Molecular Typing of Enteroviruses: Current Status and Future Prospects

Abstract

Molecular techniques for isolation and characterization of viruses from clinical and environmental samples are routinely used in virological laboratories. Identification and genotyping of enteroviruses through molecular typing is crucial since the enteroviruses are commonly present within our environment and are also associated with a number of diseases. Enteroviruses are spread through the faeco-oral route and the prevalence of these viruses in the environment is possibly a route of viral spread in the community. This study has explored the presence of different enteroviruses among the environmental as well as clinical samples from Islamabad and Rawalpindi (the twin cities), and Lahore. The samples included sewage, drinking water and blood, all of which were processed and analysed through RT-PCR based detection assays to determine the presence of virus in our community. A total of 80 sewage samples were collected from the twin cities and 10 from Lahore. Among the 80 samples from the twin cities, 45 were positive for NPEV (56.2%), 4 samples contained enterovirus (6.2%) and 1 was positive for HAV (1.2%). On the contrary, no NPEV was detected among the sewage samples from Lahore, 4 samples were positive for enterovirus (40%) and 1 was positive for HAV (10%). In the case of drinking water, 74 samples were obtained from the twin cities and 15 from Lahore. Out of the 74 samples, 2 contained NPEV (2.7%), 2 were positive for enterovirus (2.7%) and 1 sample was found to be positive for HAV (1.35%). The 15 drinking water samples from Lahore were tested and 2 of these samples were found positive for enterovirus (13.3%). Clinical samples were collected only from the twin cities and revealed 15 cases of HAV (23% out of the total 65 blood samples) all of which were associated with infection in children and predominantly in the male gender. Among the 65 samples, 28 xiii were positive for HEV infection (43%), all found among the female. Out of the 28 HEV positive females 17 (60.7%) were in the third trimester of their pregnancy. The genotyping of HEV revealed the presence of HEV1 in our study population. No other genotype was found during the course of this study. The findings of the HEV genotyping results and their dominant infections among the pregnant females is in line with evidences from other studies which have reported HEV1 to be the most predominant genotype associated with complications during the later stages of pregnancy. These findings indicate the need of wider screening and analysis within the community to identify the true disease burden associated with HEV infections. Sequencing and phylogenetic analysis of the strains isolated in this study showed close molecular relation of the NPEV strain with poliovirus strains previously reported from China. The HAV strain was in close relation with that of strains reported from India and the HEV1 strains in our study had phylogenetic relatedness with the strains reported from China and Pakistan. Overall, the sewage water from the twin cities contained high percentage of NPEV, having close phylogenetic relation with poliovirus. The clinical cases of HAV have been identified among the children and HEV has been found to be infecting the female population, with greater percentage of infections among the pregnant females. Together, the results from the environmental and the clinical samples suggest that different enteroviruses are present in Pakistan.