<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0206</schemaVersion>

    <documentType>3/A</documentType>

    <periodOfReport>2022-01-06</periodOfReport>

    <dateOfOriginalSubmission>2022-01-25</dateOfOriginalSubmission>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001658551</issuerCik>
        <issuerName>Amylyx Pharmaceuticals, Inc.</issuerName>
        <issuerTradingSymbol>AMLX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001543112</rptOwnerCik>
            <rptOwnerName>Morningside Venture Investments Ltd</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O THC MANAGEMENT SERVICES S.A.M.</rptOwnerStreet1>
            <rptOwnerStreet2>3-5 AVENUE DES CITRONNIERS</rptOwnerStreet2>
            <rptOwnerCity>MONACO</rptOwnerCity>
            <rptOwnerState>O9</rptOwnerState>
            <rptOwnerZipCode>MC 98000</rptOwnerZipCode>
            <rptOwnerStateDescription>MONACO</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001914583</rptOwnerCik>
            <rptOwnerName>MVIL, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O 22ND FLOOR, HANG LUNG CENTRE</rptOwnerStreet1>
            <rptOwnerStreet2>2-20 PATERSON ST.</rptOwnerStreet2>
            <rptOwnerCity>CAUSEWAY BAY, HONG KONG</rptOwnerCity>
            <rptOwnerState>K3</rptOwnerState>
            <rptOwnerZipCode></rptOwnerZipCode>
            <rptOwnerStateDescription>HONG KONG</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series A Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1409035</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Explanation of Responses</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series B Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>6410964</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Explanation of Responses</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series C-1 Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>974107</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Explanation of Responses</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series C-2 Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1621544</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Explanation of Responses</value>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Each share of Series A, Series B, Series C-1 and Series C-2 preferred stock (collectively the &quot;Preferred Stock&quot;) is convertible on a one-for-one basis into Common Stock at any time at the election of the Reporting Person and will automatically convert upon the closing of the Issuer's initial public offering into the number of shares of the Issuer's Common Stock shown in column 3 without payment or further consideration. The Preferred Stock has no expiration date.</footnote>
        <footnote id="F2">Frances Anne Elizabeth Richard, Jill Marie Franklin, Peter Stuart Allenby Edwards and Cheung Ka Ho are the directors of Morningside Venture Investments Limited (&quot;Morningside&quot;) and share voting and dispositive power with respect to the securities held by Morningside and MVIL, LLC (&quot;MVIL LLC&quot;), Morningside's wholly-owned subsidiary.  Cheng Yee Wing Betty and Wong See Wai are the managers of MVIL LLC and share voting and dispositive power with respect to the securities held by MVIL LLC.  Ms. Cheng and Mr. Wong each disclaim ownership of the securities owned by MVIL LLC.</footnote>
        <footnote id="F3">The shares of Series C-2 preferred stock are held by MVIL LLC.</footnote>
    </footnotes>

    <remarks>The Reporting Persons are jointly filing this Form 3 pursuant to Rule 16a-3(j) under the Exchange Act.</remarks>

    <ownerSignature>
        <signatureName>/s/ Frances Anne Elizabeth Richard, for Morningside Venture Investments Limited</signatureName>
        <signatureDate>2022-03-17</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Cheng Yee Wing Betty, for MVIL, LLC</signatureName>
        <signatureDate>2022-03-17</signatureDate>
    </ownerSignature>
</ownershipDocument>
