG-A), SEQ ID NO:
23 (ZIKV DVG-B), SEQ ID NO:
24 (ZIKV DVG-C), SEQ ID NO:
25 (ZIKV DVG-D), SEQ ID NO:
26 (ZIKV DVG-E), SEQ ID NO:
27 (ZIKV DVG-F), SEQ ID NO:
28 (ZIKV DVG-G), SEQ ID NO:
29 (ZIKV DVG-H), SEQ ID NO:
30 (ZIKV DVG-I), SEQ ID NO:
31 (ZIKV DVG-J), SEQ ID NO:
32 (ZIKV DVG-K), SEQ ID NO:
33 (ZIKV DVG-L), SEQ ID NO:
34 (CHIKV DVG-IV1), SEQ ID NO:
35 (CHIKV DVG-IV2), SEQ ID NO:
36 (CHIKV DVG-IV3), SEQ ID NO:
37 (CHIKV DVG-IV4), SEQ ID NO:
38 (CHIKV DVG-IH1), SEQ ID NO:
39 (CHIKV DVG-IU1), SEQ ID NO:
40 (CHIKV DVG-CV1), SEQ ID NO:
41 (CHIKV DVG-CV2), SEQ ID NO:
42 (CHIKV DVG-CV3), SEQ ID NO:
43 (CHIKV DVG-CV4), SEQ ID NO:
44 (CHIKV DVG-CH1), SEQ ID NO:
45 (CHIKV DVG-CH2), SEQ ID NO:
46 (CHIKV DVG-CH3), SEQ ID NO:
47 (CHIKV DVG-CM1), SEQ ID NO:
48 (CHIKV DVG-CU1), SEQ ID NO:
49 (CHIKV DVG-CU2), SEQ ID NO:
50 (CHIKV DVG-CA1), SEQ ID NO:
51 (CHIKV DVG-CA2), SEQ ID NO:
52 (CHIKV DVG-CA3), SEQ ID NO:
53 (CHIKV DVG-CA4), SEQ ID NO:
55 (RV DVG A01a-TIP-01), SEQ ID NO:
56 (RV DVG A01a-TIP-02), SEQ ID NO:
57 (RV DVG A01a-TIP-03), SEQ ID NO:
58 (RV DVG A01a-TIP-04), SEQ ID NO:
59 (RV DVG A01a-TIP-05), SEQ ID NO:
60 (RV DVG A01a-TIP-06), SEQ ID NO:
62 (RV DVG A16-TIP-01), SEQ ID NO:
63 (RV DVG A16-TIP-02), SEQ ID NO:
64 (RV DVG A16-TIP-03), SEQ ID NO:
65 (RV DVG A16-TIP-04), SEQ ID NO:
66 (RV DVG A16-TIP-05), SEQ ID NO:
89 (RV DVG C15-TIP-01), SEQ ID NO:
90 (RV DVG C15-TIP-02), SEQ ID NO:
91 (RV DVG C15-TIP-03), SEQ ID NO:
92 (RV DVG C15-TIP-04), SEQ ID NO:
68 (RV DVG B14-TIP-01), SEQ ID NO:
69 (RV DVG B14-TIP-02), SEQ ID NO:
70 (RV DVG B14-TIP-03), SEQ ID NO:
71 (RV DVG B14-TIP-04), SEQ ID NO:
72 (RV DVG B14-TIP-05), SEQ ID NO:
73 (RV DVG B14-TIP-06), SEQ ID NO:
74 (RV DVG B14-TIP-07), SEQ ID NO:
75 (RV DVG B14-TIP-08), SEQ ID NO:
76 (RV DVG B14-TIP-09), SEQ ID NO:
77 (RV DVG B14-TIP-10), SEQ ID NO:
78 (RV DVG B14-TIP-11), SEQ ID NO:
79 (RV DVG B14-TIP-12), SEQ ID NO:
80 (RV DVG B14-TIP-13), SEQ ID NO:
81 (RV DVG B14-TIP-14), SEQ ID NO:
82 (RV DVG B14-TIP-15), SEQ ID NO:
83 (RV DVG B14-TIP-16), SEQ ID NO:
84 (RV DVG B14-TIP-17), SEQ ID NO:
85 (RV DVG B14-TIP-18), SEQ ID NO:
86 (RV DVG B14-TIP-19), SEQ ID NO:
87 (RV DVG B14-TIP-20), SEQ ID NO:93 (YFV DVG-A), SEQ ID NO:
94 (YFV DVG-B), SEQ ID NO:
95 (YFV DVG-C), SEQ ID NO:
96 (YFV DVG-D), SEQ ID NO:
97 (YFV DVG-E), SEQ ID NO:
98 (YFV DVG-F), SEQ ID NO:
99 (YFV DVG-G), SEQ ID NO:
100 (YFV DVG-H), SEQ ID NO:
101 (YFV DVG-I), SEQ ID NO:
102 (YFV DVG-J), SEQ ID NO:
103 (YFV DVG-K), SEQ ID NO:
104 (YFVDVG-L), SEQ ID NO:105 (WNV DVG-1), SEQ ID NO:
106 (WNV DVG-2), SEQ ID NO:
107 (WNV DVG-3), SEQ ID NO:
108 (WNV DVG-4), SEQ ID NO:
109 (WNV DVG-5), SEQ ID NO:
110 (WNV DVG-6), SEQ ID NO:
111 (SARS-CoV-2 DVG_1), SEQ ID NO:
112 (SARS-CoV-2 DVG_2) and SEQ ID NO:
113 (SARS-CoV-2 DVG_3), or a polynucleotide having at least 70% identity, more preferably at least 80% identity;
more preferably at least 90% identity, more preferably at least 91% identity, more preferably at least 92% identity, more preferably at least 93% identity, more preferably at least 94% identity, more preferably at least 95% identity, more preferably at least 96% identity, more preferably at least 97% identity, more preferably at least 98% identity, or more preferably at least 99% identity with one of these sequences..

127 more elements

Dependencies are inferred from the claim text.

Facts

Application: 17/907,424Filed 26 Mar 2021
Priority: 27 Mar 2020
Published: 8 Jun 2023
Term ends: Not estimatedThe source records don’t support an estimate.

Classification14 codes

C12N 7/00
Viruses
C12N 2770/20021
Coronaviridae: viruses as such, e.g. new isolates, mutants or their genomic sequences
C12N 2770/20034
Coronaviridae: use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
C12N 2770/24021
Flaviviridae: viruses as such, e.g. new isolates, mutants or their genomic sequences

Family

Application63/000,998Us provisional application · filed 27 Mar 2020
US 2023/0174953 A1This patent

From the US filing history. Foreign family members aren’t listed.

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