AVIGEN INC \DE
424B3, 1999-07-08
IN VITRO & IN VIVO DIAGNOSTIC SUBSTANCES
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                                                     Filed Pursuant to 424(B)(3)
                                                                 File #333-79925

PROSPECTUS

                                  AVIGEN, INC.

                                2,653,482 SHARES

                                  COMMON STOCK

THE SELLING STOCKHOLDERS:       The selling stockholders identified in this
                                prospectus are selling 2,653,482 shares of our
                                common stock. Of these shares 2,211,235 shares
                                of common stock were sold to the selling
                                stockholders by us in private financings and
                                442,247 are issuable upon the exercise of
                                warrants sold to the selling stockholders in the
                                financings.

                                We are not selling any shares of our common
                                stock under this prospectus and will not receive
                                any of the proceeds from the sale of shares by
                                the selling stockholders.

OFFERING PRICE:                 The selling stockholders may sell the shares of
                                common stock described in this prospectus in a
                                number of different ways and at varying prices.
                                We provide more information about how they may
                                sell their shares in the section titled "Plan of
                                Distribution" on page 14.

TRADING MARKET:                 Our common stock is listed on the Nasdaq
                                National Market under the symbol "AVGN." On July
                                2, 1999, the closing sale price of our common
                                stock, as reported on the Nasdaq National
                                Market, was $5.75.

RISKS:                          INVESTING IN OUR COMMON STOCK INVOLVES A HIGH
                                DEGREE OF RISK. SEE "RISK FACTORS" BEGINNING ON
                                PAGE 3.

     The shares offered or sold under this prospectus have not been approved by
the Securities and Exchange Commission or any state securities commission, nor
have these organizations determined that this prospectus is accurate or
complete. Any representation to the contrary is a criminal offense.

                  The date of this prospectus is July 2, 1999

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                               PROSPECTUS SUMMARY

     Avigen is a leader in the development of gene therapy products derived from
adeno-associated virus, which we refer to as "AAV," for the treatment of
inherited and acquired diseases. Our proposed gene therapy products are designed
for in vivo administration to achieve the production of therapeutic proteins
within the body. We are developing two broad-based proprietary gene delivery
technologies: AAV vectors and the Targeted Vector Integration (TVI") system. We
believe AAV vectors can be used to deliver genes for the treatment of brain,
liver and prostate cancer, anemia, hemophilia, hyperlipidemia and metabolic
storage diseases. We also believe our TVI system will allow us to pursue more
effective treatments for blood cell-related diseases, including sick cell
anemia, beta-thalassemia and human immunodeficiency virus infection.

     The mailing address and telephone number of our principal executive office
is 1201 Harbor Bay Parkway, #1000, Alameda, California 94502, (510) 748-7150.
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                                  RISK FACTORS

     Investing in Avigen's common stock is very risky. You should be able to
bear a complete loss of your investment. You should carefully consider the
following factors, in addition to the other information in this prospectus,
before investing in our stock.

WE EXPECT TO CONTINUE TO OPERATE AT A LOSS AND WE MAY NEVER ACHIEVE
PROFITABILITY

     We cannot be certain that we will ever achieve and sustain profitability.
To date, we have been engaged in research and development activities and have
not generated any revenues from product sales. As of March 31, 1999, we had an
accumulated deficit of $34.1 million. The process of developing our products
will require significant research and development, preclinical testing and
clinical trials, as well as regulatory approval. We expect these activities,
together with our general and administrative expenses, to result in operating
losses for the foreseeable future. Our ability to achieve profitability is
dependent, in part, on our ability to successfully complete development of our
proposed products, obtain required regulatory approvals and manufacture and
market our products directly or through partners.

WE MUST SECURE ADDITIONAL FINANCING, OTHERWISE WE WILL NOT BE ABLE TO DEVELOP
OUR PRODUCTS AND MAINTAIN OUR NASDAQ LISTING

     We will require substantial additional funding to complete the research and
development activities currently contemplated, to commercialize our proposed
products and to maintain minimum Nasdaq continued listing requirements. If we do
not obtain such funds, we will not be able to develop our products or maintain
our Nasdaq listing.

     Our future capital requirements. We anticipate that our existing capital
resources will be adequate to fund our needs for at least the next 12 months.
Our future capital requirements will depend on many factors, including:

     - continued scientific progress in research and development programs;

     - the scope and results of preclinical studies and clinical trials;

     - the time and costs involved in obtaining regulatory approvals;

     - the costs involved in filing, prosecuting and enforcing patent claims;

     - competing technological developments;

     - the cost of manufacturing scale-up;

     - the cost of commercialization activities; and

     - other factors which may not be within our control.

     We intend to seek additional funding through public or private equity or
debt financing, when market conditions allow. If we raise additional funds by
issuing equity securities, there may be further dilution to existing
stockholders. We cannot assure you that we will be able to enter into such
financing arrangements on acceptable terms or at all. Without such additional
funding, we may be required to delay, reduce the scope of or eliminate one or
more of our research or development programs.

     Our need to maintain our Nasdaq listing. We believe that maintaining our
listing on the Nasdaq National Market is central to our ability to raise
additional funds as well as to provide liquidity to investors. We failed
temporarily to meet the Nasdaq net tangible asset listing requirement at June
30, 1998. However, the proceeds from a recent financing allowed us to meet the
Nasdaq net tangible asset listing requirement, on a proforma basis,

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for the first quarter of fiscal 1999. We may be required to generate sufficient
revenue or raise additional capital to maintain Nasdaq listing requirements in
fiscal year 2000.

OUR PRODUCTS MUST UNDERGO RIGOROUS CLINICAL TESTING AND REGULATORY APPROVALS,
WHICH COULD SUBSTANTIALLY DELAY OR PREVENT US FROM MARKETING OUR PRODUCTS

     We are engaged in the development of gene therapy products derived from
adeno-associate virus ("AAV") for the treatment of inherited and acquired
diseases. Prior to marketing in the United States, any drug developed by us must
undergo rigorous preclinical and clinical testing and an extensive regulatory
approval process implemented by the FDA. If we do not receive these necessary
approvals, we will not be able to generate substantial revenues and will not
become profitable. At the present time, we believe that our products will be
regulated as biologics by the FDA. We cannot be certain that our products will
be cleared for marketing by the FDA or that any approved products can be
successfully marketed. Satisfaction of such regulatory requirements, which
includes satisfying the FDA that the product is both safe and efficacious,
typically takes several years or more depending on the type, complexity and
novelty of the product, and requires a substantial commitment of resources. We
may encounter significant delays or excessive costs in our efforts to secure
regulatory approvals. Factors that raise uncertainty in obtaining such
regulatory approvals include:

     - gene therapy is a new and rapidly evolving technology;

     - to date, there has been only limited research and development in gene
       therapy using AAV vectors;

     - we are not aware of any gene therapy products that have obtained
       marketing approval from the United States Food and Drug Administration;

     - before obtaining regulatory approval for the commercial sale of any of
       our products under development, we must demonstrate through preclinical
       studies and clinical trials that the proposed product is safe and
       efficacious for its intended use;

     - the regulatory requirements governing gene therapy products are uncertain
       and are subject to change;

     - none of our proposed products has been tested in humans; and

     - data obtained from preclinical and clinical activities are susceptible to
       varying interpretations which could delay, limit or prevent regulatory
       approvals.

     Preclinical studies must be conducted in conformance with the FDA's Good
Laboratory Practices regulations. Before commencing clinical trials, we must
submit to and receive FDA authorization of an investigational new drug
application ("IND"). We cannot be certain that submission of an IND would result
in FDA authorization to begin clinical trials.

     Limitations once regulatory approval has been obtained. If regulatory
approval is granted for a product, such approval will be limited to those
disease states and conditions for which the product is useful, as demonstrated
through clinical trials. Furthermore, approval may require ongoing requirements
for postmarketing studies. Even if a product is approved for marketing, the
product, its manufacturer and its manufacturing facilities are continuously
subject to review and periodic inspections. Discovery of previously unknown
problems with a product, manufacturer or facility may result in restrictions on
such product or manufacturer, including withdrawal of the product from the
market. We may encounter problems with the clinical trials which will require us
to delay, suspend or terminate these trials. All of our products in research and
development may prove to have

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undesirable and unintended side effects or other characteristics that may
prevent or limit their commercial use. Because there is only limited research
regarding the safety and efficacy of AAV vectors, we believe that clinical
trials will proceed more slowly than clinical trials involving traditional drugs
and biologics.

     Consequences of failure to comply with applicable FDA or other regulatory
requirements. Failure to comply with applicable FDA or other regulatory
requirements may result in the following:

     - criminal prosecution;

     - civil penalties;

     - recall or seizure of products;

     - total or partial suspension of production or injunction; and

     - other legal or regulatory actions.

     Any such action would have a material adverse effect on our business.

WE MAY NOT BE SUCCESSFUL IN OBTAINING REQUIRED FOREIGN REGULATORY APPROVALS,
WHICH WOULD PREVENT US FROM MARKETING OUR PRODUCTS INTERNATIONALLY

     We cannot be certain that we will obtain any regulatory approvals in other
countries. In order to market our products outside of the United States, we also
must comply with numerous and varying foreign regulatory requirements
implemented by foreign health authorities. The approval procedure varies among
countries and can involve additional testing. The time required to obtain
approval may differ from that required to obtain FDA approval. The foreign
regulatory approval process includes all of the risks associated with obtaining
FDA approval set forth above, and approval by the FDA does not ensure approval
by the health authorities of any other country.

WE DO NOT HAVE EXPERIENCE IN CONDUCTING CLINICAL TRIALS, WHICH MAY CAUSE DELAYS
IN COMMENCING AND COMPLETING CLINICAL TRIALS OF OUR PRODUCTS

     Clinical trials must meet FDA regulatory requirements for Institutional
Review Board oversight and informed consent and good clinical practice
regulations. We have limited experience in conducting preclinical studies and no
experience in conducting clinical trials necessary to obtain regulatory
approval. We may not be able to conduct those clinical trials at preferred
sites, obtain sufficient test subjects or begin or successfully complete
clinical trials in a timely fashion, if at all. Furthermore, the FDA may suspend
clinical trials at any time if it believes the subjects participating in such
trials are being exposed to unacceptable health risks or if it finds
deficiencies in the IND or conduct of the investigation. We may encounter
problems in clinical trials which cause us or the FDA to delay, suspend or
terminate such trials.

     In addition to the FDA requirements, the National Institutes of Health
("NIH") has established guidelines for research involving recombinant DNA
molecules, which we use in our research. These guidelines apply to recombinant
DNA research which is conducted at or supported by the NIH. Under current
guidelines, proposals to conduct clinical research involving gene therapy at
institutions supported by the NIH must be approved by the NIH's Recombinant DNA
Advisory Committee.

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WE HAVE NO EXPERIENCE IN MANUFACTURING, MARKETING OR SELLING OUR PRODUCTS, WHICH
RAISES UNCERTAINTY IN OUR ABILITY TO COST-EFFECTIVELY MANUFACTURE OUR PRODUCTS

     Even if we are able to develop our products and obtain necessary regulatory
approvals, we have no experience in, and currently lack the resources and
capability to, manufacture or market any of our proposed products on a
commercial basis. In addition, we have not yet implemented the FDA's regulations
concerning current Good Manufacturing Practices. We may not be able to develop
adequate commercial manufacturing capabilities either on our own or through
third parties. If we are unable to manufacture our products in a cost-effective
manner, we will not become profitable. Initially, we anticipate that we will be
dependent to a significant extent on collaborative partners or other entities
for commercial scale manufacturing of our products. If we decide to establish a
commercial scale manufacturing facility, we will need substantial additional
funds and personnel and will be required to comply with extensive regulations
applicable to such facility. In addition, we do not anticipate establishing our
own sales and marketing capabilities in the foreseeable future. We may not be
able to develop adequate marketing capabilities either on our own or through
third parties.

WE NEED TO ATTRACT AND RETAIN A CORPORATE PARTNER, OTHERWISE WE MAY NOT BE ABLE
TO DEVELOP OUR PRODUCTS

     We do not currently have a corporate partner relationship with respect to
any of our technologies or potential products. Given the very high cost of
funding clinical trials and bringing a proposed product through the governmental
approval process to the commercial market, we believe that successful
development and commercialization of our technologies and products will depend
in large part on our ability to establish one or more such relationships. We may
not be able to establish relationships on favorable terms, if at all. In
addition, if we fail to raise needed future capital we could be at a
disadvantage in negotiating favorable terms with potential corporate partners.

WE MAY BE REQUIRED TO OBTAIN RIGHTS TO PROPRIETARY GENES AND OTHER TECHNOLOGIES
TO FURTHER DEVELOP OUR BUSINESS, WHICH MAY NOT BE AVAILABLE OR MAY BE COSTLY

     We currently investigate and use certain gene sequences or proteins encoded
by those sequences that are or may become patented by others. As a result, we
may be required to obtain licenses to such gene sequences or proteins or other
technology in order to test, use or market such products. For example, in
connection with our anemia program, we may need to obtain a license to a gene
for erythropoietin. We may not be able to obtain such a license on terms
favorable to us, if at all. In connection with our efforts to obtain rights to
such gene sequences or proteins, we may find it necessary to convey rights to
our technology to others. Some of our gene therapy products may require the use
of multiple proprietary technologies. Consequently, we may be required to make
cumulative royalty payments to several third parties. Such cumulative royalties
could be commercially prohibitive. We may not be able to successfully negotiate
such royalty adjustments.

IF WE DO NOT ACHIEVE CERTAIN MILESTONES WE MAY NOT BE ABLE TO RETAIN CERTAIN
LICENSES TO OUR INTELLECTUAL PROPERTY

     We have entered into agreements for the license from third parties of
certain technologies related to our gene therapy product development programs.
Certain of these license agreements provide for the achievement of development
milestones. All development milestones to date have been met with the next
milestone due August 2001. If we fail to achieve such milestones or to obtain
extensions, the licensor may terminate certain

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of the license agreements with relatively short notice to us. Termination of any
of our license agreements could have a material adverse effect on our business.

IF OUR PRODUCTS ARE NOT ACCEPTED BY PHYSICIANS AND INSURERS, WE WILL NOT BE
SUCCESSFUL

     Our success is dependent on acceptance of our gene therapy products. We
cannot assure you that our products will achieve significant market acceptance
among patients, physicians or third party payors, even if we obtain necessary
regulatory and reimbursement approvals. Failure to achieve significant market
acceptance will have a material adverse effect on our business, financial
condition and results of operations. We believe that recommendations by
physicians and health care payors will be essential for market acceptance of our
gene therapy products. In the past, there has been concern regarding the
potential safety and efficacy of gene therapy products derived from pathogenic
viruses such as retroviruses and adenoviruses. While our proposed gene therapy
products are derived from AAV which is a non-pathogenic virus, we cannot be
certain that physicians and health care payors will conclude that the technology
is safe. In addition, health care payors can indirectly affect the
attractiveness of our proposed products by regulating the maximum amount of
reimbursement they will provide for such proposed products.

EVEN IF WE BRING OUR PRODUCTS TO MARKET, WE MAY BE UNABLE TO EFFECTIVELY PRICE
OUR PRODUCTS OR OBTAIN ADEQUATE REIMBURSEMENT FOR SALES OF OUR PRODUCTS, WHICH
WOULD PREVENT OUR PRODUCTS FROM BECOMING PROFITABLE

     If we succeed in bringing our proposed products to the market, we cannot
assure you that these products will be considered cost-effective and that
reimbursement to the consumer will be available or will be sufficient to allow
us to sell our products on a competitive basis. The business and financial
condition of Avigen is affected by the efforts of government and third party
payors to contain or reduce the cost of health care through various means. In
the United States, there have been and will continue to be a number of federal
and state proposals to implement government control on pricing. In addition, the
emphasis on managed care in the United States has increased and will continue to
increase the pressure on the pricing of pharmaceutical products. We cannot
predict whether any legislative or regulatory proposals will be adopted or the
effect such proposals or managed care efforts may have on our business. In
addition, in both the United States and elsewhere, sales of medical products and
treatments are dependent, in part, on the availability of reimbursement to the
consumer from third-party payors, such as government and private insurance
plans. Third-party payors are increasingly challenging the prices charged for
medical products and services.

WE EXPECT THAT WE WILL FACE INTENSE COMPETITION, WHICH MAY LIMIT OUR ABILITY TO
BECOME PROFITABLE

     The field of gene therapy is new and rapidly evolving and is expected to
undergo significant technological change in the future. We expect increased
competition from fully integrated pharmaceutical companies and more established
biotechnology companies. Most of these companies have significantly greater
financial resources and expertise than we do in the following:

     - research and development;

     - preclinical studies and clinical trials;

     - obtaining regulatory approvals;

     - manufacturing; and

     - marketing and distribution.

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     Smaller companies may also prove to be significant competitors,
particularly through collaborative arrangements with large pharmaceutical
companies. Academic institutions, government agencies and other public and
private research organizations also conduct research, seek patent protection and
establish collaborative arrangements for product development and marketing. In
addition, these companies and institutions compete with us in recruiting and
retaining highly qualified scientific and management personnel. Our competitors
may develop more effective or more affordable products, or achieve earlier
product commercialization than we do.

     We are aware that other companies are conducting preclinical studies and
clinical trials for viral and non-viral gene therapy products. One of these
companies is supporting clinical studies for use of AAV vectors in the treatment
of cystic fibrosis.

     We believe the primary competitive factors for success in the gene therapy
field will be:

     - product efficacy;

     - safety;

     - manufacturing capability;

     - the timing and scope of regulatory approvals;

     - the timing of market introduction;

     - marketing and sales capability;

     - reimbursement coverage; and

     - price and patent position.

     Our competitors may develop more effective or more affordable products, or
achieve earlier product commercialization than we do.

OUR SUCCESS IS DEPENDENT UPON OUR ABILITY TO EFFECTIVELY PROTECT OUR PATENTS AND
PROPRIETARY RIGHTS, WHICH WE MAY NOT BE ABLE TO DO

     Our success will depend to a significant degree on our ability to obtain
patents and licenses to patent rights, preserve trade secrets, and to operate
without infringing on the proprietary rights of others. If we are not successful
in these endeavors, our business will be substantially impaired.

     To date, we have filed a number of patent applications in the United States
relating to our technologies. In addition, we have acquired exclusive and
non-exclusive licenses to certain issued patents and pending patent
applications. We cannot assure you that patents will issue from these
applications or that any patent will issue on technology arising from additional
research or, if patents do issue, that claims allowed will be sufficient to
protect our technologies.

     The patent application process takes several years and entails considerable
expense. The failure to obtain patent protection on the technologies underlying
our proposed products may have a material adverse effect on our competitive
position and business prospects. Important legal issues remain to be resolved as
to the scope of patent protection for biotechnology products, and we expect that
administrative proceedings, litigation or both will be necessary to determine
the validity and scope of our and others' biotechnology products. Such
proceedings or litigation may require a significant commitment of our resources
in the future. If patents can be obtained, we cannot assure you that any such
patents will provide us with any competitive advantage. For example, others may
independently develop similar technologies or duplicate any technology developed
by us,

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and patents may be invalidated in litigation. In addition, two of our patent
applications are co-owned with co-inventors. Under the terms of agreements with
the co-inventors, we have an option to obtain an exclusive, worldwide,
transferable, royalty-bearing license for such technology, and are currently in
discussions with one of the co-inventors to obtain such a license. If we cannot
negotiate exclusive rights to such co-owned technology, each co-inventor may
have rights to independently make, use, offer to sell or sell the patented
technology. Commercialization, assignment or licensing of such technology by a
co-inventor could have a material adverse effect on our business, financial
condition and results of operations.

     We also rely on a combination of trade secret and copyright law, employee
and third-party nondisclosure agreements and other protective measures to
protect intellectual property rights pertaining to our products and
technologies. We cannot be certain that these measures will provide meaningful
protection of our trade secrets, know-how or other proprietary information in
the event of any unauthorized use, misappropriation or disclosure of such trade
secrets, know-how or other proprietary information. In addition, the laws of
certain foreign countries do not protect our intellectual property rights to the
same extent as do the laws of the United States. We cannot assure you that we
will be able to protect our intellectual property successfully.

OTHER PERSONS MAY ASSERT RIGHTS IN OUR PROPRIETARY TECHNOLOGY, WHICH WOULD BE
COSTLY TO CONTEST OR SETTLE

     Third parties may assert patent or other intellectual property infringement
claims against us with respect to our products or technology or other matters.
There may be third-party patents and other intellectual property relevant to our
products and technology which are not known to us. We have not been accused of
infringing any third party's patent rights or other intellectual property, but
we cannot assure you that litigation asserting such claims will not be
initiated, that we would prevail in any such litigation, or that we would be
able to obtain any necessary licenses on reasonable terms, if at all. Any such
claims against us, with or without merit, as well as claims initiated by us
against third parties, can be time-consuming and expensive to defend or
prosecute and to resolve. If our competitors prepare and file patent
applications in the United States that claim technology also claimed by us, we
may have to participate in interference proceedings declared by the Patent and
Trademark Office to determine priority of invention, which could result in
substantial cost to us, even if the outcome is favorable to us. In addition, to
the extent outside collaborators apply technological information developed
independently by them or by others to our product development programs or apply
our technologies to other projects, disputes may arise as to the ownership of
proprietary rights to such technologies.

WE MAY BE UNABLE TO ATTRACT AND RETAIN THE QUALIFIED EMPLOYEES WE NEED TO BE
SUCCESSFUL

     We are highly dependent on certain members of our management and research
and development staff. The loss of any of these persons could have a material
adverse effect on our business. In addition, we rely on consultants and advisors
to assist us in formulating our research and development strategy. Recruiting
and retaining qualified technical and managerial personnel will also be critical
to our success. We cannot assure you that we will be successful in attracting
and retaining skilled personnel who generally are in high demand in the
pharmaceutical and biotechnology industries. The loss of certain key employees
or our inability to attract and retain other qualified employees could have a
material adverse effect on our business. A majority of our scientific advisors
are engaged by us on a consulting basis and are employed on a full-time basis by
employers other than

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us and some have consulting or other advisory arrangements with other entities
that may conflict or compete with their obligations to us.

WE FACE THE RISK OF PRODUCT LIABILITY CLAIMS WHICH MAY EXCEED THE SCOPE OR
AMOUNT OF OUR INSURANCE COVERAGE

     The manufacture and sale of medical products entail significant risk of
product liability claims. We currently do not carry product liability insurance
although we intend to obtain such coverage prior to commencing clinical trials.
We cannot assure you that such coverage will be adequate to protect us from any
liabilities we might incur in connection with the use or sale of our products.
In addition, we may require increased product liability coverage as additional
products are commercialized. Such insurance is expensive and in the future may
not be available on acceptable terms, if at all. A successful product liability
claim or series of claims brought against us in excess of our insurance coverage
could have a material adverse effect on our business and results of operations.
We must indemnify certain of our licensors against any product liability claims
brought against them arising out of products developed by us under these
licenses.

WE FACE RISKS FROM USING HAZARDOUS AND RADIOACTIVE MATERIALS AND MAY INCUR
ADDITIONAL COSTS TO COMPLY WITH ENVIRONMENTAL REGULATIONS

     Our research and development efforts involve the use of hazardous
materials, chemicals and various radioactive compounds. We are subject to
federal, state and local laws and regulations governing the storage, use, and
disposal of such materials and certain waste products. Although we believe that
our safety procedures for handling and disposing of such materials comply with
the standards prescribed by federal, state and local regulations, the risk of
accidental contamination or injury from these materials cannot be completely
eliminated. In the event of an accident, we could be held liable for any damages
that result and any such liability could exceed our resources. We may incur
substantial costs to comply with environmental regulations if we develop our own
commercial manufacturing facility.

OUR BUSINESS MAY BE NEGATIVELY IMPACTED BY COMPUTER FAILURES IN THE YEAR 2000

     We are aware of the issues associated with the programming code in existing
computer systems as the year 2000 approaches. Any year 2000 compliance problems
of either Avigen, our customers or vendors could have a material adverse effect
on our business, results of operations and financial condition. The "year 2000
problem" is pervasive and complex as virtually every computer operation will be
affected in some way by the rollover of the two digit year value to 00. The
issue is whether computer systems will properly recognize date-sensitive
information when the year changes to 2000. Systems that do not properly
recognize such information could generate erroneous data or fail. We are in the
process of working with our software vendors to ensure that the software that we
have licensed from third parties will operate properly in the year 2000 and
beyond. In addition, we are working with our external suppliers and service
providers to ensure that they and their systems will be able to support our
needs and, where necessary, interoperate with our server and networking hardware
and software infrastructure in preparation for the year 2000. We do not
anticipate that we will incur significant operating expenses or be required to
invest heavily in computer systems improvements to be year 2000 compliant.
However, significant uncertainty exists concerning the potential costs and
effects associated with any year 2000 compliance.

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                           FORWARD-LOOKING STATEMENTS

     This prospectus contains forward-looking statements within the meaning of
Section 27A of the Securities Act of 1933 and Section 21E of the Securities
Exchange Act of 1934, including statements regarding Avigen's drug development
programs, clinical trials, receipt of regulatory approval, capital needs,
intellectual property, expectations and intentions. The words "believe,"
"anticipate," "expect," "intend," and words of similar import are intended to
identify these statements as forward-looking statements. Such forward-looking
statements include the following:

     - our belief that AAV vectors can be used to deliver genes for the
       treatment of brain, liver and prostate cancer, anemia, hemophilia,
       hyperlipidemia and metabolic storage diseases;

     - our belief that our TVI system will allow us to pursue more effective
       treatments for blood cell-related diseases, including sick cell anemia,
       beta-thalassemia and human immunodeficiency virus infection; and

     - our expectation that our existing capital resources will be adequate to
       fund our needs for at least the next 12 months.

     Forward-looking statements necessarily involve risks and uncertainties, and
Avigen's actual results could differ materially from those anticipated in the
forward-looking statements, including those set forth under "Risk Factors" and
elsewhere in this prospectus. The factors set forth under "Risk Factors" and
other cautionary statements made in this prospectus should be read and
understood as being applicable to all related forward-looking statements
wherever they appear in this prospectus.

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                       WHERE YOU CAN GET MORE INFORMATION

     We are a reporting company and file annual, quarterly and current reports,
proxy statements and other information with the SEC. You may read and copy these
reports, proxy statements and other information at the SEC's public reference
rooms in Washington, DC, New York, NY and Chicago, IL. You can request copies of
these documents by writing to the SEC and paying a fee for the copying cost.
Please call the SEC at 1-800-SEC-0330 for more information about the operation
of the public reference rooms. Our SEC filings are also available at the SEC's
web site at "http://www.sec.gov." In addition, you can read and copy our SEC
filings at the office of the National Association of Securities Dealers, Inc. at
1735 "K" Street, Washington, DC 20006.

     The SEC allows us to "incorporate by reference" information that we file
with them, which means that we can disclose important information to you by
referring you to those documents. The information incorporated by reference is
an important part of this prospectus, and information that we file later with
the SEC will automatically update and supersede this information. We incorporate
by reference the documents listed below and any future filings we will make with
the SEC under Section 13(a), 13(c), 14 or 15(d) of the Securities Exchange Act
of 1934:

     - Annual Report on Form 10-K for the year ended June 30, 1998;

     - Quarterly Reports on Form 10-Q filed November 13, 1998, February 16, 1999
       and May 17, 1999;

     - Current Reports on Form 8-K filed October 9, 1998, January 29, 1999 and
       May 12, 1999; and

     - The description of the common stock contained in Avigen's Registration
       Statement on Form 8-A, as filed on April 22, 1996 with the SEC under the
       Securities Exchange Act of 1934.

     You may request a copy of these filings at no cost, by writing, telephoning
or e-mailing us at the following address:
                                            Avigen, Inc.
                             1201 Harbor Bay Parkway Suite 1000
                                       Alameda, CA 94502
                                          (510)748-7150
                                     http://www.Avigen.com

     This prospectus is part of a Registration Statement we filed with the SEC.
You should rely only on the information incorporated by reference or provided in
this prospectus and the Registration Statement.

                                USE OF PROCEEDS

     We will not receive any of the proceeds from the sale of the shares of
common stock offered by the selling stockholders.

                                       12
<PAGE>   13

                              SELLING STOCKHOLDERS

     In private placements concluding in April 1999 we sold to the selling
stockholders common stock and warrants to purchase common stock, and agreed to
register the common stock and the shares of common stock issuable upon the
exercise of warrants sold to those selling stockholders for resale. We also
agreed to use our best efforts to keep the Registration Statement effective for
two years, or until all of the shares are sold under the Registration Statement,
whichever comes first. Our registration of the shares of common stock does not
necessarily mean that the selling stockholders will sell all or any of the
shares.

     The following table sets forth certain information regarding the beneficial
ownership of the common stock, as of May 7, 1999, by each of the selling
stockholders.

     The information provided in the table below with respect to each selling
stockholder has been obtained from such selling stockholder. Except as otherwise
disclosed below, none of the selling stockholders has, or within the past three
years has had, any position, office or other material relationship with Avigen.
Because the selling stockholders may sell all or some portion of the shares of
common stock beneficially owned by them, we cannot estimate the number of shares
of common stock that will be beneficially owned by the selling stockholders
after this offering. In addition, the selling stockholders may have sold,
transferred or otherwise disposed of, or may sell, transfer or otherwise dispose
of, at any time or from time to time since the date on which they provided the
information regarding the shares of common stock beneficially owned by them, all
or a portion of the shares of common stock beneficially owned by them in
transactions exempt from the registration requirements of the Securities Act of
1933.

     Beneficial ownership is determined in accordance with Rule 13d-3(d)
promulgated by the Commission under the Securities Exchange Act of 1934, as
amended. Shares of common stock issuable pursuant to options, warrants and
convertible securities, to the extent such securities are currently exercisable
or convertible within 60 days of May 7, 1999, are treated as outstanding for
computing the percentage of the person holding such securities but are not
treated as outstanding for computing the percentage of any other person. Unless
otherwise noted, each person or group identified possesses sole voting and
investment power with respect to shares, subject to community property laws
where applicable. Shares not outstanding but deemed beneficially owned by virtue
of the right of a person or group to acquire them within 60 days are treated as
outstanding only for purposes of determining the number of and percent owned by
such person or group. Applicable percentages are based on 12,556,417 shares
outstanding on May 7, 1999 adjusted as required by rules promulgated by the SEC.

                                       13
<PAGE>   14

                  SHARES BENEFICIALLY OWNED PRIOR TO OFFERING

<TABLE>
<CAPTION>
                                                                           SHARES
SELLING STOCKHOLDER                                 NUMBER    PERCENT   BEING OFFERED
- -------------------                                 -------   -------   -------------
<S>                                                 <C>       <C>       <C>
Saburo Adachi(1)..................................  159,330     1.3%       159,330
Toru Tanigawa(2)..................................    9,954       *          9,954
Shuichi Ohashi(3).................................   19,914       *         19,914
Hironori Hozoji(4)................................   13,938       *         13,938
Ko Okumura(5).....................................    1,986       *          1,986
Koji Murayama(6)..................................    1,986       *          1,986
Ikuo Ogihara(7)...................................    5,970       *          5,970
Shiro Saito(8)....................................    3,978       *          3,978
Marcuard Cook & Cie S.A.(9).......................   59,748       *         59,748
Innoven FCPI (1997) FCPI no. 1(10)................   39,834       *         39,834
Innoven 1998 FCPI FCPI no. 9(11)..................  159,336     1.3        159,336
Lombard Odier & Cie(12)...........................  597,510     4.7        597,510
Pictet et Cie(13).................................  398,340     3.2        398,340
Sofragi(14).......................................   19,914       *         19,914
Pierre Charron Gestion(15)........................   43,812       *         43,812
Leven Gestion(16).................................  428,214     3.4        428,214
Clarion Offshore Fund, Ltd.(17)...................   19,914       *         19,914
Veron International Limited(18)...................  398,340     3.2        398,340
Hofung Holdings Limited(19).......................   39,834       *         39,834
Taisei Co., Ltd.(20)..............................  216,000     1.7        216,000
Claire Engleberg(21)..............................   15,630       *         15,630
</TABLE>

- -------------------------
  *  Less than 1% of the outstanding shares of common stock.

 (1) Includes 26,555 shares issuable upon exercise of warrants held by this
     selling stockholder.

 (2) Includes 1,659 shares issuable upon exercise of warrants held by this
     selling stockholder.

 (3) Includes 3,319 shares issuable upon exercise of warrants held by this
     selling stockholder.

 (4) Includes 2,323 shares issuable upon exercise of warrants held by this
     selling stockholder.

 (5) Includes 331 shares issuable upon exercise of warrants held by this selling
     stockholder.

 (6) Includes 331 shares issuable upon exercise of warrants held by this selling
     stockholder.

 (7) Includes 995 shares issuable upon exercise of warrants held by this selling
     stockholder.

 (8) Includes 663 shares issuable upon exercise of warrants held by this selling
     stockholder.

 (9) Includes 9,958 shares issuable upon exercise of warrants held by this
     selling stockholder.

(10) Includes 6,639 shares issuable upon exercise of warrants held by this
     selling stockholder.

(11) Includes 26,556 shares issuable upon exercise of warrants held by this
     selling stockholder.

                                       14
<PAGE>   15

(12) Includes 99,585 shares issuable upon exercise of warrants held by this
     selling stockholder.

(13) Includes 66,390 shares issuable upon exercise of warrants held by this
     selling stockholder.

(14) Includes 3,319 shares issuable upon exercise of warrants held by this
     selling stockholder.

(15) Includes 7,302 shares issuable upon exercise of warrants held by this
     selling stockholder.

(16) Includes 71,369 shares issuable upon exercise of warrants held by this
     selling stockholder.

(17) Includes 3,319 shares issuable upon exercise of warrants held by this
     selling stockholder.

(18) Includes 66,390 shares issuable upon exercise of warrants held by this
     selling stockholder.

(19) Includes 6,639 shares issuable upon exercise of warrants held by this
     selling stockholder.

(20) Includes 36,000 shares issuable upon exercise of warrants held by this
     selling stockholder.

(21) Includes 2,605 shares issuable upon exercise of warrants held by this
     selling stockholder.

                                       15
<PAGE>   16

                              PLAN OF DISTRIBUTION

     The shares of common stock may be sold from time to time by the selling
stockholders in one or more transactions at fixed prices, at market prices at
the time of sale, at varying prices determined at the time of sale or at
negotiated prices. The selling stockholders may offer their shares of common
stock in one or more of the following transactions:

     - on any national securities exchange or quotation service on which the
       common stock may be listed or quoted at the time of sale, including the
       Nasdaq National Market,

     - in the over-the-counter market,

     - in private transactions,

     - through options,

     - by pledge to secure debts and other obligations, or

     - a combination of any of the above transactions.

     If required, we will distribute a supplement to this prospectus to describe
material changes in the terms of the offering.

     The shares of common stock described in this prospectus may be sold from
time to time directly by the selling stockholders. Alternatively, the selling
stockholders may from time to time offer shares of common stock to or through
underwriters, broker/dealers or agents. The selling stockholders and any
underwriters, broker/dealers or agents that participate in the distribution of
the shares of common stock may be deemed to be "underwriters" within the meaning
of the Securities Act of 1933. Any profits on the resale of shares of common
stock and any compensation received by any underwriter, broker/dealer or agent
may be deemed to be underwriting discounts and commissions under the Securities
Act of 1933.

     Any shares covered by this prospectus which qualify for sale pursuant to
Rule 144 under the Securities Act of 1933 may be sold under Rule 144 rather than
pursuant to this prospectus. The selling stockholders may not sell all of the
shares they hold or may acquire upon exercise of the warrants. The selling
stockholders may transfer, devise or gift such shares by other means not
described in this prospectus.

     To comply with the securities laws of certain jurisdictions the common
stock must be offered or sold only through registered or licensed brokers or
dealers. In addition, in certain jurisdictions, the common stock may not be
offered or sold unless they have been registered or qualified for sale or an
exemption is available and complied with.

     Under the Securities Exchange Act of 1934, any person engaged in a
distribution of the common stock may not simultaneously engage in market-making
activities with respect to the common stock for five business days prior to the
start of the distribution. In addition, each selling stockholder and any other
person participating in a distribution will be subject to the Securities
Exchange Act of 1934 which may limit the timing of purchases and sales of common
stock by the selling stockholders or any such other person. These factors may
affect the marketability of the common stock and the ability of brokers or
dealers to engage in market-making activities.

     All expenses of this registration, estimated at approximately $50,000, will
be paid by Avigen. These expenses include the SEC's filing fees and fees under
state securities or "blue sky" laws. The selling stockholders will pay all
underwriting discounts and selling commissions, if any.

                                       16
<PAGE>   17

                                 LEGAL MATTERS

     Cooley Godward LLP, Palo Alto, California will give its opinion that the
shares offered in this prospectus have been, or will be upon exercise of the
warrants, validly issued and are, or will be upon exercise of the warrants,
fully paid and non-assessable.

                                    EXPERTS

     The financial statements of Avigen, Inc. appearing in Avigen's Company's
Annual Report (Form 10-K) for the year ended June 30, 1998, have been audited by
Ernst & Young LLP, independent auditors, as set forth in their report included
therein and incorporated herein by reference. Such financial statements are
incorporated herein by reference in reliance upon such report given on the
authority of such firm as experts in accounting and auditing.

                                       17
<PAGE>   18

- ------------------------------------------------------
- ------------------------------------------------------

     WE HAVE NOT AUTHORIZED ANY DEALER, SALES PERSON OR OTHER PERSON TO GIVE ANY
INFORMATION OR TO MAKE ANY REPRESENTATIONS OTHER THAN THOSE CONTAINED IN THIS
PROSPECTUS OR ANY PROSPECTUS SUPPLEMENT. YOU MUST NOT RELY ON ANY UNAUTHORIZED
INFORMATION. THIS PROSPECTUS IS NOT AN OFFER OF THESE SECURITIES IN ANY STATE
WHERE AN OFFER IS NOT PERMITTED. THE INFORMATION IN THIS PROSPECTUS IS CURRENT
AS OF JULY 2, 1999. YOU SHOULD NOT ASSUME THAT THIS PROSPECTUS IS ACCURATE AS OF
ANY OTHER DATE.

                           -------------------------

                               TABLE OF CONTENTS

<TABLE>
<CAPTION>
                                      PAGE
                                      ----
<S>                                   <C>
Prospectus Summary..................    2
Risk Factors........................    3
Forward-Looking Statements..........   11
Were You Can Find More
  Information.......................   12
Use of Proceeds.....................   12
Selling Stockholders................   13
Plan of Distribution................   16
Legal Matters.......................   17
Experts.............................   17
</TABLE>

- ------------------------------------------------------
- ------------------------------------------------------
- ------------------------------------------------------
- ------------------------------------------------------

                                2,653,482 SHARES

                                  AVIGEN, INC.

                                  COMMON STOCK
                              --------------------

                                   PROSPECTUS
                              --------------------
                                  JULY 2, 1999

- ------------------------------------------------------
- ------------------------------------------------------


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