Based on the available phylogeny of HCV sequences, HCV can be classified into at least 6 major genotypes and more than 30 genotypic subtypes. Moreover, even in patients infected with a single genotype of HCV, HCV exists in vivo as a group of variants with sequence differences between them of up to 4-8%, called quasispecies. Probably due to the lack of protective immunity, overlapping infections with different HCV strains are often seen in patients with CHC, especially in patients at very high risk of infection, such as intravenous drug addicts, hemodialysis patients and patients who have received multiple blood transfusions in the era before HCV screening was introduced to blood donors. Multiple genotypes of HCV infection have important clinicopathological implications. There are conflicting views on the finding of simultaneous infection with multiple genetic subtypes/genotypes in an established individual. Roughly two scenarios exist that lead to infection with more than one genotype: patients already infected with a single genotype are overlapping with an additional genotype of virus or are co-infected with multiple genotypes of virus. The results of studies on the frequency and clinical significance of co-infection are conflicting and may be due to problems in detecting HCV genotypes and subtypes themselves. Applied serologic methods have shown that patients infected with a single HCV genotype may all have experienced transient or insidious overlapping infections with another HCV genotype. The most commonly used genotyping method nowadays is the linear probe technique for detecting alterations in the untranslated region at the 5′ end (5′-UTR). Applying this method, multiple HCV genotypes are detected in 10.8% of those infected with a single HCV genotype and in 5% of those with mixed HCV/HIV infection. In the latter group of patients, multiple HCV genotype infection was associated with rapid HIV progression. However, it is worth noting that genotyping methods targeting the 5′-UTR may not be the best approach for detecting multiple HCV genotype infections. A common error in traditional 5′-UTR-based genotyping methods lies in distinguishing between 1α and 1b subtypes, and approximately 20% of 1α genotypes may be incorrectly classified as 1b subtypes. Since these two genotypes differ by only 1 nucleotide, more precise typing methods need to be applied to ensure the detection of multiple genotypic infections in different viral strains. Also, it is of concern that multiple genotypic HCV infections may be due to the fact that different genotypic viruses may be present in different viral storage organs. The widespread presence of the HCV genome in non-hepatic storage organs has been reported, and certain evidence supports the hypothesis that different viral strains may acquire specific hepatic tropism when compared to non-hepatic storage organs. However, this issue is still controversial and may be due to different methods of detecting HCV genotypes. To date, the clinical significance of multiple genotype infections is unclear, and the clinical validations that have been concluded so far have excluded such patients, making it difficult to evaluate the impact of multiple genotype infections on treatment response. Liver transplantation between donors and recipients infected with different genotypes of HCV provides a very useful model for studying host-virus and virus-virus interactions, although immunosuppressive therapy for anti-rejection may affect the nature of the interactions. Several groups of studies have suggested that one viral strain commonly predominates in patients with multiple infections. A French study investigated 119 cases of untreated chronic HCV infection. Ribosomal binding site sequences of HCV RNA were amplified and single strand conformation polymorphism (SSCP), linear probe techniques and clonal sequencing were applied to compare sequence differences in plasma and peripheral blood mononuclear cells (PBMC). Differences in SSCP patterns between plasma and PBMC were found in 54 (48%) of the 113 evaluable patients. 24% of patients were infected with both genotypes or genotypes and were detectable only in PBMC (n=25) or in plasma (n=2). differences in compartmentalization (a compartment is a non-morphological concept consisting of relatively independent cell populations) were more frequent in drugged patients and less frequent in the plasma of genotype 1 HCV-infected patients. Patients with mixed infection with two or more HCV strains appear to have a more durable response to pegylated interferon/ribavirin therapy. In contrast, in a large study from Alaska, USA, no compartmentalized differences were found in HCV-infected patients. Most of the mixed genotype and switch genotype infection patterns identified by 5′-UTR analysis methods could not be repeatedly confirmed by heterologous double stranded swimming analysis (HDA) methods. The technical issue of the optimal detection process must be addressed before evaluating the clinical significance of multiplex genotype HCV infection. Some studies have shown that the presence of multiple genotypes has important implications for drug selection and regimen, but this has not been widely accepted. However, it is worth noting that in clinical practice, the predominance of one viral genotype often allows only one genotype to be detected, but it should be prudent to use the results of the most recently detected genotype to determine the treatment cycle, as infection (or reactivation) with other genotypes of virus may result in changes in the dominant genotype over time. In patients who relapse after treatment, clinicians are advised to repeat genotypic testing to determine whether this activation is caused by the predominant strain of virus prior to treatment. In summary, there is an impact on the efficacy of antiviral therapy (IFN+RBV) in special populations of patients with hepatitis C (e.g., patients with hepatitis C combined with pregnancy, diabetes, renal disease, renal transplantation, psychiatric disorders, abnormal thyroid function, HIV, aplastic anemia, and patients with childhood hepatitis C, hepatitis C cirrhosis, and multiple genotype HCV infection), as well as adverse effects of IFN and RBV affect special populations with their own underlying diseases. Therefore, when administering antiviral therapy, specific problems should be analyzed and antiviral treatment strategies should be adopted carefully and rationally. It is worth noting that recent clinical studies have found that DAAs have better efficacy in antiviral therapy for special populations with CHC (e.g., CHC combined with renal disease) with fewer adverse effects, which provides more options for antiviral therapy for special populations with CHC, but multi-center, large sample clinical studies are still needed.