Researchers from Vall d’Hebron Research Institute (VHIR) have developed a new deep sequencing methodology that accurately classifies the 7 confirmed genotypes of the hepatitis C (HCV) virus, and the different subtypes. The new system also allows, for the first time, to identify infections with more than one subtype of the virus (mixed infections), the variability of the virus and possible resistance mutations.

“We are going one step further in personalized medicine, because thanks to this new system we can decide which is the treatment with greater chances of success in each patient”, reports Dr. Rafael Estaban Mur, head of the Hepatic Diseases group at VHIR and responsible of the Department of Internal Medicine and Hepatology at Vall d’Hebron University Hospital.

The two commercial available genotyping methods can only identify the main genotypes and two out of the 67 subtypes of the virus. As the efficacy of new treatments depends on the subtype, physicians do not have tools to choose the most efficient treatment.

The study, published in the Journal of Clinical Microbiology, is a collaboration between all the members of the Networked Biomedical Research Center for Hepatic and Digestive Diseases (CIBERehd), Roche and ABL. It is funded with the CDTI MINECO IDI 20110115.

Comparison with the current technologies

The scientific community has achieved major steps in the study of hepatitis C, especially in the development of new inhibitors, such as sofosbuvir and simeprevir. The combination of these new drugs has reached cure rates up to the 90 per cent in controlled clinical trials, without using the classic treatment of interferon (which causes many side effects such as depression and fever).

However, the response to the new antiviral inhibitors is different in each genotype and subtype of the HCV virus. For that reason, Dr. Esteban Mur alerts that “if physicians are not able to classify the virus properly and detect mixed infections, patients will be inefficiently treated and the therapeutic failure rate will be higher”.

To carry out this study, researchers compared the results of the new technology, using the Roche Diagnostics’ 454 deep sequencing platform, with two common technologies available in many diagnostic laboratories (Versant HCV genotype 2.0 and Real-time HCV Genotype II).

In order to compare the results of each technology, they analyzed 82 samples from patients infected with genotype 1 hepatitis C, which is the most common genotype and the most difficult one to treat. In this case, the two commercial available genotyping methods failed in 16% of the patients, whereas the new system successfully indentified all the subtypes of genotype 1 HCV, even a mixed infection.

Secondly, they analyzed 32 samples from different genotypes and subtypes of HCV-infected patients. Whereas both commercial systems were unable to identify the HCV subtype of the majority of these samples, the new methodology identified all the genotypes, subtypes and mixed infections.

In all these cases, the identification of the genotype and subtype is essential. For instance, patients with the genotype 5 can be cured after the administration of the standard treatment with interferon, however, those infected with the genotype 4 HCV virus require more aggressive treatments, adding specific inhibitors.

With the new system, Dr. Esteban Mur expects that “physicians will select the most efficient treatment, optimizing the resources available”. Besides the benefits of the new methodology for the public health system, Dr. Joan Ignasi Esteban, coordinator of the clinical part of the study, highlights that “every time that a treatment fails, the range of therapeutic options for the patient decreases, due to the onset of resistance mutations”. In this regard, the new methodology is also able to determine if the patient has developed mutations and which is the variability of the virus or, in other words, how it has evolved since the infection.

Researchers are currently working on the automation of this technology, in order to obtain results in less than 7 days.