<PAGE>   1

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                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                            ------------------------

                                  FORM 10-K/A
                            ------------------------

(MARK ONE)

     [X]  ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
          EXCHANGE ACT OF 1934

                  FOR THE FISCAL YEAR ENDED DECEMBER 31, 1999

                                       OR

     [ ]   TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
           EXCHANGE ACT OF 1934

          FOR THE TRANSITION PERIOD                TO                .

                        COMMISSION FILE NUMBER: 0-20815

                                     AVIRON
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

<TABLE>
<S>                                            <C>
                   DELAWARE                                      77-0309686
       (STATE OR OTHER JURISDICTION OF                        (I.R.S. EMPLOYER
        INCORPORATION OR ORGANIZATION)                      IDENTIFICATION NO.)
</TABLE>

           297 NORTH BERNARDO AVENUE, MOUNTAIN VIEW, CALIFORNIA 94043
          (ADDRESS OF PRINCIPAL EXECUTIVE OFFICES INCLUDING ZIP CODE)

                                 (650) 919-6500
              (REGISTRANT'S TELEPHONE NUMBER, INCLUDING AREA CODE)

           SECURITIES REGISTERED PURSUANT TO SECTION 12(b) OF THE ACT
                                      NONE

           SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT
                         COMMON STOCK, $.001 PAR VALUE

    Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
Registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. Yes [X] No [ ]

    Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K is not contained herein, and will not be contained, to the
best of Registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to this
Form 10-K. [ ]

    Based on the closing sale price of $39.6875 on March 1, 2000, the aggregate
market value of the voting stock held by non-affiliates of the Registrant was
$551,770,193.

    On March 1, 2000, there were outstanding 17,163,183 shares of the
Registrant's Common Stock.

                      DOCUMENTS INCORPORATED BY REFERENCE
                        (TO THE EXTENT INDICATED HEREIN)

--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
<PAGE>   2

                                   PART III.

ITEM 10. DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT

     The names of our executive officers, senior management and directors as of
April 27, 2000 and information about them is presented below.

<TABLE>
<CAPTION>
                  NAME                     AGE                        POSITION
                  ----                     ---                        --------
<S>                                        <C>    <C>
EXECUTIVE OFFICERS
C. Boyd Clarke...........................  51     Chief Executive Officer, President and Director
Fred Kurland.............................  50     Senior Vice President and Chief Financial Officer
Carol A. Olson...........................  42     Senior Vice President, Commercial Development

SENIOR MANAGEMENT
Edward J. Arcuri, Ph.D. .................  49     Vice President, Manufacturing
Charlene A. Friedman.....................  42     Vice President, General Counsel and Secretary
Dianne L. Mastilock......................  48     Vice President, Human Resources
Paul M. Mendelman, M.D. .................  52     Vice President, Clinical Research
Eric J. Patzer, Ph.D. ...................  51     Vice President, Development
Rayasam S. Prasad........................  47     Vice President, Technical Affairs

DIRECTORS
J. Leighton Read, M.D. ..................  49     Chairman of the Board of Directors Director
Reid W. Dennis...........................  73     Director
Dennis M. Fenton, Ph.D. .................  48     Director
Wayne T. Hockmeyer, Ph.D. ...............  55     Director
Paul H. Klingenstein.....................  44     Director
Alan C. Mendelson........................  52     Director
Bernard Roizman, Sc.D. ..................  71     Director
</TABLE>

     C. Boyd Clarke, has been our President and Chief Executive Officer since
December 1999. From 1998 until joining us, Mr. Clarke was Chief Executive
Officer and President of U.S. Bioscience, Inc., a biotechnology company. Mr.
Clarke served as President and Chief Operating Officer of U.S. Bioscience, Inc.
from 1996 to 1998. From 1977 to 1996, Mr. Clarke held a number of positions at
Merck & Co., Inc., including being the first president of Pasteur-Merieux MSD,
and most recently as Vice President of Merck Vaccines. Mr. Clarke has a B.S. in
Biochemistry, and an M.A. in History from the University of Calgary.

     Fred Kurland, has been our Senior Vice President and Chief Financial
Officer since January 1998. Prior to joining us, Mr. Kurland was Vice President
and Chief Financial Officer of Protein Design Labs, Inc., a biotechnology
company, from 1996 to 1998. From 1995 to 1996, Mr. Kurland was Vice President
and Chief Financial Officer at Applied Immune Sciences, a biotechnology company,
and from 1987 to 1995, he held a number of positions at Syntex Corporation, a
pharmaceutical company, most recently as Vice President and Controller. Mr.
Kurland, a Certified Public Accountant, holds a B.S. in Business and Economics
from Lehigh University, and an M.B.A. and a J.D. from the University of Chicago.

     Carol A. Olson, has been our Senior Vice President, Commercial Development
since May 1998. Prior to joining us, Ms. Olson was the founder and managing
director of the Churchill Madison Group, a management consulting firm focused on
building new businesses in the medical, life sciences and high technology
industries. From 1984 to 1993, Ms. Olson worked for the Hewlett Packard Company.
Ms. Olson holds a B.A. in Economics with honors from Yale University and an
M.B.A. from Stanford University.

     Edward J. Arcuri, Ph.D., has been our Vice President, Manufacturing since
July 1999. Dr. Arcuri joined us from North American Vaccine, Inc., or NAVA,
where he served as Vice President, Manufacturing Operations and Process
Development from January 1995 to July 1999. Prior to joining NAVA, Dr. Arcuri
served as Senior Director, Biological Manufacturing at Merck and Co. from 1991
to 1994. Dr. Arcuri holds a B.S. degree in Biology from the State University of
New York at Albany and a masters degree and Ph.D. in Biology from Rensselaer
Polytechnic Institute.

                                        2
<PAGE>   3

     Charlene A. Friedman has been our Vice President, General Counsel and
Secretary since April 2000. From 1999 to joining us, Ms. Friedman was a
consultant to Inamed Corporation, a medical device company. From 1996 to 1999,
Ms. Friedman held various positions at Collagen Aesthetics, Inc., a
biotechnology company, most recently as Vice President, Legal and Regulatory
Affairs, General Counsel and Assistant Secretary. From 1995 to 1996, Ms.
Friedman was an attorney with Lillick & Charles in San Francisco, California.
From 1993 to 1995, she practiced law in Boston, Massachusetts at Warner &
Stackpole. She is a member of the Massachusetts and California bars. Ms.
Friedman holds a B.A. in Ancient Greek and Latin from Tufts University and a
J.D. from Northeastern University.

     Dianne L. Mastilock, has been our Vice President, Human Resources since
February 2000, and has held various positions at Aviron since April 1999. Ms.
Mastilock joined us from Digital Link, where she served as Vice President, Human
Resources from August 1994 to April 1999. Prior to joining Digital Link, Ms.
Mastilock served as Director, Human Resources at Humphry Instruments from 1993
to 1994. Prior to that, Ms. Mastilock was Director, Human Resources at Vitaphore
Corp. from 1991 to 1993. Ms. Mastilock holds a B.S. degree in Recreation and
Leisure Studies from San Jose State University and a Masters degree in Human
Resources and Organizational Development from the University of San Francisco.

     Paul M. Mendelman, M.D., has been our Vice President, Clinical Research
since 1996. Dr. Mendelman also is currently consulting professor in the
Department of Pediatrics at the Stanford University School of Medicine. Prior to
joining Aviron, Dr. Mendelman was Director, Clinical Research, Infectious
Diseases for Merck Research Laboratories, a pharmaceutical company, since 1991.
From 1983 to 1991, Dr. Mendelman was Clinical Instructor, Assistant Professor
and then Associate Professor of Pediatrics at the University of Washington. Dr.
Mendelman holds a B.S. and an M.D. from Ohio State University and is a fellow of
the American Academy of Pediatrics.

     Eric J. Patzer, Ph.D., has been our Vice President, Development since 1996.
Prior to joining the company, Dr. Patzer held various positions with Genentech,
Inc, a pharmaceutical company, since 1981, most recently as Vice President,
Development. Dr. Patzer holds a B.S. in Mechanical Engineering from The
Pennsylvania State University and a Ph.D. in Microbiology from the University of
Virginia.

     Rayasam (Ray) S. Prasad, has been our Vice President, Technical Affairs
since September 1999. Mr. Prasad joined Aviron from Chiron Vaccines, the global
vaccines business unit of Chiron Corporation, a biotechnology company, where he
served as Head of Regulatory, Quality and Drug Safety from October 1994 to
September 1999. Mr. Prasad also served as Director of Quality Assurance for
Therapeutics and Vaccines at Chiron. Prior to joining Chiron, Mr. Prasad held
positions in quality assurance and biological manufacturing operations at
Genentech from 1986 to 1994, and Burroughs Wellcome Co. from 1981 to 1986. Mr.
Prasad holds a B.S. in Pharmacy from Andhra University, India.

     J. Leighton Read, M.D., a founder of Aviron, has been our Chairman since
1992, Chief Executive Officer from 1992 until 1999 and was Chief Financial
Officer from 1992 until 1996. In 1989, he co-founded Affymax N.V. with Dr.
Alejandro Zaffaroni, serving initially as its Executive Vice President and Chief
Operating Officer and later, from 1990 to 1991, as President of the Pharma
Division and as a Managing Director of the parent company. From 1991 to 1993,
Dr. Read was a principal with Interhealth Limited, an investment partnership.
Prior to 1989, Dr. Read held appointments at the Harvard Medical School and
School of Public Health. He has served on the boards of a number of private
biotechnology companies and is currently on the board of CV Therapeutics, Inc.,
and AxyS Pharmaceuticals, Inc. both of which are biotechnology companies. Dr.
Read holds a B.S. in Biology and Psychology from Rice University and an M.D.
from the University of Texas Health Science Center at San Antonio.

     Reid W. Dennis, has been a member of our board of directors since 1992. Mr.
Dennis has been active in venture capital investments since 1952. He founded
Institutional Venture Partners, or IVP, a venture capital firm, in 1980, and has
acted as a General Partner of IVP since that time. He is currently a director of
Cohesion Technologies, as well as several private companies. Mr. Dennis holds a
B.S. in Electrical Engineering and an M.B.A. from Stanford University.

     Dennis M. Fenton, Ph.D. became a member of our board of directors in March
2000. In February 2000 Dr. Fenton was appointed Executive Vice President of
Amgen, a biotechnology company. From January 1995

                                        3
<PAGE>   4

to February 2000, Dr. Fenton served as the Senior Vice President Operations, of
Amgen. From August 1992 to January 1995, Dr. Fenton served as Senior Vice
President, Sales and Marketing of Amgen. Dr. Fenton served as Amgen's Vice
President, Process Development, Facilities and Manufacturing Services, from 1991
to 1992. Dr. Fenton previously had served as Vice President, Pilot Plant
Operations and Clinical Manufacturing, from 1988 to 1991, and as Director, Pilot
Plant Operations, from 1985 to 1988. Dr. Fenton received a B.A. from Manhattan
College in New York and a Ph.D. in Microbiology from Rutgers University.

     Wayne T. Hockmeyer, Ph.D., became a member of our board of directors in
March 2000. Dr. Hockmeyer founded MedImmune Inc., a biotechnology company, in
April 1988 and currently serves as its Chairman and Chief Executive Officer and
was elected to serve on its board of directors in May 1988. He became Chairman
of the board of directors of MedImmune Inc. in May 1993. From 1986 to 1988, Dr.
Hockmeyer served as Vice President, Research and Development, of Praxis
Biologics, Inc. From 1980 to 1986, Dr. Hockmeyer served as Chairman of the
Department of Immunology, Walter Reed Army Institute of Research. Dr. Hockmeyer
is a member of the Maryland Economic Development Commission, a member of the
Board of Directors of Digene Corporation serves on the Advisory Board of the
University of Maryland Biotechnology Institute, is a member of Board of Advisors
of the Institute of Human Virology, is a Member of the Board of Directors of the
High Technology Council of Maryland, is Chairman of the Maryland Bioscience
Alliance and a member of the University of Maryland University College Graduate
School Advisory Board, Executive Programs. Dr. Hockmeyer received a B.S. degree
from Purdue University and a Ph.D. from the University of Florida.

     Paul H. Klingenstein, has been a member of our board of directors since
1993. Mr. Klingenstein has been a General Partner of Aberdare Ventures since
1999. From 1986 until 1997, he was at Accel Partners where he was a General
Partner since 1988. In 1997, he served as a consultant to the Rockefeller
Foundation and to E.M. Warburg, Pincus & Co. Asia, Ltd. He is a director of
several private healthcare and internet companies. Mr. Klingenstein holds an
A.B. from Harvard University and an M.B.A. from Stanford University.

     Alan C. Mendelson, has been a member of our board of directors since April
2000 and was our Secretary since our inception until April 2000. Mr. Mendelson
is a senior partner of Cooley Godward LLP and has been with the firm since 1973.
He currently heads the firm's companies and life sciences groups and is a member
of its Management Committee. Mr. Mendelson served as Managing Partner of Cooley
Godward's Palo Alto office from May 1990 to March 1995 and November 1996 to
September 1997. He served as Secretary and Acting General Counsel of Amgen, Inc.
from April 1990 to April 1991 and as Acting General Counsel of Cadence Design
Systems, Inc. from November 1995 to June 1996. Mr. Mendelson serves as the
secretary of a number of private and public companies and is a member of the
board of directors of Axys Pharmaceuticals, Inc., Isis Pharmaceuticals, Inc. and
US Search.com, Inc. Mr. Mendelson received a A.B. in Political Science from the
University of California, Berkeley and a J.D. from Harvard Law School.

     Bernard Roizman, Sc.D., has been a member of our board of directors since
1992. Dr. Roizman has been the Joseph Regenstein Distinguished Service Professor
of Virology at the University of Chicago since 1984. He holds B.A. and M.S.
degrees from Temple University and an Sc.D. from The Johns Hopkins University.
Dr. Roizman is also a member of our Scientific Advisory Board.

                                        4
<PAGE>   5

SECTION 16(A) BENEFICIAL OWNERSHIP REPORTING COMPLIANCE

     Section 16(a) of the Securities Exchange Act requires our directors and
executive officers, and persons who own more than ten percent of a registered
class of our equity securities, to file with the SEC initial reports of
ownership and reports of changes in ownership of Common Stock and other equity
securities of Aviron. Officers, directors and greater than ten percent
stockholders are required by SEC regulation to furnish us with copies of all
Section 16(a) forms they file.

     To our knowledge, based solely on a review of the copies of such reports
furnished to us and written representations that no other reports were required,
during the fiscal year ended December 31, 1999, all Section 16(a) filing
requirements applicable to its officers, directors and greater than ten percent
beneficial owners were complied with; except that Fred Kurland filed one late
report covering one transaction for the sale of 776 shares of Common Stock and
Carol A. Olson filed one late report covering two transactions for the purchase
of an aggregate of 1,500 shares of Common Stock.

                                        5
<PAGE>   6

ITEM 11. EXECUTIVE COMPENSATION

COMPENSATION OF DIRECTORS

     Since June 1998, each of our non-employee directors has received cash
compensation for their services, in addition to being eligible for reimbursement
for their expenses incurred in connection with attendance at Board and Committee
meetings in accordance with our policy. In March 2000, the Board approved
increases in the cash compensation paid to each non-employee director. The
retainer was increased from $1,000 per month to $1,250 per month. Compensation
paid for each Board meeting attended was increased from $500 to $2,500.
Compensation for each Committee meeting attended was increased from $300 to
$500. In addition, a director who participates in a Board or Committee meeting
telephonically shall receive compensation in the amount of 50% of the applicable
meeting fee provided the Board or Committee meeting lasts at least thirty (30)
minutes. Should a Committee meeting fall on the same date as a Board meeting,
such non-employee director shall receive only the Board meeting attendance
stipend of $2,500.

     Each of our non-employee directors also receives stock option grants under
our 1996 Non-Employee Directors' Stock Option. In April 2000, our Board of
Directors approved an amendment to the Directors' Plan, subject to stockholder
approval, to increase the maximum number of shares of Common Stock that may be
issued pursuant to options granted under the Directors' Plan from 200,000 shares
to 350,000 shares. The Directors' Plan is administered by the Board of
Directors, unless the Board delegates administration to a committee comprised of
not less than two members of the Board.

     Option grants under the Directors' Plan are non-discretionary. Pursuant to
the terms of the Directors' Plan, each person who is first elected as a
non-employee director is automatically granted an option to purchase 15,000
shares of Common Stock upon such election. This is the non-employee director's
initial grant. In addition, on December 31, of each year, each non-employee
director who has served as a non-employee director since December 31 of the
immediately preceding year is automatically granted an option to purchase 3,000
shares of Common Stock. This is the non-employee director's annual grant. If the
non-employee director has not served as a director since December 31 of the
immediately preceding year they will receive a prorated annual grant. In April
2000, our Board of Directors approved an amendment to the Directors' Plan,
subject to stockholder approval, to increase the initial grant from 15,000
shares to 20,000 shares and to increase the annual grant from 3,000 shares to
10,000 shares.

     The exercise price of options under the Directors' Plan is equal to 100% of
the fair market value of the Common Stock subject to the option on the date of
the grant. Options granted under the Directors' Plan may not be exercised until
the date upon which such optionee has provided one year of continuous service as
a non-employee director following the date of such option grant. The initial
grant and annual grant vest in one-third increments on the anniversary date of
such option grant. The term of options granted under the Directors' Plan is ten
years. The Directors' Plan will terminate in March 2006, unless earlier
terminated by the Board.

     In the event of a merger, consolidation, reverse reorganization,
dissolution, sale of substantially all of our assets, or certain changes in the
beneficial ownership of our securities representing at least a 50% change of
such ownership, the options outstanding under the Directors' Plan will
automatically become fully vested and will terminate if not exercised prior to
such event.

     During the last fiscal year, we granted options under the Directors' Plan
covering 3,000 shares to each of Mr. Dennis, Mr. Klingenstein, Dr. Roizman, and
Dr. Shaw, at an exercise price per share of $15.6875, the fair market value of
such Common Stock on the date of grant. As of March 31, 2000, options for an
aggregate of 990 shares of our Common Stock have been exercised under the
Directors' Plan.

COMPENSATION OF EXECUTIVE OFFICERS

     The following table shows for the fiscal years ended December 31, 1999,
December 31, 1998, and December 31, 1997, compensation awarded or paid to, or
earned by, our Chief Executive Officers and our two other executive officers at
December 31, 1999. Dr. Read served as our Chief Executive Officer until

                                        6
<PAGE>   7

Mr. Clarke joined us in December 1999. Amounts under the column "All Other
Compensation" include group term life insurance paid by us on behalf of the
executive officers.

                           SUMMARY COMPENSATION TABLE

<TABLE>
<CAPTION>
                                                                              LONG-TERM
                                                                             COMPENSATION
                                                                                AWARDS
                                           ANNUAL COMPENSATION               ------------
                                 ----------------------------------------     SECURITIES
                                                             OTHER ANNUAL     UNDERLYING     ALL OTHER
  NAME AND PRINCIPAL POSITION    YEAR    SALARY     BONUS    COMPENSATION      OPTIONS      COMPENSATION
  ---------------------------    ----   --------   -------   ------------    ------------   ------------
<S>                              <C>    <C>        <C>       <C>             <C>            <C>
C. Boyd Clarke.................  1999   $ 24,628        --          --         600,000         $5,025(1)
  President and Chief            1998         --        --          --              --             --
  Executive Officer              1997         --        --          --              --             --
J. Leighton Read, M.D..........  1999    300,000   $75,000          --          50,000          1,056
  Chairman and Chief             1998    275,000    50,000          --         250,000            290
  Executive Officer              1997    260,000    80,000     $31,726(2)       25,000            574
Fred Kurland...................  1999    245,000    20,000          --          30,000          1,032
  Senior Vice President and      1998    223,955    25,000          --         100,000            283
  Chief Financial Officer        1997         --        --          --              --             --
Carol A. Olson.................  1999    250,000    20,000          --          60,000            354
  Senior Vice President,         1998    143,013    40,000          --         166,617             93
  Commercial Development         1997         --        --          --              --             --
</TABLE>

---------------
(1) Represents payment by us of a housing allowance in the amount of $5,025.

(2) Includes $20,739 of reimbursement for income taxes and $10,987 in income tax
    gross-up in connection with the early exercise of stock options in 1996.

                       STOCK OPTION GRANTS AND EXERCISES

     The following tables show for the fiscal year ended December 31, 1999,
information regarding options granted to and held at year end by the executive
officers listed in the "Summary Compensation Table" above.

                             OPTION GRANTS IN 1999

     The exercise price of each option was equal to the fair market value of our
common stock on the date of grant. The exercise price may be paid in cash, in
shares of our common stock valued at fair value on the exercise date or through
a cashless exercise procedure involving a same-day sale of the purchased shares.

     The potential realizable value is calculated based on the ten-year term of
the option at the time of grant. Stock price appreciation of 5% and 10% is
assumed pursuant to rules promulgated by the Securities and Exchange Commission
and does not represent our prediction of our stock price performance. The
potential realizable values at 5% and 10% appreciation are calculated by:

     - multiplying the number of shares of common stock subject to a given
       option by the exercise price per share;

     - assuming that the aggregate stock value derived from that calculation
       compounds at the annual 5% or 10% rate shown in the table until the
       expiration of the options; and

     - subtracting from that result the aggregate option exercise price.

     The shares listed in the following table under "Number of Securities
Underlying Options Granted" are subject to vesting. Certain of the stock options
listed in the table vest ratably over fifty months and certain vest upon
achievement of milestones. Each of the options has a ten-year term, subject to
earlier termination if the optionee's service with us ceases. Under certain
circumstances following a change of control, the vesting of such option grants
may accelerate and become immediately exercisable. Mr. Clarke's options were
granted outside the 1996 Equity Incentive Plan. See the section below entitled
"Employment Agreements and

                                        7
<PAGE>   8

Change in Control Arrangements" for a description of our agreements with Mr.
Clarke and Dr. Read concerning stock options that have been granted to them.

     Percentages shown under "Percent of Total Options Granted in 1999" are
based 1,626,000 options granted to our employees and directors during 1999.

<TABLE>
<CAPTION>
                                                                                         POTENTIAL REALIZABLE
                                         INDIVIDUAL GRANTS                                 VALUE AT ASSUMED
                            -------------------------------------------                    ANNUAL RATES OF
                            NUMBER OF                                                        STOCK PRICE
                            SECURITIES    PERCENT OF                                       APPRECIATION FOR
                            UNDERLYING   TOTAL OPTIONS                                       OPTION TERM
                             OPTIONS      GRANTED IN                      EXPIRATION   ------------------------
                             GRANTED         1999        EXERCISE PRICE      DATE          5%           10%
                            ----------   -------------   --------------   ----------   ----------   -----------
<S>                         <C>          <C>             <C>              <C>          <C>          <C>
C. Boyd Clarke............   600,000         36.90%         $16.750        11/30/09    $6,320,391   $16,017,112
J. Leighton Read, M.D.....    50,000          3.08%          21.375         2/23/09       672,131     1,703,312
Fred Kurland..............    30,000          1.85%          24.125         1/27/09       455,162     1,153,471
Carol A. Olson............    30,000          1.85%          24.125         1/27/09       455,162     1,153,471
                              30,000          1.85%          21.375         2/23/09       403,279     1,021,987
</TABLE>

                          1999 YEAR-END OPTION VALUES

     During the fiscal year ended December 31, 1999, no shares were acquired on
exercise by executive officers listed in the "Summary Compensation Table" above.
Amounts shown under the column "Value of Unexercised In-the-Money Options at
December 31, 1999" are based on the closing price of our Common Stock ($15.8125)
on December 31, 1999, as reported on the Nasdaq Stock Market, without taking
into account any taxes that may be payable in connection with the transaction,
multiplied by the number of shares underlying the option, less the exercise
price payable for these shares. As of December 31, 1999, none of the options
held by Mr. Clarke or Mr. Kurland were in-the-money.

<TABLE>
<CAPTION>
                                                 NUMBER OF SECURITIES
                                                UNDERLYING UNEXERCISED           VALUE OF UNEXERCISED
                                                      OPTIONS AT                 IN-THE-MONEY OPTIONS
                                                  DECEMBER 31, 1999              AT DECEMBER 31, 1999
                                             ----------------------------    ----------------------------
                  NAME                       EXERCISABLE    UNEXERCISABLE    EXERCISABLE    UNEXERCISABLE
                  ----                       -----------    -------------    -----------    -------------
<S>                                          <C>            <C>              <C>            <C>
C. Boyd Clarke...........................            0         600,000              --              --
J. Leighton Read, M.D....................      137,000         188,000        $107,313         $50,500
Fred Kurland.............................       52,600          77,400              --              --
Carol A. Olson...........................      101,997         135,400        $  3,938         $ 9,188
</TABLE>

EMPLOYMENT AGREEMENTS AND CHANGE IN CONTROL ARRANGEMENTS

     In November 1999, we issued an Offer Letter to Mr. Clarke to join us as
President, Chief Executive Officer and Director. The terms of the offer provide
that Mr. Clarke shall receive a monthly salary of $28,333.33 (equivalent to
$340,000 on an annual basis). Mr. Clarke is also eligible for a cash retention
bonus of $100,000 per year for the first five years of his employment, an annual
cash performance bonus of up to 60% of his salary and the standard benefits
package we offer to our employees. In addition, the Board granted to Mr. Clarke
an aggregate of 600,000 shares of our Common Stock at $16.75 per share, the fair
market value on the date of grant. We have also provided Mr. Clarke with an
interest free loan in the amount of $500,000 to be used toward the purchase of a
home in the San Francisco Bay Area. In the event Mr. Clarke is terminated
without cause he will receive one year's salary, bonus, health coverage and
continued vesting of his stock options for up to one year. In the event Mr.
Clarke is terminated following a change in control of Aviron, he will receive
two years' salary and bonus, two years health coverage, full vesting on his
stock options and other severance payments.

     In December 1999, we entered into a Non-Officer Chairman Employment
Agreement with Dr. Read. The terms of this agreement provide for compensation to
be paid to Dr. Read in exchange for his continuing services to us as Chairman of
our Board of Directors. This compensation includes an annual salary of $300,000,
provided that Dr. Read devote at least 20 hours a week to his position as
Chairman. Dr. Read is also eligible for the standard benefits package we offer
to our employees and provides for acceleration of the vesting

                                        8
<PAGE>   9

of all of his stock options upon a change in control of Aviron. The term of the
agreement is December 6, 1999 to December 31, 2000; however, the agreement may
be terminated by either party before December 31, 2000.

     In April 2000, our board of directors adopted management continuity
agreements for our executive officers and members of senior management, other
than C. Boyd Clarke, our President and Chief Executive Officer. These agreements
are intended to provide our executive officers and members of senior management
with financial security and sufficient income and encouragement to remain with
Aviron through a change of control of the company. If within 18 months of a
change of control, the individual's employment is terminated, actually or
constructively, the agreements will provide: (a) for a lump sum salary payment
equal to the sum of (1) the individual's base annual salary rate in effect
immediately preceding the date of the change of control, and (2) the
individual's target bonus for the fiscal year in which the change of control
occurs, (b) that all outstanding stock options for the individual will vest and
become immediately exercisable, and (c) that the individual will be entitled
(but not obligated) to continue health care coverage for one year and at the
individual's own expense for an additional six months. If pursuant to a change
of control, the acquiring company does not assume or substitute the individual's
outstanding stock options, then the vesting and exercisability of such stock
options will accelerate.

                                        9
<PAGE>   10

ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

     The following table sets forth certain information regarding the beneficial
ownership of our common stock as of April 14, 2000, by:

     - all those known by us to be beneficial owners of more than five percent
       of our common stock;

     - each of our directors and nominees;

     - each of our executive officers; and

     - all executive officers, directors and nominees as a group.

     Beneficial ownership is determined in accordance with the rules of the
Securities and Exchange Commission and generally includes voting or investment
power with respect to securities. Beneficial ownership also includes shares of
Common Stock subject to options that are currently exercisable or exercisable
within 60 days of April 14, 2000. These shares, however, are not deemed
outstanding for the purposes of computing the percentage ownership of each other
person. Percentage of ownership is based on 20,625,940 shares of Common Stock
outstanding on April 14, 2000. Unless otherwise indicated, the address of each
of the individuals and entities named below is: c/o Aviron, 297 North Bernardo
Avenue, Mountain View, CA 94043.

<TABLE>
<CAPTION>
                                                                     BENEFICIAL OWNERSHIP
                                                       -------------------------------------------------
                                                                                NUMBER OF
                                                          SHARES ISSUABLE         SHARES
                                                        PURSUANT TO OPTIONS     (INCLUDING
                                                        EXERCISABLE WITHIN     NUMBER SHOWN
                                                            60 DAYS OF           IN FIRST     PERCENTAGE
                  BENEFICIAL OWNER                        APRIL 14, 2000         COLUMN)       OF TOTAL
                  ----------------                     ---------------------   ------------   ----------
<S>                                                    <C>                     <C>            <C>
5% STOCKHOLDER
  Biotech Invest, S.A................................              --           2,655,286       12.87%
     Swiss Bank Tower
     Panama 1, Republic of Panama
DIRECTORS AND EXECUTIVE OFFICERS
  J. Leighton Read, M.D.(1)..........................         175,000             471,885        2.27%
  C. Boyd Clarke.....................................              --                  --           *
  Reid W. Dennis(2)..................................           6,000              40,671           *
  Dennis M. Fenton, Ph.D.............................              --                  --           *
  Wayne T. Hockmeyer, Ph.D...........................              --                  --           *
  Paul H. Klingenstein...............................          16,050              32,779           *
  Alan C. Mendelson(3)...............................              --              11,892
  Bernard Roizman, Sc.D..............................          15,600             189,600           *
  Carol A. Olson(4)..................................         124,257             127,915           *
  Fred Kurland.......................................          65,600              66,502           *
  All executive officers, directors and nominees as a
     group (10 persons)..............................         402,507             941,244        4.48%
</TABLE>

---------------
 *  Represents beneficial ownership of less than 1% of the outstanding shares of
    our Common Stock.

(1) Includes an aggregate of 32,000 shares held by The Travis Read 1993 Trust
    and The Haley Read 1993 Trust of which Robert Fitzwilson is the trustee. Dr.
    Read disclaims beneficial ownership of the shares held by the trusts.

(2) Includes 3,546 shares held by Institutional Venture Management V, of which
    Mr. Dennis is a general partner. Mr. Dennis disclaims beneficial ownership
    of the shares held by Institutional Venture Management V, except to the
    extent of his pecuniary interest therein.

(3) Includes 9,911 shares held by Cooley Godward LLP, of which Mr. Mendelson is
    a partner. Mr. Mendelson disclaims beneficial ownership of the shares held
    by Cooley Godward LLP, except to the extent of his pecuniary interest
    therein.

(4) Includes 500 shares held by Carol A. Olson, custodian for John Gregory Olson
    (UCAUTMA). Ms. Olson disclaims beneficial ownership of the shares held by
    the trust.

                                       10
<PAGE>   11

ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS

     We have entered into indemnity agreements with our executive officers and
directors and members of senior management which provide, among other things,
that we will indemnify these persons, under the circumstances and to the extent
provided for therein, for expenses, damages, judgments, fines and settlements he
or she may be required to pay in actions or proceedings which he or she is or
may be made a party by reason of his or her position as a director, officer or
other agent of Aviron, and otherwise to the full extent permitted under Delaware
law and our Bylaws.

     We have entered into employment agreements with C. Boyd Clarke, our
President and Chief Executive Officer, and J. Leighton Read, M.D., our Chairman
of the Board of Directors. We also intend to enter into management continuity
agreements with our executive officers and members of senior management. See the
section above entitled "Executive Compensation -- Employment Agreements and
Change in Control Arrangements" for a description of these agreements.

                                       11
<PAGE>   12

                                   SIGNATURES

     Pursuant to the requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, the Registrant has duly caused this Form 10-K/A to be
signed on its behalf by the undersigned, thereunto duly organized, on April 28,
2000.

                                          AVIRON

                                          By:      /s/ C. BOYD CLARKE
                                            ------------------------------------
                                                       C. Boyd Clarke
                                               President and Chief Executive
                                                           Officer

     Pursuant to the requirements of the Securities Exchange Act of 1934, this
report has been signed below by the following persons on behalf of the
Registrant in the capacities and on the dates stated.

<TABLE>
<CAPTION>
                      SIGNATURE                                     TITLE                     DATE
                      ---------                                     -----                     ----
<C>                                                    <C>                               <S>
                 /s/ C. BOYD CLARKE                       President, Chief Executive     April 28, 2000
-----------------------------------------------------  Officer and Director (Principal
                   C. Boyd Clarke                             Executive Officer)

                  /s/ FRED KURLAND                     Senior Vice President and Chief   April 28, 2000
-----------------------------------------------------    Financial Officer (Principal
                    Fred Kurland                           Financial and Accounting
                                                                   Officer)

             /s/ J. LEIGHTON READ, M.D.*                    Chairman of the Board        April 28, 2000
-----------------------------------------------------
               J. Leighton Read, M.D.

                 /s/ REID W. DENNIS*                               Director              April 28, 2000
-----------------------------------------------------
                   Reid W. Dennis

            /s/ DENNIS M. FENTON, PH.D.*                           Director              April 28, 2000
-----------------------------------------------------
               Dennis M. Fenton, Ph.D.

           /s/ WAYNE T. HOCKMEYER, PH.D.*                          Director              April 28, 2000
-----------------------------------------------------
              Wayne T. Hockmeyer, Ph.D.

              /s/ PAUL H. KLINGENSTEIN*                            Director              April 28, 2000
-----------------------------------------------------
                Paul H. Klingenstein

                                                                   Director
-----------------------------------------------------
                  Alan C. Mendelson

             /s/ BERNARD ROIZMAN, SC.D.*                           Director              April 28, 2000
-----------------------------------------------------
               Bernard Roizman, Sc.D.

               *By: /s/ C. BOYD CLARKE
  ------------------------------------------------
                   C. Boyd Clarke
                  Attorney-in-Fact
</TABLE>

                                       12
<PAGE>   13

                                 EXHIBIT INDEX

<TABLE>
<CAPTION>
 ITEM                             DESCRIPTION
 ----                             -----------
<C>       <S>
   3.1    Bylaws of the Registrant(2).
   3.2    Restated Certificate of Incorporation of the Registrant(2).
   4.1    Reference is made to Exhibits 3.1 and 3.2.
   4.2    Specimen Stock Certificate(1).
   4.3    Warrant for Series A Preferred Stock, issued to The Mount
          Sinai School of Medicine of the City of New York(1).
   4.4    Warrant for Series A Preferred Stock, issued to The Mount
          Sinai School of Medicine of the City of New York(1).
   4.5    Warrant for Series A Preferred Stock, issued to The Mount
          Sinai School of Medicine of the City of New York(1).
   4.6    Warrant or Series A Preferred Stock, issued to The Mount
          Sinai School of Medicine of the City of New York(1).
   4.7    Warrant for Series C Preferred Stock, issued to Raymond,
          James & Associates(1).
   4.8    Investors Rights Agreement, dated July 18, 1995, among the
          Registrant and the investors named therein(1).
   4.9    Common Stock Purchase Agreement between the Registrant and
          Biotech Target, S.A., dated as of March 27, 1997(3).
   4.10   Rights Agreement between the Registrant and BankBoston,
          N.A., dated as of October 8, 1997(5).
   4.11   Common Stock Purchase Agreement between the Registrant and
          American Home Products Corporation, dated as of December 16,
          1999(14).
   4.12   Common Stock Purchase Agreement between the Registrant and
          American Home Products Corporation, dated as of December 30,
          1999(14).
   4.13   Common Stock Purchase Agreement between the Registrant and
          American Home Products Corporation, dated as of February 3,
          2000(14).
   4.14   Warrant for Common Stock, issued to University of
          Michigan(14).
 +10.1    License Agreement between the Registrant and ARCH
          Development Corporation, dated July 1, 1992(1).
 +10.2    Technology Transfer Agreement between the Registrant and The
          Mount Sinai School of Medicine of the City University of New
          York, dated February 9, 1993(1).
 +10.3    Materials Transfer and Intellectual Property Agreement
          between the Registrant and the Regents of the University of
          Michigan, dated February 24, 1995(1).
  10.4    Stock Transfer Agreement between the Registrant and the
          Regents of the University of Michigan, dated February 24,
          1995(1).
 +10.5    Development and License Agreement between the Registrant and
          Sang-A Pharm. Co., Ltd., dated May 3, 1995(1).
 +10.6    Cooperative Research and Development Agreement between the
          Registrant and the National Institutes of Health, dated May
          30, 1995(1).
 +10.7    Heads of Agreement between the Registrant and SmithKline
          Beecham Biologicals S.A., dated October 8, 1995(1).
 +10.8    Manufacturing and Development Agreement between the
          Registrant and Evans Medical Limited, dated November 7,
          1995(1).
 *10.9    1996 Equity Incentive Plan(1).
 *10.10   1996 Non-Employee Directors' Stock Option Plan(1).
 *10.11   1996 Employee Stock Purchase Plan(1).
</TABLE>
<PAGE>   14

<TABLE>
<CAPTION>
 ITEM                             DESCRIPTION
 ----                             -----------
<C>       <S>
  10.12   Industrial lease between the Registrant and the Vanni
          Business Park General Partnership, dated August 29, 1995(1).
 +10.13   First Amendment to License Agreement between the Registrant
          and ARCH Development Corporation dated March 15, 1996(1).
 +10.14   Biological Materials License Agreement between the
          Registrant and the National Institutes of Health, dated May
          31, 1996(1).
 +10.15   Contract Manufacture Agreement between the Registrant and
          Evans Medical Limited, dated as of April 16, 1997(4).
 +10.16   Production Agreement between the Registrant and Packaging
          Coordinators, Inc., dated as of October 31, 1997(6).
  10.17   Facility Reservation Agreement between the Registrant and
          Packaging Coordinators, Inc., dated as of October 31,
          1997(6).
 +10.18   Influenza Vaccine Collaboration and License Distributor
          Agreement between the Registrant and CSL Limited, dated June
          19, 1998(7).
 +10.19   Supply Agreement between the Registrant and Becton Dickinson
          and Company dated July 1, 1998(8).
 +10.20   United States License and Co-Promotion Agreement between the
          Registrant and Wyeth Lederle Vaccines dated January 11,
          1999(9).
 +10.21   International FluMist(TM) License Agreement between the
          Registrant and Wyeth dated January 11, 1999(9).
 +10.22   FluMist(TM) Supply Agreement between the Registrant and
          Wyeth Lederle Vaccines dated January 11, 1999(9).
 +10.23   Credit Agreement between the Registrant and American Home
          Products Corporation dated January 11, 1999(9).
 +10.24   Letter Amendment to the Materials Transfer and Intellectual
          Property Agreement between the Registrant and the Regents of
          the University of Michigan dated February 24, 1999(10).
  10.25   Real Property Lease by and between the Registrant and
          Spieker Properties, L.P. dated February 5, 1999(11).
 +10.26   First Amendment to the Influenza Vaccine Collaboration and
          License and Distribution Agreement by and between the
          Registrant and CSL Limited, A.C.N. dated June 7, 1999(11).
  10.27   Loan and Security Agreement by and between the Registrant
          and Transamerica Business Credit Corporation dated June 23,
          1999(11).
  10.28   Master Loan and Security Agreement by and between the
          Registrant and FINOVA Capital Corporation dated July 23,
          1999(12).
 +10.29   Amended and Restated Contract Manufacture Agreement by and
          between the Registrant and Medeva Pharma Limited dated June,
          1999, as amended.(13)
  10.30   Real Property Lease by and between the Registrant and MELP
          VII L.P., dated October 12, 1999(14).
  10.31   Offer Letter, as amended, by and between the Registrant and
          C. Boyd Clarke, dated November 24, 1999(14).
  10.32   Employment Agreement by and between the Registrant and J.
          Leighton Read, dated December 6, 1999(14).
  10.33   Amendment No. 1 to Stock Transfer Agreement by and between
          the Registrant and The Regents of the University of
          Michigan, dated February 16, 2000(14).
  23.1    Consent of Ernst & Young LLP, Independent Auditors(13).
  24.1    Power of Attorney. See Signature Page(14).
  27.1    Financial Data Schedule(14).
</TABLE>
<PAGE>   15

---------------
  +  Confidential treatment has been granted for portions of this exhibit.

  *  Compensatory Plan or Agreement

 (1) Incorporated by reference to the correspondingly numbered exhibit to our
     Registration Statement on Form S-1, File No. 333-05209, filed June 5, 1996,
     as amended.

 (2) Incorporated by reference to the correspondingly numbered exhibit to our
     Quarterly Report on Form 10-Q, File No. 0-20815, for the quarter ended
     September 30, 1996, filed December 20, 1996.

 (3) Incorporated by reference to the correspondingly numbered exhibit to our
     Quarterly Report on Form 10-Q for the quarter ended March 31, 1997, File
     No. 0-20815, filed May 15, 1997.

 (4) Incorporated by reference to the correspondingly numbered exhibit to our
     Current Report on Form 8-K, File No. 0-20815, dated April 16, 1997 and
     filed July 21, 1997.

 (5) Incorporated by reference to the correspondingly numbered exhibit to our
     Current Report on Form 8-K, File No. 0-20815, dated October 8, 1997 and
     filed October 10, 1997.

 (6) Incorporated by reference to the correspondingly numbered exhibit to our
     Registration Statement on Form S-3, File No. 333-41649, filed December 10,
     1997.

 (7) Incorporated by reference to the correspondingly numbered exhibit to our
     Quarterly Report on Form 10-Q for the quarter ended June 30, 1998, File No.
     0-20815, filed August 14, 1998.

 (8) Incorporated by reference to the correspondingly numbered exhibit to our
     Quarterly Report on Form 10-Q for the quarter ended September 30, 1998,
     File No. 0-20815, filed November 16, 1998.

 (9) Incorporated by reference to the correspondingly numbered exhibit to our
     Annual Report on Form 10-K for the year ended on December 31, 1998, File
     No. 0-20815 filed March 31, 1999.

(10) Incorporated by reference to the correspondingly numbered exhibit to our
     Quarterly Report on Form 10-Q for the quarter ended March 31, 1999, File
     No. 0-20815, filed May 13, 1999.

(11) Incorporated by reference to the correspondingly numbered exhibit to our
     Quarterly Report on Form 10-Q for the quarter ended June 30, 1999, File No.
     0-20815, filed August 13, 1999.

(12) Incorporated by reference to the correspondingly numbered exhibit to our
     Quarterly Report on Form 10-Q for the quarter ended September 30, 1999,
     File No. 0-20815, filed November 15, 1999.

(13) Incorporated by reference to the correspondingly numbered exhibit to our
     Annual Report on Form 10-K/A for the year ended December 31, 1999, File No.
     0-20815, filed April 3, 2000.

(14) Incorporated by reference to the corresponding numbered exhibit to our
     Annual Report on Form 10-K for the year ended December 31, 1999, File No.
     02815, filed March 8, 2000.