Professional Documents
Culture Documents
WO2020008254A1
WO2020008254A1
World Intel 1P v )
O mition % (0 OO
0 000 OO
International Bureau (10) International Publication Number
./
(43) International Publication Date / WO 2020/008254 Al
09 January 2020 (09.01.2020) WIPOIPCT
(51) International Patent Classification: Sylvia; 1021 West Hastings Street, 9th Floor, Vanvouver,
CO7K 16/12 (2006.01) CI2N 1/19 (2006.01) BC V6E 0C3 (CA).
AGIK 39/42 (2006.01) CI2N 1721 (2006.01)
(81) Designated States (unless otherwise indicated, for every
AGIP
CO7K 3112
16/00 (2006.01)
(2006.01) CI2N 1513 (2006.01)
CI2P21/00 2006.01) kind of national protection available): AE, AG, AL, AM,
CO7K 16/08 (2006.01)
i CH0B 40/08 (2006.01)
i AO,
CA, AT, AU,
CH, AZ, BA,
CL, CN, CO, BB,
CR, BG,
CU, BI, BN, DJ,
CZ, DE, BR, DK,
BW, DM,
BY, DO,
BZ,
(21) International Application Number: DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN,
PCT/IB2019/000687 HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP,
KR KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME,
(22) International Filing Date:
MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ,
04 June 2019 (04.06.:2019) OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA.
(25) Filing Language: English SC,SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN,
(26) Publication Language: English
TR, TT. TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
(84) Designated States (unless otherwise indicated, for every
(30) Priority Data: kind of regional protection available): ARIPO (BW, GH,
62/680,736 05 June 2018 (05.06.2018) us GM.KE. LR LS, MW. MZ, NA.RW, SD. SL. ST, §7. TZ.
(71) Applicant: NOVOBIND LIVESTOCK THERA- UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ,
PEUTICS INC. [CA/CAJ; 1021 West Hastings Street, 9th TM), European (AL, AT, BE, BG. CH, CY. CZ, DE, DK,
Floor, Vancouver, Be, VGE OC3 (CA). EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV,
SLOUTET,o Slade,
o, Andrew;
Vo1021 WestBC Hastings
VO oChStreet, 9th TR OAPL(EE B, . G, C CW. G, GN. G0, GW.
(72) Inventors: ABNOUSI, Hamlet; 1021 West Hastings MC, MK, MT.NL, NO. PL. PT. RO. RS, SE. SI. SK. SM.
(54) Title: ANTIBODIES AGAINST AQUACULTURE DISEASE-CAUSING AGENTS AND USES THEREOF
FIG. 1A
CH2
CH2
w0 20207008254 A1 [l
CH3
CH3
(57) Abstract: Described herein are methods and antibodies useful for reducing, eliminating, or preventing infection with a bacterial
or viral population in an aquatic animal. Also described herein are antigens useful for targeting by heavy chain antibodies and VHH
fragments for reducing a bacterial or viral population in an aquatic animal.
Published:
— with international search report (Art. 21(3))
— before the expiration of the time limit for amending the
claims and to be republished in the event of receipt of
amendments (Rule 48.2(h))
WO 2020/008254 PCT/1B2019/000687
[0002] This invention relates to methods and compositions for the control of microorganisms in
aquaculture and uses thereof.
[0003] Losses to the aquaculture industry following contamination of livestock with pathogens
are a global burden. With a growing global population and no significant increase in the amount
of farm land available to agriculture, there is a need to produce larger quantities of food without
using more space. Aquaculture is an especially attractive use of this space because the feed
conversion ratio for aquaculture organisms is roughly 1:1, whereas the ratio for larger farmed
sources of protein is 1:3 or higher . Losses to the global aquaculture industry due to pathogens
is estimated to be around 40%, or $6 billion USD per annum @ Traditional treatment of animals
with antibiotics is a major contributor to the emergence of multi-drug resistant organisms and is
widely recognized as an unsustainable solution to controlling contamination of livestock. There
is a need for the development of pathogen-specific molecules that inhibit infection or association
of the pathogen with the host, without encouraging resistance.
[0004] With reference to the definitions set out below, described herein are polypeptides
comprising heavy chain variable region fragments (VuHs) whose intended use includes
applications in aquaculture, diagnostics, in vitro assays, feed, therapeutics, substrate
identification, nutritional supplementation, bioscientific and medical research, and companion
diagnostics. Also described herein are polypeptides comprising VyHs that bind to and decrease
the virulence of disease-causing agents in aquaculture. Further to these descriptions, set out
below are the uses of polypeptides that comprise VyHs in methods of reducing transmission and
severity of disease in host animals, including their use as an ingredient in a product. Further
described are the means to produce, characterize, refine and modify VuHs for this purpose
WO 2020/008254 PCT/1B2019/000687
INCORPORATION BY REFERENCE
[0005] All publications, patents, and patent applications mentioned in this specification are
herein incorporated by reference to the same extent as if each individual publication, patent, or
patent application was specifically and individually indicated to be incorporated by reference.
[0006] The novel features of the invention are set forth with particularity in the appended
claims. A better understanding of the features and advantages of the present invention will be
obtained by reference to the following detailed description that sets forth illustrative
embodiments, in which the principles of the invention are utilized, and the accompanying
drawings of which:
FIGS. 1A-1B: Panel A shows a schematic of camelid heavy chain only antibodies and their
relationship to VyH domains. Panel B illustrates the framework regions (FRs) and
complementarity determining regions (CDRs) of the VyH domain
FIGS. 2A-2F: Show phage ELISA binding data for V4H antibodies of this disclosure.
FIG. 3: Shows binding of a selection of recombinantly expressed and purified ViH antibodies
to PirA using a protein pull-down assay.
FIG. 4: Shows the stability of a selection of recombinantly expressed and purified VuH
antibodies to PirA in shrimp midgut extract fluids.
DEFINITIONS
[0007] In describing the present invention, the following terminology is used in accordance with
the definitions below.
[0008] In the following description, certain specific details are set forth in order to provide a
thorough understanding of various embodiments. However, one skilled in the art will understand
that the embodiments provided may be practiced without these details. Unless the context
requires otherwise, throughout the specification and claims which follow, the word “comprise”
and variations thereof;, such as, “comprises” and “comprising” are to be construed in an open,
inclusive sense, that is, as “including, but not limited to.” As used in this specification and the
appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the
content clearly dictates otherwise. It should also be noted that the term “or” is generally
employed in its sense including “and/or” unless the content clearly dictates otherwise. Further,
headings provided herein are for convenience only and do not interpret the scope or meaning of
the claimed embodiments,
WO 2020/008254 PCT/1B2019/000687
1) Host
[0009] As referred to herein, “host”, “host organism”, “recipient animal”, “host animal” and
variations thereof refer to the intended recipient of the product when the product constitutes a
feed. In certain embodiments, the host is a crustacean, a shellfish, a shrimp or a prawn.
2) Shellfish
mussels, scallops, cockles, whelks, winkles, shrimp, prawns, crawfish, crayfish, lobster, crabs,
krill and barnacles.
3) Aquaculture-specific
[0011] As referred to herein, “aquaculture”, “aquatic” and variations thereof refer to the
cultivation or dwelling of organisms, including animals and plants, in water.
4) Pathogens
[0012] As referred to herein, “pathogen”, “pathogenic”, and variations thereof refer to virulent
microorganisms, that can be associated with host organisms, that give rise to a symptom or set
of symptoms in that organism that are not present in uninfected host organisms, including the
reduction in ability to survive, thrive, reproduce. Without limitation, pathogens encompass
parasites, bacteria, viruses, prions, protists, fungi and algae. In certain embodiments, the
pathogen is a bacterium belonging to the Vibrio genus. In certain embodiments, the pathogen is
the White Spot Syndrome Virus.
[0013] “Virulence”, “virulent” and variations thereof refer to a pathogen’s ability to cause
symptoms in a host organism. “Virulence factor” refers to nucleic acids, plasmids, genomic
islands, genes, peptides, proteins, toxins, lipids, macromolecular machineries or complexes
thereof that have a demonstrated or putative role in infection
[0014] “Disease-causing agent” refers to a microorganism, pathogen or virulence factor with a
demonstrated or putative role in infection
5) Bacteria
[0015] As referred to herein, “bacteria”, “bacterial” and variations thereof refer, without
6) Viruses
[0016] As referred to herein, “virus”, “viral” and variations thereof refer, without limitation, to
the White Spot Syndrome Virus, or any other viral species associated with aquatic organisms or
host organisms.
7) Antibodies
[0017] A schematic of camelid heavy chain only antibodies and their relationship to VyH
domains and complementarity determining regions (CDRs) is shown in FIG. 1. (Panel A). A
camelid heavy chain only antibody consists of two heavy chains linked by a disulphide bridge.
Each heavy chain contains two constant immunoglobulin domains (CH2 and CH3) linked
through a hinge region to a variable immunoglobulin domain (ViH). (Panel B) are derived from
single VyH domains. Each VyH domain contains an amino acid sequence of approximately 110-
130 amino acids. The VgH domain consists of the following regions starting at the N-terminus
(N): framework region 1 (FR1), complementarity-determining region 1 (CDR1), framework
region 2 (FR2), complementarity-determining region 2 (CDR2), framework region 3 (FR3),
complementarity-determining region 3 (CDR3), and framework region 4 (FR4). The domain
ends at the C-terminus (C). The complementarity-determining regions are highly variable,
determine antigen binding by the antibody, and are held together in a scaffold by the framework
regions of the VyuH domain. The framework regions consist of more conserved amino acid
sequences; however, some variability exists in these regions.
[0018] As referred to herein “VyH” refers to an antibody or antibody fragment comprising a
single heavy chain variable region which may be derived from natural or synthetic sources.
NBXs referred to herein are an example of a ViH. In a certain aspect a VyH may lack a portion
of a heavy chain constant region (CH2 or CH3), or an entire heavy chain constant region.
[0019] As referred to herein “heavy chain antibody” refers to an antibody that comprises two
heavy chains, and lacking the two light chains normally found in a conventional antibody. The
heavy chain antibody may originate from a species of the Camelidae family or Chondrichthyes
class. Heavy chain antibodies retain specific binding to an antigen in the absence of any light
chain
[0020] As referred to herein “specific binding”, “specifically binds” or variations thereof refer to
binding that occurs between an antibody and its target molecule that is mediated by at least one
complementarity determining region (CDR) of the antibody’s variable region. Binding that is
between the constant region and another molecule, such as Protein A or G, for example, does not
a single chain antibody, a variable region fragment of a heavy chain antibody, a nanobody, a
polypeptide or an immunoglobulin new antigen receptor (IgNAR)
[0022] As referred to herein an “antibody originates from a species” when any of the CDR
regions of the antibody were raised in an animal of said species. Antibodies that are raised in a
certain species and then optimized by an in vitro method (e.g., phage display) are considered to
have originated from that species.
[0023] As referred to herein “conventional antibody” refers to any full-sized immunoglobulin
that comprises two heavy chain molecules and two light chain molecules joined together by a
disulfide bond. In certain embodiments, the antibodies, compositions, feeds, products, and
(IPNV), infectious hypodermal and hematopoietic necrosis virus (IHHNV), taura syndrome
virus (TSV) and white spot bacilloform virus (WSBV), hepatopancreatic parvo-like virus
(HPV), reo-like virus, monodon baculovirus (MBV), baculoviral midgut GI and necrosis virus
(BMN)), algae, prions, protists, parasites, fungi, peptides, proteins and nucleic acids. To our
knowledge, an effective, non-vaccine-based treatment against any of these disease-causing
agents has yet to be developed for commercial use.
[0032] Existing methods fail to acknowledge the limited immune development of aquatic
organisms affected by the pathogens listed above, and as such rely on the host organism to
generate protection against disease-causing agents. This approach is limited by the inadequacies
of the host organism’s immune system and therefore does not provide an effective means of
protection. This problem is circumvented by introducing exogenous peptides into the host that
neutralize the virulence and spread of the disease-causing agent without eliciting the host
immune response. Moreover, the methods described herein provide scope for the adaptation and
refinement of neutralizing peptides, which provides synthetic functionality beyond what the host
is naturally able to produce.
[0033] Antibody heavy chain variable region fragments (VyHs) are small (12-15 kDa) proteins
that comprise specific binding regions to antigens. When introduced into an animal, ViHs bind
and neutralize the effect of disease-causing agents i situ. Owing to their smaller mass, they are
less susceptible than conventional antibodies, such as previously documented IgYs, to cleavage
by enzymes found in host organisms, more resilient to temperature and pH changes, more
soluble, have low systemic absorption and are easier to recombinantly produce on a large scale,
making them more suitable for use in animal therapeutics than conventional antibodies
Antibodies for preventing or reducing virulence (summary)
[0034] In one aspect, the present invention provides a polypeptide or pluralities thereof
comprising a VyH or VyHs that bind disease-causing agents to reduce the severity and
transmission of disease between and across species. In certain embodiments, the VyH is
supplied to host animals. In certain embodiments, the VyH is an ingredient of a product.
Binding to reduce virulence
[0035] In another aspect, the present invention provides a polypeptide or pluralities thereof
comprising a VygH or VyHs that bind disease-causing agents, and in doing so, reduce the ability
of the disease-causing agent to exert a pathological function or contribute to a disease
phenotype. In certain embodiments, binding of the V4H(s) to the disease-causing agent reduces
the rate of replication of the disease-causing agent. In certain embodiments, binding of the
ViH(s) to the disease-causing agent reduces the ability of the disease-causing agent to bind to its
cognate receptor. In certain embodiments, binding of the Vy4H(s) to the disease-causing agent
WO 2020/008254 PCT/IB2019/000687
8
reduces the ability of the disease-causing agent to interact with another molecule or molecules
In certain embodiments, binding of the VyH(s) to the disease-causing agent reduces the mobility
or motility of the disease-causing agent. In certain embodiments, binding of the VyzH(s) to the
disease-causing agent reduces the ability of the disease-causing agent to reach the site of
infection. In certain embodiments, binding of the VyH(s) to the disease-causing agent reduces
the ability of the disease-causing agent to cause cell death.
Antibodies derived from llamas
[0036] In a further aspect, the present invention provides a method for the inoculation of
Camelid or other species with recombinant virulence factors, the retrieval of mRNA encoding
VuH domains from lymphocytes of the inoculated organism, the reverse transcription of mRNA
encoding VyH domains to produce cDNA, the cloning of cDNA into a suitable vector and the
recombinant expression of the VyH from the vector. In certain embodiments, the camelid can be
embodiments, the inoculated species can be, without limitation, any organism that can produce
single domain antibodies, including cartilaginous fish, such as a member of the Chondrichthyes
class of organisms, which includes for example sharks, rays, skates and sawfish. In certain
embodiments, the heavy chain antibody comprises a sequence set forth in Table 1. In certain
embodiments, the heavy chain antibody comprises an amino acid sequence with at least 80%,
90%, 95%, 97%, 99%, or 100% identity to any sequence disclosed in Table 1. In certain
embodiments, the heavy chain antibody possesses a CDRI1 set forth in Table 2. In certain
embodiments, the heavy chain antibody possesses a CDR2 set forth in Table 2. In certain
embodiments, the heavy chain antibody possesses a CDR3 set forth in Table 2
selected from the list of host animals described, with that list being representative but not
limiting. In certain embodiments, the route of administration to a recipient animal can be, but is
not limited to: introduction to the alimentary canal orally or rectally, provided to the exterior
surface (for example, as a spray or submersion), provided to the medium in which the animal
dwells (including air and water based media), provided by injection, provided intravenously,
provided via the respiratory system, provided via diffusion, provided via absorption by the
endothelium or epithelium, or provided via a secondary organism such as a yeast, bacterium,
algae, bacteriophages, plants and insects. In certain embodiments, the host animal is a shellfish.
In certain embodiments, the host animal is shrimp
Feed product
[0039] In a further aspect, the present invention provides a polypeptide or pluralities thereof
comprising a VyzH or VyHs that bind disease-causing agents and are administered to host
animals in the form of a product. The form of the product is not limited, so long as it retains
binding to the disease-causing agent in the desired form. In certain embodiments, the product is
feed, pellet, nutritional supplement, premix, therapeutic, medicine, or feed additive, but is not
100 mg/kg of body weight. In certain embodiments, VyHs are administered to recipient animals
at a concentration less than 1 mg/kg of body weight. In certain embodiments, VyHs are
administered to recipient animals at a concentration less than 500 mg/kg of body weight. In
certain embodiments, ViyHs are administered to recipient animals at a concentration less than
100 mg/kg of body weight. In certain embodiments, VyHs are administered to recipient animal
WO 2020/008254 PCT/IB2019/000687
28
at a concentration less than 50 mg/kg of body weight. In certain embodiments, VyHs are
administered to recipient animals at a concentration less than 10 mg/kg of body weight.
Feeding frequency
[0041] In a further aspect, the present invention provides a polypeptide or pluralities thereof
comprising a VygH or VyHs that bind disease-causing agents and are administered to host
animals as part of a product at any suitable dosage frequency. In practice, the suitable dosage
frequency is that at which the product offers any protection against a disease-causing agent, and
depends on the delivery method, delivery schedule, the environment of the recipient animal, the
size of the recipient animal, the age of the recipient animal and the health condition of the
recipient animal, among other factors. In certain embodiments, the dosage frequency can be but
is not limited to: constantly, at consistent specified frequencies under an hour, hourly, at
specified frequencies throughout a 24-hour cycle, daily, at specified frequencies throughout a
week, weekly, at specified frequencies throughout a month, monthly, at specified frequencies
throughout a year, annually, and at any other specified frequency greater than 1 year.
Feed additives
[0042] In a further aspect, the present invention provides a polypeptide or pluralities thereof
comprising a VgH or ViHs that bind disease-causing agents and are administered to host
animals as part of a product that also comprises other additives or coatings. In practice, the most
suitable coating or additive depends on the method of delivery, the recipient animal, the
environment of the recipient, the dietary requirements of the recipient animal, the frequency of
delivery, the age of the recipient animal, the size of the recipient animal, the health condition of
the recipient animal In certain embodiments, these additives and coatings can include, but are
not limited to the following list and mixtures thereof: a vitamin, an antibiotic, a hormone, 1
peptone, shrimp meal, krill, algae, B-cyclodextran, alginate, gum, tragacanth, pectin and gelatin.
Non-feed uses
[0043] In a further aspect, the present invention provides a polypeptide or pluralities thereof
comprising a VygH or VyHs that bind disease-causing agents, and can be used in a non-feed use,
such as but not limited to: a diagnostic kit, an ELISA-based assay, a western blot assay, an
immunofluorescence assay, or a FRET assay, in its current form and/or as a polypeptide
conjugated to another molecule. In certain embodiments, the conjugated molecule is can be but
is not limited to: a fluorophore, a chemiluminescent substrate, an antimicrobial peptide, a
nucleic acid or a lipid.
WO 2020/008254 PCT/1B2019/000687
29
Antigens
[0044] In a further aspect, the present invention provides a polypeptide or pluralities thereof
comprising a VyH or VyHs that bind disease-causing agents, including toxins, produced by a
species of Vibrio. In certain embodiments, the Vibrio species is capable of harbouring the pVA-
1 plasmid. In certain embodiments, the species does not belong to the Vibrio genus but is
capable of harbouring disease-causing agents shared by Vibrio species, such as but not limited to
the pVA-1 plasmid. In certain embodiments, the Vibrio species refers to both current and
reclassified organisms. In certain embodiments, the Vibrio species is V. adaptatus, V. aerogenes,
V. aestivus, V. aestuarianus, V. agarivorans, V. albensis, V. alfacsensis, V. alginolyticus, V.
[0045] In certain embodiments, the VyH or plurality thereof is capable of binding to two or
more disease-causing agents, originating from the same or different species. In certain
embodiments, the disease-causing agent is a polypeptide with 60%, 70%, 80%, 90%, 95%, 98%,
99%, or 100% amino acid sequence identity to PirA (SEQ ID 25). In certain embodiments, the
disease-causing agent is a polypeptide with 60%, 70%, 80%, 90%, 95%, 98%, 99%, or 100%
amino acid sequence identity to PirB (SEQ ID 26). In certain embodiments, the disease-causing
agent is an exposed peptide, protein, protein complex, nucleic acid, lipid, or combination
thereof, that is associated to the surface of the Fibrio bacterium. In certain embodiments, the
disease-causing agent is a pilus, fimbria, flagellum, secretion system or porin. In certain
embodiments, the disease-causing agent is the Vibrio bacterium
[0046] In a further aspect, the present invention provides a polypeptide or pluralities thereof
comprising a VygH or VyHs that bind disease-causing agents produced by White Spot Syndrome
Virus. In certain embodiments, the disease-causing agent is a polypeptide with 60%, 70% 80%,
90%, 95%, 98%, 99%, or 100% amino acid sequence identity VP24 (SEQ ID 27). In certain
embodiments, the disease-causing agent is a polypeptide with 60%, 70% 80%, 90%, 95%, 98%,
WO 2020/008254 W PCT/IB2019/000687
99%, or 100% amino acid sequence identity to VP28 (SEQ ID 28). In certain embodiments, the
disease-causing agent is viral protein associated with or hypothesised to be associated with the
envelope of the White Spot Syndrome Virus. In certain embodiments, the disease-causing agent
is the White Spot Syndrome Virus.
SEQ ID 25:
PirA
>tr|AOA085YLCO|AOAO085YLCO_VIBPH JHE-like toxin PirA-like OS=Vibrio
PFMAGGWKVAKSHVVQRDETYHLQRPDNAFYHQRIVVINNGASRGFCTIYYH
SEQ ID 26:
PirB
>tr|AOA085YLC1|A0A085YLC1_VIBPH JHE-like toxin PirB-like OS=Vibrio
parahaemolyticus OX=670 GN=BTO19_25780 PE=4 SV=1
MTNEYVVTMSSLTEFNPNNARKSYLFDNYEVDPNYAFKAMVSFGLSNIPYAGGFLSTL
WNIFWPNTPNEPDIENIWEQLRDRIQDLVDESIIDAINGILDSKIKETRDKIQDINETIENFG
YAAAKDDYIGLVTHYLIGLEENFKRELDGDEWLGYAILPLLATTVSLQITYMACGLDY
KDEFGFTDSDVHKLTRNIDKLYDDVSSYITELAAWADNDSYNNANQDNVYDEVMGAR
KPNMFGERRNRIVKIESWNSIEIHY YNRVGRLKLTYENGEVVELGKAHKYDEHYQSIEL
NGAYIKYVDVIANGPEAIDRIVFHFSDDRTFVVGENSGKPSVRLQLEGHFICGMLADQE
GSDKVAAFSVAYELFHPDEFGTEK
SEQ ID 27:
VP24
MHMWGVYAAILAGLTLILVVISIVVTNIELNKKLDKKDKDAYPVESEIINLTINGVARGN
HFNFVNGTLQTRNYGKVYVAGQGTSDSELVKKKGDIILTSLLGDGDHTLNVNKAESKE
LELYARVYNNTKRDITVDSVSLSPGLNATGREFSANKFVLYFKPTVLKKNRINTLVFGA
TFDEDIDDTNRHYLLSMRFSPGNDLFKVGEK
SEQ ID 28
VP28
MDLSFTLSVVSAILAITAVIAVFIVIFRYHNTVTKTIETHTGNIETNMDENLRIPVTAEVGS
GYFKMTDVSFDSDTLGKIKIRNGKSDAQMKEEDADLVITPVEGRALEVTVGQNLTFEG
TFKMWNNTSRKINITGMQMVPKINPSKAFVGSSNTSSFTPVSIDEDEVGTFVCGTTFGAP
IAATAGGNLFDMYVHVTYSGTETE
EXAMPLES
[0047] The following illustrative examples are representative of the embodiments of the
applications, systems and methods described herein and are not meant to be limiting in any way.
[0048] While preferred embodiments of the present invention are shown and described herein, it
will be obvious to those skilled in the art that such embodiments are provided by way of
example only. Numerous variations, changes, and substitutions will now occur to those skilled
in the art without departing from the invention. It should be understood that various alternatives
to the embodiments of the invention described herein may be employed in practicing the
invention,
1. Production of antigens
[0049] Recombinant antigens can be purified from an £. coli expression system. For example,
the gene for an antigen can be expressed at 18°C in £. coli BL21 (DE3) cells grown overnight in
autoinducing media (Formedium). Cells are then lysed by sonication in buffer A (250 mM
NaCl, 50 mM CaCl,, 20 mM Imidazole and 10 mM HEPES, pH 7.4) with 12.5 ug/ml DNase I,
and 1X Protease inhibitor cocktail (Bioshop). The lysate is cleared by centrifugation at 22000 x
g for 30 minutes at 4°C , and is then applied to a 5 ml HisTrap HP column (GE Healthcare) pre-
equilibrated with buffer A, washed with ten column volumes of buffer A and eluted with a
gradient of 0% to 60% (vol/vol) buffer B (250 mM NaCl, 50 mM CaCl,, 500 mM imidazole
and10 mM HEPES, pH 7.4). The protein is then dialyzed overnight in the presence of TEV
against buffer C (250 mM NaCl, 10 mM HEPES, pH 7.4 and 5 mM B-mercaptoethanol) at 4°C
The dialyzed protein is applied to a HisTrap HP column (GE Biosciences) pre-equilibrated with
buffer C. 6xHis-tagged TEV and 6xHis-tag are bound to the column and the antigen is collected
in the flowthrough. The sample is dialyzed overnight against buffer D (5 mM NaCl and 10 mM
Tris pH 8.8) and then applied to a 5 ml HiTrap Q HP column (GE Healthcare). The protein is
eluted with a gradient of 0% to 50% (vol/vol) buffer E (1.0 M NaCl and 10 mM Tris pH 8.8).
Lastly, the elution is loaded onto a Superdex 75 Increase 10/300 GL gel filtration column (GE
Healthcare) using buffer F (400 mM NaCl and 20 mM HEPES pH 7.4). The protein sample is
then concentrated to 1 mg/mL using Amicon concentrators with appropriate molecular weight
cut-off (MWCO; Millipore). The purified protein is stored at =80°C.
WO 2020/008254 PCT/1B2019/000687
32
Panning
[0051] RNA isolated from purified llama lymphocytes is used to generate cDNA for cloning
into phagemids. The resulting phagemids are used to transform £. coli TG-1 cells to generate a
library of expressed VyH genes. The phagemid library size can be ~2.5 x 10” total transformants
and the estimated number of phagemid containing VyH inserts can be estimated to be ~100%.
High affinity antibodies are then selected by panning against the Vibrio or WSSV antigens used
for llama immunization. At least two rounds of panning are performed and antigen-binding
clones arising from rounds 2 or later are identified using phage ELISA. Antigen-binding clones
are sequenced, grouped according to their CDR regions, and prioritized for soluble expression in
E. coli and antibody purification.
[0052] Figure 2 shows the Phage ELISA results for all antibodies of this disclosure. Black bars
show binding to wells coated with the antigen specified in Tables 1 and 2 dissolved in
phosphate-buffered saline (PBS). Grey bars are negative controls that show binding to wells
coated with PBS only. In all cases binding to the antigen target is at least 50% above binding to
the PBS-coated wells. Panel A shows the results for NBX0401 to NBX0406. Panel B shows the
results for NBX0601 to NBX0630. Panel C shows the results for NBX063 1 to NBX0637,
NBX0813 to NBX0825, NBX0845, NBX0846, and NBX0849. Panel D shows the results for
NBX0638 to NBX0650, and NBX0826 to NBX0844. Panel E shows the results for NBX0850 to
NBX0865, and NBX09001 to NBX09011. Panel F shows the results for NBX0722 to
the column using an FPLC with a linear gradient between buffer A and buffer B (10 mM
HEPES, pH 7.5, 500 mM NaCl, 500 mM Imidazole). NBX proteins are dialyzed overnight to
PBS and concentrated to ~1.5 mg/ml.
3. Protein Pull-downs
[0055] Approximately 0.1 mg of antigen is incubated with NBX at a 1:5 molar ratio in 200 pl of
binding buffer (10 mM phosphate buffer pH7.4 and 500 mM NaCl) for 30 minutes at room
temperature, and then applied onto a column containing Ni-NTA (nickel-nitrilotriacetic acid}
resin pre-equilibrated with the binding buffer. Protein mixture and the resin are incubated for 30
minutes before the resin is washed with the binding buffer and then with the binding buffer plus
20 mM Imidazole. Bound proteins are eluted with 100 pl of 1 M imidazole, pH 7.4. The
presence or absence of NBX in the various fractions is analyzed on an SDS-PAGE gel. A
protein solution containing only the NBX is also applied to a separate column to assess non-
specific binding of the NBX to the resin
[0056] Figure 3 shows representative results for four unique NBXs. For each of the four
antibodies shown, the lanes are as follows. (1) Starting material of PirA(*) and NBX(") mixture
prior to application to Ni-NTA resin. (2) Flow-through of PirA and NBX through the Ni-NTA
WO 2020/008254 o PCT/IB2019/000687
resin. (3) Final wash of the Ni-NTA resin prior to protein elution. (4) Elution of PirA and NBX
from the Ni-NTA resin. (5) Elution from Ni-NTA resin to which only NBX was applied. (6)
Final wash of Ni-NTA resin to which only NBX was applied. (7) NBX(") only mixture prior to
application to Ni-NTA resin. NBXs that can successfully be pulled down by PirA are those that
appear in the lane 4 elution but not in the lane 5 elution. For each gel a ladder of proteins of
known sizes in kilodaltons (kDa) are shown for reference.
4. Protein stability in shrimp intestinal tract fluid
[0057] Thaw frozen shrimp midgut extract and NBX at room temperature, and immediately
place on ice. Spin shrimp midgut extract and protein at 10,000 RCF for 1 minute to pellet and
remove any precipitation. Prechill PBS and saline on ice. Label and prechill 8 x 0.2 mL strip
tubes on ice. Set up two reactions in volumes of 10 pl on ice. The first reaction contains no
shrimp midgut extract and consists of 5 ug NBX in 3.2 L PBS and 4.8 pL of 150 mM NaCl.
The second reaction contains shrimp midgut extract and is generated using the following ratios:
2.4 uL shrimp midgut extract, 5 ug NBX in 0.8 pL PBS, and 4.8 uL of 150 mM NaCl. The
tubes are incubated on ice for 5 minutes (corresponds to time = 0 minutes in Figure 1) followed
by 26°C for up to 24 hours. The final incubation temperature (26°C) is the internal temperature
of a shrimp. After incubation, add 8 pL of preheated 2X SDS sample buffer to stop the reaction.
Boil at 95-100°C for 5 minutes. The stability of each NBXs is assessed by the presence or
absence of the NBX on an 18% SDS-PAGE gel.
[0058] Figure 4 shows representative results for four unique NBXs. For each of the four
antibodies shown SDS-PAGE gels are arranged from left to right as follows. A ladder of
proteins of known sizes in kilodaltons (kDa) are shown for reference. The next two lanes show
the NBX at the beginning and end of the experiment in the absence of shrimp midgut extract.
These lanes show that the NBX is not degraded over time in the absence of shrimp midgut
extract. The subsequent lane shows the appearance of the shrimp midgut extract at the start of
the experiment without NBX added. This lane allows for the visualization of naturally occurring
proteins in the extract. The subsequent 7-9 lanes show the time course of NBX stability in the
shrimp midgut extract. These lanes allow for the visualization of the relative stability of the
NBX. The longer the full-sized NBX can be visualized on the gel the more stable it is. The final
lane shows the shrimp midgut extract in the absence of NBX at the endpoint of the assay.
[0059] All publications, patent applications, issued patents, and other documents referred to in
this specification are herein incorporated by reference as if each individual publication, patent
application, issued patent, or other document is specifically and individually indicated to be
incorporated by reference in its entirety. Definitions that are contained in text incorporated by
reference are excluded to the extent that they contradict definitions in this disclosure.
WO 2020/008254 s PCT/IB2019/000687
Withyachumnarnkul, B., Itathitphaisarn, O., Bass, D. (2017). New paradigms to help solve the
global aquaculture disease crisis. PLos Pathogens, 13(2), pp. 1-6
3.Lee, C. T, Chen, T. I, Yang, Y. T, Ko, T. P,, Huang, Y. T., Huang,, J. Y., Huang, M.
F., Lin, S.J, Chen, C. Y, Lin, S. S, Lightner, D. V., Wang, H. C., Wang, A. H. J., Wang, H. C.,
Schofield, P., Mohney, L. L., Nunan, L. M., Navarro, S. A. (2012) Historic emergence, impact
and current status of shrimp pathogens in the Americas, Journal of Invertebrate Pathology, 110
(2), pp. 174-183
[0061] While preferred embodiments of the present invention have been shown and described
herein, it will be obvious to those skilled in the art that such embodiments are provided by way
of example only. Numerous variations, changes, and substitutions will now occur to those
skilled in the art without departing from the invention. It should be understood that various
alternatives to the embodiments of the invention described herein may be employed in practicing
WO 2020/008254 PCT/IB2019/000687
36
the invention. It is intended that the following claims define the scope of the invention and that
methods and structures within the scope of these claims and their equivalents be covered
thereby
WO 2020/008254 PCT/1B2019/000687
37
CLAIMS
WHAT IS CLAIMED IS:
9. The polypeptide of any one of claims 1 to 7, wherein the variable region fragment
of the heavy chain antibody comprises a complementarity determining region 1 (CDR1) as set
forth in any one of SEQ ID Nos: 7 to 12 or 151 to 272, a complementarity determining region 2
(CDR2) as set forth in any one of SEQ ID Nos: 13 to 18 or 273 to 394, and a complementarity
determining region 3 (CDR3) as set forth in any one of SEQ ID Nos: 19 to 24 or 395 to 516.
10 The polypeptide of any one of claims 1 to 7, wherein the amino acid sequence of
the VyH comprises:
(a) a CDRI sequence set forth in SEQ ID No: 7, a CDR2 sequence set forth
in SEQ ID No: 13, and a CDR3 sequence set forth in SEQ ID No: 19.
(b) a CDRI sequence set forth in SEQ ID No: 8, a CDR2 sequence set forth
in SEQ ID No: 14, and a CDR3 sequence set forth in SEQ ID No: 20
(c) a CDRI sequence set forth in SEQ ID No: 10, a CDR2 sequence set forth
in SEQ ID No: 16, and a CDR3 sequence set forth in SEQ ID No: 22.
WO 2020/008254 . PCT/IB2019/000687
(d) a CDRI sequence set forth in SEQ ID No: 11, a CDR2 sequence set forth
in SEQ ID No: 17, and a CDR3 sequence set forth in SEQ ID No: 23.
(e) a CDRI sequence set forth in SEQ ID No: 175, a CDR2 sequence set
forth in SEQ ID No: 297, and a CDR3 sequence set forth in SEQ ID No: 419.
[63) a CDRI sequence set forth in SEQ ID No: 218, a CDR2 sequence set
forth in SEQ ID No: 340, and a CDR3 sequence set forth in SEQ ID No: 462.
(g a CDRI sequence set forth in SEQ ID No: 219, a CDR2 sequence set
forth in SEQ ID No: 341, and a CDR3 sequence set forth in SEQ ID No: 463
(h) a CDRI sequence set forth in SEQ ID No: 243, a CDR2 sequence set
forth in SEQ ID No: 365, and a CDR3 sequence set forth in SEQ ID No: 487.
11 A polypeptide complex, wherein the polypeptide comprises a first component
polypeptide and a second component polypeptide, wherein the first component polypeptide and
the second component polypeptide are not covalently linked together and are coupled together
by a protein-protein interaction, a small molecule-protein interaction, or a small molecule-small
molecule interaction, wherein each of the first and the second component polypeptides comprise
a VzH which specifically binds an aquaculture-associated pathogen.
12 The polypeptide of any one of claims 1 to 10 or the polypeptide complex of claim
11, wherein the aquaculture-associated pathogen is a shellfish-associated bacterium
13 The polypeptide of any one of claims 1 to 10 or the polypeptide complex of claim
11, wherein the aquaculture-associated bacteria comprises a species of Vibrio
14. The polypeptide of any one of claims 1 to 10 or the polypeptide complex of claim
11, wherein the species of Vibrio is selected from the list consisting of V. adaptatus, V.
aerogenes, V. aestivus, V. aestuarianus, V. agarivorans, V. albensis, V. alfacsensis, V.
15 The polypeptide or the polypeptide complex of claim 14, wherein the VyH
specifically binds a Vibrio virulence factor
16 The polypeptide or the polypeptide complex of claim 14, wherein the VyH
specifically binds an antigen or polypeptide at least 60%, 70%, 80%, 90%, 95%, 98%, 99%, or
17. The polypeptide or the polypeptide complex of claim 15, wherein the Vibrio
virulence factor is PirA polypeptide, PirA-like toxin polypeptide, PirB polypeptide, or PirB-like
toxin.
18 The polypeptide of any one of claims 1 to 10 or the polypeptide complex of claim
11, wherein the aquaculture-associated pathogen is White Spot Syndrome Virus.
19 The polypeptide of any one of claims 1 to 10 or the polypeptide complex of claim
11, wherein the VyH specifically binds an antigen or polypeptide at least 60%, 70%, 80%, 90%,
95%, 98%, 99%, or 100% identical to SEQ IDs Nos: 27 or 28 or combinations thereof.
20. The polypeptide of any one of claims 1 to 10 or the polypeptide complex of claim
11, wherein the VyH specifically binds a polypeptide from VP24 or VP28, and combinations
thereof.
21 The polypeptide of any one of claims 1 to 10 or the polypeptide complex of claim
11, wherein the VyH can be pulled-down in a protein-protein binding assay by any of SEQ ID
Nos: 25 or 26 or 27 or 28
22 The polypeptide of any one of claims 1 to 10 or the polypeptide complex of claim
11, wherein the VyH survives in shrimp midgut extract for at least 1 minute, 5 minutes, 15
30 The cell of claim 29, wherein the bacteria is of the genus Escherichia.
31 The cell of claim 29, wherein the bacteria is a probiotic bacterium.
WO 2020/008254 w PCT/IB2019/000687
32 The cell of claim 31, wherein the probiotic bacteria is selected from the group
consisting of the genus Bacillus, the genus Lactobacillus, the genus Bifidobacteriunt.
33 The polypeptide of any one of claims 1 to 10 or 12 to 22 or the polypeptide
complex of any one of claims 11 to 22 further comprising a vitamin, an antibiotic, a hormone, an
glucan, vegetable extracts, peptone, shrimp meal, krill, algae, B-cyclodextran, alginate, gum,
tragacanth, pectin, gelatin, an additive spray, a toxin binder, a short chain fatty acid, a medium
chain fatty acid, yeast, a yeast extract, sugar, a digestive enzyme, a digestive compound, an
essential mineral, an essential salt, or fibre.
34 A method of producing the polypeptide of any one of claims 1 to 10 or 12 to 22
or the polypeptide complex of any one of claims 11 to 22, comprising (a) incubating a cell of
any one of claims 25 to 32 in a medium suitable for secretion of the polypeptide from the cell;
and (b) purifying the polypeptide from the medium.
35. The polypeptide of any one of claims 1 to 10 or 12 to 22 or the polypeptide
complex of any one of claims 11 to 22 for use in reducing or preventing a fish or shellfish-
associated bacterial or viral infection in a human individual or a fish or shellfish
36 The polypeptide of any one of claims 1 to 10 or 12 to 22 or the polypeptide
complex of any one of claims 11 to 22 for use in reducing transmission or preventing
transmission of a fish or shellfish-associated bacterial or viral infection from a fish or shellfish to
another fish or shellfish or a human individual
37. The use of claim 35 or 36, wherein the shellfish is a species of crustaceans,
bivalvia, gastropods, cephalopods, octopus, squid, cuttlefish, clams, oysters, mussels, scallops,
cockles, whelks, winkles, shrimp, prawns, crawfish, crayfish, lobster, crabs, krill and barnacles.
38. The use of claim 35 or 36, wherein the fish is a species of catfish, carp, tilapia,
o2
|
|
ciz
FIG. 1B
VHH
Amino Acid Sequence
i
Antigen-Coated
FES-Coated
e
ey
E——
e
Antigen-Coated
2 s, i
a
S
§ e—
i
s
NBX Number
NBX Number
@ I sz
FIG.2B
FIG.2A
s
* — s
2/7
i
s
O
it
P
— i
e o - @ i
£=1 (=3 f=1 £=3
s
oM pereo) gad Sy s
MM paeo) uabguy Sy s
2150
WO 2020/008254
i
2 < o
= S =
0.8
10
13 PoIR0D S8d STy
MM paIEo] usBiuy SOy
WO 2020/008254 PCT/1B2019/000687
317
B
e Antigen-Coated
== PBS-Coated
4. Upper Limit of Detec s S
g T oad
R
33
§ L
w0
2 8 2
34
<
8
14
J bR LE N . A " N . A
SEESSSES
FPEIPIIFSEFFPLEL
PP PP
S SSSSSSSSSSS
NBX Number
WO 2020/008254 PCT/1B2019/000687
47
FIG. 2D
- Antigen-Coated
trd
W PRS-Costed
Agen Antigen Coated Wellf
Bg5; PBS Coated Well
L
N STEIR
LR IL s i<kks ‘ B bbb§
LEER L. N
SRR
RO
HBX Number
PCT/1B2019/000687
k=l Wfi
m d - s &v\v
Q% i B
Q8 Am:*.@v
5 O K
2 0 e RN
NEX Number
NBX Number
&g G
-" KA
L %9,
FIG. 2E
FIG. 2F
&.r
S
517
gp@@,@
Aantigen-Coated
%%,
PES-Coated
o
& » ~
—
- P &m.%
1,
119 PoIEOD SHd Py (4
e
B
HiBp payeoD uabyuy By
WO 2020/008254
8.5
284
- -
Hep pEIeDD S84 Py
o, payeoz uaBhuy %hy
SP8OXaN
XEN - ¢
QWL WPz HST Mz MZOF OB ST §
B daiys iBpiu duiniys
QZ80XEN SZO0XaN
¥ "Old
International application No.
INTERNATIONAL SEARCH REPORT
PCT/IB2019/000687
A, CLASSIFICATION OF SUBJECT MATTER
IPC: CO7K 16/12 2006.01), AGIK 39/42 (2006.01), AGIP31/12(200601), CO7K 16/00(2006.01),
CO7K 16/08 (2006.01), CI2N 1/19 (2006.01) (more IPCs on the last page)
According to International Patent Classification (IPC) or to both national classification and IPC
B. FIELDS SEARCHED
Documentation searched other than minimum documentation to the extent that such documents are included in the fields searched
Electronic database(s) consulted during the intemational scarch (name of database(s) and, where practicable, search terms used)
[Databases: CIPO library discovery tool, Scopus, PubmedCentral, Questel-Orbit, GQPAT, GeneSeq Protein, Uniprot, RefSeq, GenPept, IPI,
IGBLAST Protein, PDB protein, ENSEMBL.
[Keywords: heavy chain antibody, Vhh, nanobody, vibrio, aquaculture associated pathogen, whitc spot syndrome virus.
SEQ ID NO: 1-6 and 29-150 @80% identity, 7-24 and 151-516 @100% identity.
C. DOCUMENTS CONSIDERED TO BE RELEVANT
Category* Citation of document, with indication, where appropriate, of the relevant passages Relevant to claim No.
Panning anti-LPS nanobody as a capture target to enrich Vibrio fluvialis” Biochem Biophys Res
P,X | Commun.2019 May 7: 512(3):531-536. doi: 10.1016/j.bbrc.2019.03.104. Epub 2019 Mar 22. 1-40
*the whole document®
[V Further documents are listed in the continuation of Box C. ¥ Sce patent family annex.
+[special categories of cited documents: “1 [later document published after the intemational filing date or priority
“A” |document defining the general state of the art which is not considered date and not in conflict with the application but cited to understand
to be of particular relevance the principle or theory underlying the invention
“D” |document cited by the applicant in the international application “X” [document of particular relevance; the claimed invention cannot be
“E |earlier application or patent but published on or after the international considered novel or cannot be considered to involve an inventive
filing date step when the document is taken alone
“L” |document which may throw doubts on priority claim(s) or which is “Y” [document of particular relevance; the claimed invention cannot be
cited to establish the publication date of another citation or other considered to involve an inventive step when the document is
special reason (as specified) combined with one or more other such documents, such combination
0" |document referring to an oral disclosure, use, exhibition or other means being obvious to a person skilled in the art
& |document member of the same patent family
“P |document published prior to the international filing date but later than
b date claimod
Date of the actual completion of the international search Date of mailing of the international scarch report
12 December 2019 (12-12-2019) 12 December 2019 (12-12-2019)
Category* | Citation of document, with indication, where appropriate, of the relevant passages Relevant to claim No.
1. With regard to any nucleotide and/or amino acid sequence disclosed in the interational application, the international search was carried out
on the basis of a sequence listing:
a [ forming part of the international application as filed:
I in the form ofan Annex C/ST.25 text file.
™' on paper or in the form of an image file.
b. [ furnished together with the international application under PCT Rule 13fer.1(a) for the purposes of intemational scarch only in the
form ofan Annex C/ST.25 text file.
¢. ¥ furnished subsequent to the international filing date for the purposes of international search only:
[¥in the form of an Annex C/ST.25 text file (Rule 137er.1(a)).
I™ on paper or in the form of an image file (Rule 13fer.1(b) and Administrative Instructions, Section 713).
2. I Tnaddition, 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 beyond the application
as filled, as appropriate, were furnished.
3.Additional comments:
Form PCT/ISA/210 (continuation of first sheet (1)) (July 2019) Page 2016
International application No.
INTERNATIONAL SEARCH REPORT PCT/IB2019/000687
CI2N 1/21 (2006.01), CI2N 15/13 (2006.01), CI2P 21/00 (2006.01), C40B 40/08 (2006.01)