Cytomegalovirus Drug Resistance by Next Generation Sequencing, Ganciclovir, Foscarnet, Cidofovir, Maribavir, and Letermovir

3004615

Cytomegalovirus Drug Resistance by Next Generation Sequencing, Ganciclovir, Foscarnet, Cidofovir, Maribavir, and Letermovir 3004615

Method

Massively Parallel Sequencing

Provides antiviral susceptibility information for ganciclovir, foscarnet, cidofovir, maribavir, and letermovir. Intended for patients with viral load >2.6 log IU/mL.

Cytomegalovirus (CMV) is a common infection among both children and adults that is generally asymptomatic in infected immunocompetent children and adults, but can lead to serious complications in neonates, pregnant individuals, immunocompromised individuals, and transplant recipients. Next generation sequencing can be used to test for CMV antiviral resistance with greater sensitivity to detect resistant subpopulations than traditional Sanger sequencing. This test sequences resistance-associated mutations in the UL27, UL54, UL56, and UL97 genes to assess resistance to ganciclovir, foscarnet, cidofovir, maribavir, and letermovir.

The reference sequence for CMV antiviral resistance testing is Merlin strain genbank ID NC_006273.

Test Interpretation

Limitations

Specimens with viral loads <2.6 log IU/mL may fail to amplify, thus producing indeterminate results.
This test detects populations down to 10% of the total population, which may account for resistance interpretation differences between methods.

Evaluated Mutations

*UL27* Variants
Variant	Cidovir	Foscarnet	Ganciclovir	Maribavir	Letermovir	Confirmed by Phenotyping
A269T	—	—	—	P	—	Y
A406V^,	—	—	—	P	—	Y
C415*^,	—	—	—	P	—	Y
D534Y	—	—	—	P	—	Y
E22*	—	—	—	P	—	Y
K89N	—	—	—	S	—	Y
L193F	—	—	—	P	—	Y
L335P^,	—	—	—	R	—	Y
L426F	—	—	—	P	—	Y
R233S^,	—	—	—	P	—	Y
R448P	—	—	—	P	—	Y
V353E	—	—	—	P	—	Y
W153R	—	—	—	P	—	Y
W362*	—	—	—	P	—	Y
W362R	—	—	—	P	—	Y

*UL54* Variants
Variant	Cidovir	Foscarnet	Ganciclovir	Maribavir	Letermovir	Confirmed by Phenotyping
883-884ins	—	—	—	—	—	N
981-982del^,^,^,^,^,^,^,^,^,^,	R	R	R	—	—	Y
A505V^,	P	S	P	—	—	Y
A543P^,	R	S	R	—	—	Y
A809V^,^,^,^,^,^,^,^,^,	P	R	R	—	—	Y
A834P^,^,	R	R	R	—	—	Y
A987G^,^,^,^,^,^,	R	S	R	—	—	Y
A987V^,	S	R	S	—	—	Y
C524del^,	R	S	R	—	—	Y
C539G^,	R	S	R	—	—	Y
C539R^,	R	S	R	—	—	Y
C590F	S	R	S	—	—	Y
D301N^,^,^,	R	S	R	—	—	Y
D413A^,^,	R	S	R	—	—	Y
D413E^,^,^,^,^,^,^,	R	S	R	—	—	Y
D413N^,	R	S	R	—	—	Y
D413Y^,	R	S	R	—	—	Y
D515E^,^,	P	P	R	—	—	Y
D515G	S	S	S	—	—	Y
D515Y^,^,^,^,	P	P	R	—	—	Y
D542E^,	R	S	S	—	—	Y
D588E^,^,	S	R	S	—	—	Y
D588N^,^,^,^,	P	R	R	—	—	Y
D594N	S	S	S	—	—	Y
E303D^,	R	S	R	—	—	Y
E303G^,	R	S	R	—	—	Y
E756D^,^,	S	R	S	—	—	Y
E756G	S	R	S	—	—	Y
E756K^,^,^,^,^,^,^,^,	P	R	R	—	S	Y
E756Q^,^,^,	S	R	S	—	—	Y
E951D^,	S	R	R	—	—	Y
E989D	P	R	R	—	—	Y
F412C^,^,^,^,^,	R	S	R	—	—	Y
F412L^,^,	R	S	R	—	—	Y
F412S^,^,^,	R	S	R	—	—	Y
F412V^,^,^,	R	S	R	—	—	Y
F595I^,^,	S	R	S	—	—	Y
G841A^,^,	R	R	R	—	—	Y
G841S	S	P	P	—	—	Y
G971D	S	S	S	—	—	Y
H600L	R	R	R	—	—	Y
I521T^,^,	R	S	R	—	—	Y
I722V	R	S	R	—	—	N
I726T^,	P	S	P	—	—	Y
I726V^,	R	S	R	—	—	Y
K493N	R	R	R	—	—	Y
K500N^,^,	R	S	R	—	—	Y
K513E^,^,^,^,	R	S	R	—	—	Y
K513N^,^,^,^,^,^,	R	S	R	—	—	Y
K513Q	R	S	R	—	—	Y
K513R^,^,^,	R	S	R	—	—	Y
K513T	R	S	R	—	—	Y
K805Q^,^,^,^,	R	S	S	—	—	Y
L501F^,^,^,^,^,	R	S	R	—	—	Y
L501I^,^,^,^,^,	R	S	R	—	—	Y
L516M	S	S	S	—	—	Y
L516P^,	R	S	R	—	—	Y
L516R^,^,	R	S	R	—	—	Y
L516W^,	R	S	R	—	—	Y
L545F	R	S	R	—	—	Y
L545S^,^,^,^,^,	R	S	R	—	—	Y
L545W^,^,^,	R	S	R	—	—	Y
L565V	P	R	P	—	—	Y
L773V^,^,	R	R	R	—	—	Y
L776M^,^,	S	R	R	—	—	Y
L802M^,^,^,^,^,^,^,^,^,	S	R	P	—	—	Y
L802V	S	S	P	—	—	Y
L862F	S	S	P	—	—	Y
L897P	—	—	S	—	—	Y
L957F^,^,	S	S	R	—	—	Y
M393K^,	R	R	R	—	—	N
M393R^,	R	R	R	—	—	N
M844T^,	S	R	S	—	—	Y
M844V^,	S	R	R	—	—	Y
N408D^,^,^,^,^,^,^,^,	R	S	R	—	—	Y
N408H	R	S	R	—	—	Y
N408K^,^,^,^,	R	S	R	—	—	Y
N408S^,^,	R	S	R	—	—	Y
N410K^,^,	R	S	R	—	—	Y
N495K^,^,^,	S	R	S	—	—	Y
P488R^,	R	S	R	—	—	Y
P497S	R	S	P	—	—	Y
P522A^,^,	R	S	R	—	—	Y
P522S^,^,^,^,^,	R	S	R	—	—	Y
P522T	R	S	R	—	—	Y
P829S^,^,	S	S	R	—	—	Y
Q578H^,^,^,^,	R	R	R	—	—	Y
Q578L^,	S	P	P	—	—	Y
Q783R	S	P	P	—	—	Y
Q807A	—	R	—	—	—	Y
R1052C	S	S	S	—	—	Y
S290R^,	S	R	P	—	—	Y
S585A^,^,	S	R	S	—	—	Y
T419M	—	R	S	—	—	N
T503A	R	S	R	—	—	Y
T503I^,^,^,^,	R	S	R	—	—	Y
T552N^,^,^,	S	R	R	—	—	Y
T700A^,^,^,^,^,^,^,	P	R	S	—	—	Y
T813S^,^,	R	R	R	—	—	Y
T821I^,^,^,^,^,	S	R	R	—	—	Y
T838A^,^,	S	R	S	—	—	Y
V526L^,	R	S	R	—	—	Y
V715A^,	S	R	S	—	—	Y
V715M^,^,^,^,^,^,^,	S	R	S	—	—	Y
V781I^,^,^,	S	R	P	—	—	Y
V787A^,^,	S	R	R	—	—	Y
V787E^,	R	R	R	—	—	Y
V787I	—	R	—	—	—	N
V787L^,^,^,^,^,	S	R	R	—	—	Y
V812L^,^,^,^,^,^,^,^,	R	R	R	—	—	Y
V823A	R	S	R	—	—	Y
V946L^,^,	S	R	S	—	—	Y
Y751H	R	S	R	—	—	N

*UL56* Variants
Variant	Cidovir	Foscarnet	Ganciclovir	Maribavir	Letermovir	Confirmed by Phenotyping
A365S^,	—	—	—	—	R	Y
C25F	—	—	—	—	R	Y
C325F^,	—	—	—	—	R	Y
C325R^,	—	—	—	—	R	Y
C325W^,	—	—	—	—	R	Y
C325Y^,^,^,	—	—	—	—	R	Y
E237D^,^,	—	—	—	—	R	Y
E237G^,	S	S	—	—	R	Y
F261C^,	—	—	—	—	R	Y
F261L^,^,	—	—	—	—	R	Y
F261S	—	—	—	—	R	N
K258E	—	—	—	—	R	Y
L241P^,^,^,	—	—	—	—	R	Y
L254F^,	—	—	—	—	R	Y
L257F^,^,	—	—	—	—	R	Y
L257I^,	—	—	—	—	R	Y
L328V^,	—	—	—	—	R	Y
M329T^,^,	—	—	—	—	R	Y
N232Y	—	—	—	—	R	Y
N368D^,	—	—	—	—	R	Y
Q204R	—	—	—	—	P	Y
R369G^,	—	—	—	—	R	Y
R369M^,^,	—	—	—	—	R	Y
R369S^,^,	—	—	—	—	R	Y
R369T^,	S	S	S	—	R	Y
S229F^,	—	—	—	—	R	Y
T244K^,	—	—	—	—	R	Y
T244R	—	—	—	—	R	N
V231A^,	—	—	—	—	R	Y
V231L^,^,^,^,	—	—	—	—	R	Y
V236A^,	—	—	—	—	R	Y
V236L^,	—	—	—	—	R	Y
V236M^,^,^,^,^,	S	S	S	—	R	Y
Y321C^,	—	—	—	—	R	Y

*UL97* Variants
Variant	Cidovir	Foscarnet	Ganciclovir	Maribavir	Letermovir	Confirmed by Phenotyping
590-593del^,	S	S	R	—	—	Y
590-600del^,	—	—	R	—	—	N
590-603del^,	—	—	R	—	—	N
590-607del	—	—	R	—	—	N
591-594del^,^,^,	—	—	R	—	—	Y
591-607del^,	—	—	R	—	—	Y
595-603del^,^,^,^,	—	S	R	—	—	Y
597-598del^,	—	—	R	—	—	Y
597-599del^,	—	—	R	—	—	Y
597-603del	—	—	—	—	—	N
600-601del^,^,^,	—	—	R	—	—	Y
601-602del^,	—	—	R	—	—	Y
601-603del^,	S	S	R	—	—	Y
A590T^,^,	—	—	R	—	—	N
A591D^,^,	—	—	R	—	—	N
A591V^,^,	—	—	R	—	—	Y
A594E^,^,	—	—	R	—	—	Y
A594G^,^,	—	—	R	—	—	Y
A594P^,^,^,^,	—	—	R	—	—	Y
A594S^,	—	—	R	—	—	Y
A594T^,^,^,^,^,^,^,	—	—	R	—	—	Y
A594V^,^,^,^,^,^,^,^,^,^,	—	—	R	—	—	Y
A606D^,^,	—	—	P	—	—	N
A613V^,^,	—	—	R	—	—	Y
A619V^,	—	—	S	—	—	Y
A674T^,	—	—	S	—	—	Y
C480F^,	—	—	R	R	—	Y
C480R^,	—	—	R	R	—	Y
C518Y^,^,	—	—	R	—	—	Y
C592F	—	—	R	—	—	N
C592G^,^,^,^,^,^,^,^,^,^,	S	S	R	—	—	Y
C603R^,^,^,	—	—	R	—	—	Y
C603S^,^,^,	—	—	P	—	—	Y
C603W^,^,^,^,^,^,^,	S	S	R	—	—	Y
C603Y^,^,	—	—	R	—	—	N
C607F^,^,^,	—	—	R	—	—	Y
C607Y^,^,^,^,^,^,^,	—	S	R	—	—	Y
D456N^,	—	—	R	R	—	Y
D605E^,^,	—	—	S	—	—	Y
E362D	—	—	R	S	—	Y
E596D^,	—	—	S	—	—	Y
E596G^,^,^,^,^,^,	—	—	R	—	—	Y
E596Q	—	—	R	—	—	Y
E596Y^,	—	—	R	—	—	Y
E596del^,	—	—	R	—	—	Y
E655K^,	—	—	S	—	—	Y
F342S^,^,^,	—	—	R	R	—	Y
F342Y^,	—	—	R	R	—	Y
G598S^,^,	—	—	R	—	—	Y
G598V^,	—	—	R	—	—	N
H411L^,^,	—	—	—	R	—	Y
H411N^,^,	—	—	—	R	—	Y
H411Y^,^,^,	—	—	—	R	—	Y
H520Q^,^,^,^,	S	S	R	—	—	Y
I610T^,	—	—	R	—	—	Y
K355M^,^,	—	—	R	R	—	Y
K355del	—	—	R	R	—	Y
K359E^,	—	—	R	S	—	Y
K359N	—	—	R	S	—	Y
K359Q^,	—	—	R	S	—	Y
K599E^,	—	—	S	—	—	Y
K599M^,	—	—	R	—	—	N
K599R^,	—	—	S	—	—	Y
K599T^,^,	S	—	R	—	—	Y
K599del^,	—	—	R	—	—	Y
L337M^,	—	—	—	R	—	Y
L348V	—	—	S	R	—	Y
L397R^,^,	—	—	S	R	—	Y
L405P^,	—	—	R	—	—	Y
L595F^,^,^,^,	—	—	R	—	—	Y
L595S^,^,^,^,^,^,^,^,	—	—	R	—	—	Y
L595T^,^,	S	S	R	—	—	N
L595W^,^,^,^,^,	—	—	R	—	—	Y
L595del^,^,^,^,^,	—	—	R	—	—	Y
L600I^,	—	—	S	—	—	Y
L600del^,^,^,^,^,^,	—	—	R	—	—	Y
L634Q^,	—	—	S	—	—	Y
M460I^,^,^,^,^,^,^,^,	S	S	R	—	—	Y
M460L^,	—	—	R	—	—	N
M460T^,^,	—	—	R	—	—	Y
M460V^,^,^,^,^,^,^,^,^,^,	—	S	R	—	—	Y
M615V^,	—	—	S	—	—	Y
N597D^,	—	—	S	—	—	Y
N597I^,	—	—	R	—	—	N
P521L^,	—	—	R	R	—	Y
T409M^,^,	—	—	—	R	—	Y
T601M^,	—	—	S	—	—	Y
T601del^,^,	—	—	R	—	—	Y
V345I	—	—	S	S	—	Y
V353A^,^,	—	—	—	R	—	Y
V356G^,^,	—	—	R	R	—	Y
V466G^,^,^,	—	—	R	R	—	Y
Y617H^,	—	—	S	—	—	Y
Y617del^,	—	—	R	R	—	Y
* = stop codon del = deletion R = "Resistant." Resistant indicates evidence of drug resistance compared with a wild-type virus. P = "Possible Resistance." Possible resistance indicates mutations were detected with borderline-level drug resistance or conflicting resistance status reported in the literature. S = "Sensitive." Ignored by the plugin and reported as additional variant. — = No known resistance-association or phenotypically confirmed sensitivity to specified drug. Ignored in the analysis. Y = "Yes." Mutation's resistance profile was confirmed by marker transfer/phenotyping experiments. N = "No." Mutation's resistance profile has not been confirmed by marker transfer/phenotyping experiments.

Cihlar T, Fuller MD, Cherrington JM. Characterization of drug resistance-associated mutations in the human cytomegalovirus DNA polymerase gene by using recombinant mutant viruses generated from overlapping DNA fragments. J Virol. 1998;72(7):5927-5936.

Cherrington JM, Fuller MD, Lamy PD, et al. In vitro antiviral susceptibilities of isolates from cytomegalovirus retinitis patients receiving first- or second-line cidofovir therapy: relationship to clinical outcome. J Infect Dis. 1998;178(6):1821-1825.

Baldanti F, Underwood MR, Stanat SC, et al. Single amino acid changes in the DNA polymerase confer foscarnet resistance and slow-growth phenotype, while mutations in the UL97-encoded phosphotransferase confer ganciclovir resistance in three double-resistant human cytomegalovirus strains recovered from patients with AIDS. J Virol. 1996;70(3):1390-1395.

Goldner T, Hewlett G, Ettischer N, et al. The novel anticytomegalovirus compound AIC246 (letermovir) inhibits human cytomegalovirus replication through a specific antiviral mechanism that involves the viral terminase. J Virol. 2011;85(20):10884-10893.

Wolf DG, Yaniv I, Ashkenazi S, et al. Emergence of multiple human cytomegalovirus ganciclovir-resistant mutants with deletions and substitutions within the UL97 gene in a patient with severe combined immunodeficiency. Antimicrob Agents Chemother. 2001;45(2):593-595.

Wong DD, van Zuylen WJ, Hamilton ST, et al. Patient-derived cytomegaloviruses with different ganciclovir sensitivities from UL97 mutation retain their replication efficiency and some kinase activity in vitro. Antimicrob Agents Chemother. 2019;63(9):e02425-18.

Feedback

Cytomegalovirus Drug Resistance by Next Generation Sequencing, Ganciclovir, Foscarnet, Cidofovir, Maribavir, and Letermovir

Test Interpretation

Limitations

Evaluated Mutations

References