Cytomegalovirus (CMV) Genotype
Cytomegalovirus (CMV) Genotype
This test is used to detect antiviral resistance in patients with CMV infection.
Test Summary
Cytomegalovirus (CMV) Genotype
Clinical use
- Detect antiviral resistance in patients with cytomegalovirus (CMV) infection
Clinical background
CMV is a member of the Herpesviridae family that infects about 60% of people in the United States by age 40.1 After initial infection, CMV remains latent indefinitely and can reactivate at any time.2,3 Although CMV infections are usually asymptomatic or mild in healthy people, they are more serious in people with compromised immune systems, such as transplant recipients and people with HIV.3,4 In these patients, initial or reactivated CMV infection can cause severe disease, transplant rejection, and death.3–5
Although CMV infection can usually be treated or prevented with antiviral drugs (ie, ganciclovir/valganciclovir, cidofovir, foscarnet, letermovir, and maribavir), the virus can develop genetic mutations that confer resistance to 1 or more of these drugs.3,4 Resistance can make the drug(s) ineffective and is associated with greater morbidity and mortality.3,4 About 5% to 12% of transplant recipients treated with ganciclovir develop resistance,6 but the prevalence is higher in certain patient populations, including2,5,6
- Lung and intestinal transplant recipients
- Transplant recipients with donor-positive, recipient-negative CMV serostatus
- Patients with prolonged exposure to subtherapeutic doses of anti-CMV drugs
- Patients who are highly immunosuppressed
According to guidelines from the American Society of Transplantation Infectious Diseases Community of Practice and the Transplantation Society International CMV Consensus Group, antiviral resistance should be suspected when CMV infection is refractory to treatment.2,6 CMV infection is considered refractory when, after ≥2 weeks of appropriately dosed antiviral therapy, CMV viral load fails to decrease by >1 log10 or CMV disease fails to improve.2,6,7
According to the same guidelines, suspected antiviral resistance should be confirmed by genotypic resistance testing, which involves testing for CMV mutations that are known to confer resistance. Most resistance-conferring mutations are found in the UL54, UL56, and UL97 genes.3,4,6 Because drug targets differ, mutations in certain genes confer resistance to certain drugs (Table 1).3,4
Table 1. Genes Associated With Resistance to Anti-CMV Drugs
Gene3,4 |
Encoded drug target |
Drug(s) affected by mutations |
UL54 |
DNA polymerase |
(Val)ganciclovir, cidofovir, foscarnet |
UL56 |
Terminase complex |
Letermovir |
UL97 |
Phosphotransferase |
(Val)ganciclovir, maribavir |
Quest Diagnostics offers 3 genotypic tests for CMV drug resistance that detect mutations in the UL54, UL56, and/or UL97 genes (Table 2). Detected mutations are compared to a database of known resistance-conferring mutations to predict whether the infection is resistant to each anti-CMV drug. Testing all 3 genes (test code 13947) predicts resistance for all 5 FDA-approved anti-CMV drugs, but testing fewer genes may be appropriate for certain patients, including those for whom letermovir resistance does not need to be determined (test code 13948) and those for whom only letermovir resistance needs to be determined (test code 13949).
Table 2. Available Genotypic Tests for CMV Drug Resistance
Test code |
Test name |
Gene(s) (codons) sequenced |
Drug(s) for which resistance is predicted |
13949 |
Cytomegalovirus (CMV) Genotype (UL56) |
UL56 (codons 70-570) |
Letermovir |
13948 |
Cytomegalovirus (CMV) Genotype (UL97/UL54) |
UL54 (codons 235-1,045) |
(Val)ganciclovir, cidofovir, foscarnet, maribavir |
13947 |
Cytomegalovirus (CMV) Genotype (UL97/UL54/UL56) |
UL54 (codons 235-1,045) |
(Val)ganciclovir, cidofovir, foscarnet, letermovir, maribavir |
The genotypic tests offered by Quest use next-generation sequencing (NGS), which is more sensitive than traditional Sanger sequencing, potentially allowing resistance to be detected earlier.3 In particular, NGS tests can detect smaller mutant subpopulations than Sanger sequencing tests (mutation reporting threshold: 15% for Quest NGS tests vs 20%-30% for Sanger sequencing tests).3–5
Individuals suitable for testing
- Patients with suspected refractory or resistant CMV infection
Method
- Polymerase chain reaction, NGS, and bioinformatic analysis
- Analytical sensitivity (limit of detection): 500 IU/mL (whole blood), 2,000 IU/mL (plasma)
- Analytical specificity: 100%
Interpretive information
Test results include a list of the mutations detected, if any, and corresponding predictions of resistance to each specified drug (resistance predicted, resistance probable, or resistance not predicted). Probable resistance indicates a lower level of evidence for resistance than predicted resistance (eg, mutations found in clinical isolates but unconfirmed by recombinant phenotyping). A result of TNP (test not performed) indicates that a genotype could not be obtained from the sample, which may be due to insufficient viral load, mutations at the priming sites, or the presence of polymerase chain reaction inhibitors.
Genotypic tests for CMV drug resistance have the following limitations:
- Test results do not include mutations that are present in <15% of the viral population. However, the clinical significance of such minority mutations is unknown.5
- Because the tests are most accurate at viral loads ≥500 IU/mL, results for specimens with lower viral loads should be interpreted with caution.4
- The tests cannot account for mutations outside the specified gene regions (Table 2) or mutations whose effects on drug susceptibility have not yet been determined.
References
- Fowler K, Mucha J, Neumann M, et al. A systematic literature review of the global seroprevalence of cytomegalovirus: possible implications for treatment, screening, and vaccine development. BMC Public Heal. 2022;22(1):1659. doi:10.1186/s12889-022-13971-7
- Razonable RR, Humar A. Cytomegalovirus in solid organ transplant recipients—guidelines of the American Society of Transplantation Infectious Diseases Community of Practice. Clin Transplant. 2019;33(9):e13512. doi:10.1111/ctr.13512
- Grgic I, Gorenec L. Human cytomegalovirus (HCMV) genetic diversity, drug resistance testing and prevalence of the resistance mutations: a literature review. Trop Med Infect Dis. 2024;9(2):49. doi:10.3390/tropicalmed9020049
- Pham JH, Razonable RR. Management of resistant and refractory cytomegalovirus infections after transplantation. Expert Rev Anti-Infect Ther. Published September 5, 2024. doi:10.1080/14787210.2024.2399647
- Alsanea MS, Al-Qahtani AA, Almaghrabi RS, et al. Diagnosis of human cytomegalovirus drug resistance mutations in solid organ transplant recipients—a review. Diagnostics. 2024;14(2):203. doi:10.3390/diagnostics14020203
- Kotton CN, Kumar D, Caliendo AM, et al. The third international consensus guidelines on the management of cytomegalovirus in solid-organ transplantation. Transplantation. 2018;102(6):900-931. doi:10.1097/tp.0000000000002191
- Ljungman P, de la Camara R, Robin C, et al. Guidelines for the management of cytomegalovirus infection in patients with haematological malignancies and after stem cell transplantation from the 2017 European Conference on Infections in Leukaemia (ECIL 7). Lancet Infect Dis. 2019;19(8):e260-e272. doi:10.1016/s1473-3099(19)30107-0
Content reviewed 10/2024
This test is used to detect antiviral resistance in patients with CMV infection.
Test Summary
Cytomegalovirus (CMV) Genotype
Clinical use
- Detect antiviral resistance in patients with cytomegalovirus (CMV) infection
Clinical background
CMV is a member of the Herpesviridae family that infects about 60% of people in the United States by age 40.1 After initial infection, CMV remains latent indefinitely and can reactivate at any time.2,3 Although CMV infections are usually asymptomatic or mild in healthy people, they are more serious in people with compromised immune systems, such as transplant recipients and people with HIV.3,4 In these patients, initial or reactivated CMV infection can cause severe disease, transplant rejection, and death.3–5
Although CMV infection can usually be treated or prevented with antiviral drugs (ie, ganciclovir/valganciclovir, cidofovir, foscarnet, letermovir, and maribavir), the virus can develop genetic mutations that confer resistance to 1 or more of these drugs.3,4 Resistance can make the drug(s) ineffective and is associated with greater morbidity and mortality.3,4 About 5% to 12% of transplant recipients treated with ganciclovir develop resistance,6 but the prevalence is higher in certain patient populations, including2,5,6
- Lung and intestinal transplant recipients
- Transplant recipients with donor-positive, recipient-negative CMV serostatus
- Patients with prolonged exposure to subtherapeutic doses of anti-CMV drugs
- Patients who are highly immunosuppressed
According to guidelines from the American Society of Transplantation Infectious Diseases Community of Practice and the Transplantation Society International CMV Consensus Group, antiviral resistance should be suspected when CMV infection is refractory to treatment.2,6 CMV infection is considered refractory when, after ≥2 weeks of appropriately dosed antiviral therapy, CMV viral load fails to decrease by >1 log10 or CMV disease fails to improve.2,6,7
According to the same guidelines, suspected antiviral resistance should be confirmed by genotypic resistance testing, which involves testing for CMV mutations that are known to confer resistance. Most resistance-conferring mutations are found in the UL54, UL56, and UL97 genes.3,4,6 Because drug targets differ, mutations in certain genes confer resistance to certain drugs (Table 1).3,4
Table 1. Genes Associated With Resistance to Anti-CMV Drugs
Gene3,4 |
Encoded drug target |
Drug(s) affected by mutations |
UL54 |
DNA polymerase |
(Val)ganciclovir, cidofovir, foscarnet |
UL56 |
Terminase complex |
Letermovir |
UL97 |
Phosphotransferase |
(Val)ganciclovir, maribavir |
Quest Diagnostics offers 3 genotypic tests for CMV drug resistance that detect mutations in the UL54, UL56, and/or UL97 genes (Table 2). Detected mutations are compared to a database of known resistance-conferring mutations to predict whether the infection is resistant to each anti-CMV drug. Testing all 3 genes (test code 13947) predicts resistance for all 5 FDA-approved anti-CMV drugs, but testing fewer genes may be appropriate for certain patients, including those for whom letermovir resistance does not need to be determined (test code 13948) and those for whom only letermovir resistance needs to be determined (test code 13949).
Table 2. Available Genotypic Tests for CMV Drug Resistance
Test code |
Test name |
Gene(s) (codons) sequenced |
Drug(s) for which resistance is predicted |
13949 |
Cytomegalovirus (CMV) Genotype (UL56) |
UL56 (codons 70-570) |
Letermovir |
13948 |
Cytomegalovirus (CMV) Genotype (UL97/UL54) |
UL54 (codons 235-1,045) |
(Val)ganciclovir, cidofovir, foscarnet, maribavir |
13947 |
Cytomegalovirus (CMV) Genotype (UL97/UL54/UL56) |
UL54 (codons 235-1,045) |
(Val)ganciclovir, cidofovir, foscarnet, letermovir, maribavir |
The genotypic tests offered by Quest use next-generation sequencing (NGS), which is more sensitive than traditional Sanger sequencing, potentially allowing resistance to be detected earlier.3 In particular, NGS tests can detect smaller mutant subpopulations than Sanger sequencing tests (mutation reporting threshold: 15% for Quest NGS tests vs 20%-30% for Sanger sequencing tests).3–5
Individuals suitable for testing
- Patients with suspected refractory or resistant CMV infection
Method
- Polymerase chain reaction, NGS, and bioinformatic analysis
- Analytical sensitivity (limit of detection): 500 IU/mL (whole blood), 2,000 IU/mL (plasma)
- Analytical specificity: 100%
Interpretive information
Test results include a list of the mutations detected, if any, and corresponding predictions of resistance to each specified drug (resistance predicted, resistance probable, or resistance not predicted). Probable resistance indicates a lower level of evidence for resistance than predicted resistance (eg, mutations found in clinical isolates but unconfirmed by recombinant phenotyping). A result of TNP (test not performed) indicates that a genotype could not be obtained from the sample, which may be due to insufficient viral load, mutations at the priming sites, or the presence of polymerase chain reaction inhibitors.
Genotypic tests for CMV drug resistance have the following limitations:
- Test results do not include mutations that are present in <15% of the viral population. However, the clinical significance of such minority mutations is unknown.5
- Because the tests are most accurate at viral loads ≥500 IU/mL, results for specimens with lower viral loads should be interpreted with caution.4
- The tests cannot account for mutations outside the specified gene regions (Table 2) or mutations whose effects on drug susceptibility have not yet been determined.
References
- Fowler K, Mucha J, Neumann M, et al. A systematic literature review of the global seroprevalence of cytomegalovirus: possible implications for treatment, screening, and vaccine development. BMC Public Heal. 2022;22(1):1659. doi:10.1186/s12889-022-13971-7
- Razonable RR, Humar A. Cytomegalovirus in solid organ transplant recipients—guidelines of the American Society of Transplantation Infectious Diseases Community of Practice. Clin Transplant. 2019;33(9):e13512. doi:10.1111/ctr.13512
- Grgic I, Gorenec L. Human cytomegalovirus (HCMV) genetic diversity, drug resistance testing and prevalence of the resistance mutations: a literature review. Trop Med Infect Dis. 2024;9(2):49. doi:10.3390/tropicalmed9020049
- Pham JH, Razonable RR. Management of resistant and refractory cytomegalovirus infections after transplantation. Expert Rev Anti-Infect Ther. Published September 5, 2024. doi:10.1080/14787210.2024.2399647
- Alsanea MS, Al-Qahtani AA, Almaghrabi RS, et al. Diagnosis of human cytomegalovirus drug resistance mutations in solid organ transplant recipients—a review. Diagnostics. 2024;14(2):203. doi:10.3390/diagnostics14020203
- Kotton CN, Kumar D, Caliendo AM, et al. The third international consensus guidelines on the management of cytomegalovirus in solid-organ transplantation. Transplantation. 2018;102(6):900-931. doi:10.1097/tp.0000000000002191
- Ljungman P, de la Camara R, Robin C, et al. Guidelines for the management of cytomegalovirus infection in patients with haematological malignancies and after stem cell transplantation from the 2017 European Conference on Infections in Leukaemia (ECIL 7). Lancet Infect Dis. 2019;19(8):e260-e272. doi:10.1016/s1473-3099(19)30107-0
Content reviewed 10/2024