13D Filing: James E. Flynn and AveXis Inc (AVXS)

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

[Rule 13d-101]

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO §
24.13d-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO § 240.13D-2(a)

(Amendment No. 2)*

AveXis,
Inc.

(Name
of Issuer)

Common
Stock, par value $0.0001 per share

(Title
of Class of Securities)

05366U100

(CUSIP
Number)

(Name,
Address and Telephone Number of Person Authorized to Receive Notices and Communications)

May
30, 2017

(Date
of Event which Requires Filing of this Statement)

If the filing person
has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing
this schedule because of §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box ☐.

Note: Schedules
filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See § 240.13d-7
for other parties to whom copies are to be sent.

(Continued on following
pages)

(Page 1 of 15 Pages)

* The remainder of this cover page shall be filled out for a
reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment
containing information which would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page
shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”)
or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however,
see the Notes).

SCHEDULE 13D

(1) Comprised of 413,611 shares held by Deerfield Special Situations
Fund, L.P., 88,000 shares held by Deerfield Partners, L.P. and 112,000 shares held by Deerfield International Master Fund, L.P.

 SCHEDULE 13D

 SCHEDULE 13D

 SCHEDULE 13D

SCHEDULE 13D

SCHEDULE 13D

(2) Comprised of 413,611 shares held by Deerfield Special Situations
Fund, L.P., 88,000 shares held by Deerfield Partners, L.P., 1,623,089 shares held by Deerfield Private Design Fund III, L.P.,
112,000 shares held by Deerfield International Master Fund, L.P. and 15,428 shares of Common Stock underlying options held by
Jonathan Leff, a partner in Deerfield Management Company, L.P. and a former director of the Issuer.

SCHEDULE 13D

(3) Comprised of 1,623,089 shares held by Deerfield Private
Design Fund III, L.P.

SCHEDULE 13D

(4) Comprised of 413,611 shares held by Deerfield Special Situations
Fund, L.P., 88,000 shares held by Deerfield Partners, L.P., 1,623,089 shares held by Deerfield Private Design Fund III, L.P.,
112,000 shares held by Deerfield International Master Fund, L.P. and 15,428 shares of Common Stock underlying options held by
Jonathan Leff, a partner in Deerfield Management Company, L.P. and a former director of the Issuer.

This Amendment No. 2 (this “Amendment”)
to Schedule 13D amends the Schedule 13D (as previously amended, the “Schedule 13D”) filed by (i) Deerfield Mgmt,
L.P. (“Deerfield Mgmt”), (ii) Deerfield Special Situations Fund, L.P. (“Deerfield Special Situations
Fund”), (iii) Deerfield Management Company, L.P. (“Deerfield Management”), (iv) Deerfield Private
Design Fund III, L.P. (“Deerfield Private Design Fund III”), (v) Deerfield Partners, L.P. (“Deerfield
Partners”), (vi) Deerfield International Master Fund, L.P. (“Deerfield International Master Fund”),
(vii) Deerfield Mgmt III, L.P. (“Deerfield Mgmt III”) and (viii) James E. Flynn, a natural person (“Flynn”
and collectively with Deerfield Mgmt, Deerfield Special Situations Fund, Deerfield Management, Deerfield Private Design Fund III,
Deerfield Partners, Deerfield International Master Fund and Deerfield Mgmt III, the “Reporting Persons”), with
respect to the securities of AveXis, Inc. (the “Company”), on February 19, 2016, as amended by Amendment No.
1 to the Schedule 13D filed on February 2, 2017. Deerfield Special Situations Fund, Deerfield Private Design Fund III, Deerfield
Partners and Deerfield International Master Fund are collectively referred to herein as the “Funds.”

Capitalized terms used herein but not otherwise defined herein
shall have the meanings ascribed to them in the Schedule 13D.

Item 4.        Purpose of the Transaction

Item 4 of the Schedule 13D is hereby amended by adding the
following:

As previously disclosed by the Company, Jonathan Leff, a partner
of Deerfield Management, did not stand for re-election to the Company’s board of directors at the Company’s 2017 annual
meeting of stockholders (the “Annual Meeting”). Accordingly, Mr. Leff’s term as a director expired on May 30,
2017, the date of the Annual Meeting.

Item 5.        Interest in Securities of the Issuer.

Items 5(a), (b) and (c) of the Schedule 13D are hereby amended
and restated in their entirety as follows:

(a)

(1)       Deerfield
Mgmt

Percentage
of shares: 2.21%*

(2)        Deerfield
Management

Percentage
of shares: 8.10%*

(3)        Deerfield
Special Situations Fund

Number of shares: 413,611

Percentage
of shares 1.49%*

(4)       Deerfield
Private Design Fund III

Number of shares: 1,623,089

Percentage of shares: 5.84%*

(5)       Deerfield
Partners

Number of Shares: 88,000

Percentage of Shares: 0.32%*

(6)       Deerfield
International Master Fund

Number of Shares: 112,000

Percentage of Shares: 0.40%*

(7)       Deerfield
Mgmt III

Number of shares: 1,623,089
(comprised of shares held by Deerfield Private Design Fund III)

Percentage of shares: 5.84%*

(8)       Flynn

Percentage of shares: 8.10%*

*Percentage beneficial ownership reported herein reflects 27,794,558
shares of Common Stock outstanding as of May 11, 2017, as reported in the Company’s Quarterly Report on Form 10-Q for the
quarterly period ended March 31, 2017.

(b)

(1)        Deerfield
Mgmt

Sole power to vote or direct the vote: 0

Shared power to vote or direct the vote:
613,611

Sole power to dispose or to direct the disposition:
0

Shared power to dispose or direct the disposition:
613,611

(2)       Deerfield
Management

Sole power to vote or direct the vote: 0

Shared power to vote or direct the vote:
2,252,128

Sole power to dispose or to direct the disposition:
0

Shared power to dispose or direct the disposition:
2,252,128

(3)       Deerfield
Special Situations Fund

Sole power to vote or direct the vote: 0

Shared power to vote or direct the vote:
413,611

Sole power to dispose or to direct the disposition:
0

Shared power to dispose or direct the disposition:
413,611

(4)       Deerfield
Private Design Fund III

Sole power to vote or direct the vote: 0

Shared power to vote or direct the vote:
1,623,089

Sole power to dispose or to direct the disposition:
0

Shared power to dispose or direct the disposition:
1,623,089

(5)       Deerfield
Partners

Sole power to vote or direct the vote: 0

Shared power to vote or direct the vote:
88,000

Sole power to dispose or to direct the disposition:
0

Shared power to dispose or direct the disposition:
88,000

(6)       Deerfield
International Master Fund

Sole power to vote or direct the vote: 0

Shared power to vote or direct the vote:
112,000

Sole power to dispose or to direct the disposition:
0

Shared power to dispose or direct the disposition:
112,000

(7)       Deerfield
Mgmt III

Sole power to vote or direct the vote: 0

Shared power to vote or direct the vote:
1,623,089

Sole power to dispose or to direct the disposition:
0

Shared power to dispose or direct the disposition:
1,623,089

(8)       Flynn

Sole power to vote or direct the vote: 0

Shared power to vote or direct the vote:
2,252,128

Sole power to dispose or to direct the disposition:
0

Shared power to dispose or direct the disposition:
2,252,128

Flynn is the sole member of the general
partner of each of Deerfield Mgmt, Deerfield Mgmt III and Deerfield Management. Deerfield Mgmt is the general partner, and Deerfield
Management is the investment advisor, of Deerfield Special Situations Fund, Deerfield Partners and Deerfield International Master
Fund. Deerfield Mgmt III is the general partner, and Deerfield Management is the investment advisor, of Deerfield Private Design
Fund III. Pursuant to an arrangement between Deerfield Management and Leff, for so long as Leff is employed by Deerfield Management,
any compensation that Leff receives from the Issuer is for the economic benefit of Deerfield Management and must be transferred
to Deerfield Management, for no consideration, subject to applicable restrictions on transfer. See Item 6 of the Schedule 13D for
additional information regarding such arrangement.

(c) No Reporting Person has effected any
transactions in the Company’s securities since the initial filing of the Schedule 13D. The changes in the percentage of Common
Stock beneficially owned by each Reporting Person reflected in this Amendment have resulted solely from an increase in the number
of shares of Common Stock outstanding.

SIGNATURE

After reasonable inquiry
and to the best of their knowledge and belief, the undersigned certify that the information set forth in this statement is true,
complete and correct.

Dated: May 31, 2017