Limits...
Advanced molecular surveillance of hepatitis C virus.

Rossi LM, Escobar-Gutierrez A, Rahal P - Viruses (2015)

Bottom Line: HCV exploits complex molecular mechanisms, which result in a high degree of intrahost genetic heterogeneity.Here, we review molecular aspects associated with HCV transmission, as well as the most recent technological advances used for virus and host characterization.Additionally, the cornerstone discoveries that have defined the pathway for viral characterization are presented and the importance of implementing advanced HCV molecular surveillance is highlighted.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Institute of Bioscience, Language and Exact Science, Sao Paulo State University, Sao Jose do Rio Preto, SP 15054-000, Brazil. liv.rossi@yahoo.com.

ABSTRACT
Hepatitis C virus (HCV) infection is an important public health problem worldwide. HCV exploits complex molecular mechanisms, which result in a high degree of intrahost genetic heterogeneity. This high degree of variability represents a challenge for the accurate establishment of genetic relatedness between cases and complicates the identification of sources of infection. Tracking HCV infections is crucial for the elucidation of routes of transmission in a variety of settings. Therefore, implementation of HCV advanced molecular surveillance (AMS) is essential for disease control. Accounting for virulence is also important for HCV AMS and both viral and host factors contribute to the disease outcome. Therefore, HCV AMS requires the incorporation of host factors as an integral component of the algorithms used to monitor disease occurrence. Importantly, implementation of comprehensive global databases and data mining are also needed for the proper study of the mechanisms responsible for HCV transmission. Here, we review molecular aspects associated with HCV transmission, as well as the most recent technological advances used for virus and host characterization. Additionally, the cornerstone discoveries that have defined the pathway for viral characterization are presented and the importance of implementing advanced HCV molecular surveillance is highlighted.

Show MeSH

Related in: MedlinePlus

Advanced HCV molecular surveillance. The main components required for advanced molecular surveillance of HCV are listed. Global databases containing comprehensive information concerning transmission events are used as a source of information to draw conclusions about viral spread. Advanced molecular tools and data mining analyses are required to accurately identify the nuances driving the transmission of HCV.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4379565&req=5

viruses-07-01153-f006: Advanced HCV molecular surveillance. The main components required for advanced molecular surveillance of HCV are listed. Global databases containing comprehensive information concerning transmission events are used as a source of information to draw conclusions about viral spread. Advanced molecular tools and data mining analyses are required to accurately identify the nuances driving the transmission of HCV.

Mentions: Importantly, the requirement for the establishment of a database-type of molecular surveillance network that is feasible for international surveillance networks is the standardization of the input data. Several initiatives involving international partnerships and pilot studies have been initiated for an array of pathogens including HCV [219,223,224]. Data sharing is critical for an interdisciplinary approach in order to tackle a problem [223]. The introduction of NGS in routine diagnostics is likely to further boost HCV integrative surveillance. By applying analytical tools to genomic data for HCV, public health scientists can track specific mutations that confer the ability to resist drugs or link them to transmission networks. However, the information provided by raw genomic sequences of pathogens must be integrated with knowledge about the host biology as well as societal and environmental factors in order to understand the etiology of epidemics and to anticipate their trajectories [223]. Therefore, the development of a diagnostic pipeline critically relies on database exhaustiveness that can match the rapid growth of databases prompted by NGS. A typical blast analysis of millions of sequences after de novo assembly into larger contigs against the whole NCBI database using relaxed criteria is time- and resource-consuming for diagnostics. In contrast, stringent mapping of non-assembled reads in a comprehensive database in conjunction with long sequence reads will likely improve the overall process. Thus, an HCV integrative molecular surveillance tool should ideally be web-based and include both viral and host factors as well as epidemiological data (Figure 6) [220]. In addition to international public and private sequence databases, the ideal HCV integrative database should be enriched with data obtained from ongoing molecular surveillance projects and outbreak investigations, supplemented if at all possible with sequence information from cases identified in hepatitis clinics and blood banks [117]. As a result, comprehensive analyses including human genetics, phylogenetics and data mining could be easily attained locally by researchers in the field with minimal effort at an affordable cost for local state public health laboratories (Figure 6).


Advanced molecular surveillance of hepatitis C virus.

Rossi LM, Escobar-Gutierrez A, Rahal P - Viruses (2015)

Advanced HCV molecular surveillance. The main components required for advanced molecular surveillance of HCV are listed. Global databases containing comprehensive information concerning transmission events are used as a source of information to draw conclusions about viral spread. Advanced molecular tools and data mining analyses are required to accurately identify the nuances driving the transmission of HCV.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4379565&req=5

viruses-07-01153-f006: Advanced HCV molecular surveillance. The main components required for advanced molecular surveillance of HCV are listed. Global databases containing comprehensive information concerning transmission events are used as a source of information to draw conclusions about viral spread. Advanced molecular tools and data mining analyses are required to accurately identify the nuances driving the transmission of HCV.
Mentions: Importantly, the requirement for the establishment of a database-type of molecular surveillance network that is feasible for international surveillance networks is the standardization of the input data. Several initiatives involving international partnerships and pilot studies have been initiated for an array of pathogens including HCV [219,223,224]. Data sharing is critical for an interdisciplinary approach in order to tackle a problem [223]. The introduction of NGS in routine diagnostics is likely to further boost HCV integrative surveillance. By applying analytical tools to genomic data for HCV, public health scientists can track specific mutations that confer the ability to resist drugs or link them to transmission networks. However, the information provided by raw genomic sequences of pathogens must be integrated with knowledge about the host biology as well as societal and environmental factors in order to understand the etiology of epidemics and to anticipate their trajectories [223]. Therefore, the development of a diagnostic pipeline critically relies on database exhaustiveness that can match the rapid growth of databases prompted by NGS. A typical blast analysis of millions of sequences after de novo assembly into larger contigs against the whole NCBI database using relaxed criteria is time- and resource-consuming for diagnostics. In contrast, stringent mapping of non-assembled reads in a comprehensive database in conjunction with long sequence reads will likely improve the overall process. Thus, an HCV integrative molecular surveillance tool should ideally be web-based and include both viral and host factors as well as epidemiological data (Figure 6) [220]. In addition to international public and private sequence databases, the ideal HCV integrative database should be enriched with data obtained from ongoing molecular surveillance projects and outbreak investigations, supplemented if at all possible with sequence information from cases identified in hepatitis clinics and blood banks [117]. As a result, comprehensive analyses including human genetics, phylogenetics and data mining could be easily attained locally by researchers in the field with minimal effort at an affordable cost for local state public health laboratories (Figure 6).

Bottom Line: HCV exploits complex molecular mechanisms, which result in a high degree of intrahost genetic heterogeneity.Here, we review molecular aspects associated with HCV transmission, as well as the most recent technological advances used for virus and host characterization.Additionally, the cornerstone discoveries that have defined the pathway for viral characterization are presented and the importance of implementing advanced HCV molecular surveillance is highlighted.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Institute of Bioscience, Language and Exact Science, Sao Paulo State University, Sao Jose do Rio Preto, SP 15054-000, Brazil. liv.rossi@yahoo.com.

ABSTRACT
Hepatitis C virus (HCV) infection is an important public health problem worldwide. HCV exploits complex molecular mechanisms, which result in a high degree of intrahost genetic heterogeneity. This high degree of variability represents a challenge for the accurate establishment of genetic relatedness between cases and complicates the identification of sources of infection. Tracking HCV infections is crucial for the elucidation of routes of transmission in a variety of settings. Therefore, implementation of HCV advanced molecular surveillance (AMS) is essential for disease control. Accounting for virulence is also important for HCV AMS and both viral and host factors contribute to the disease outcome. Therefore, HCV AMS requires the incorporation of host factors as an integral component of the algorithms used to monitor disease occurrence. Importantly, implementation of comprehensive global databases and data mining are also needed for the proper study of the mechanisms responsible for HCV transmission. Here, we review molecular aspects associated with HCV transmission, as well as the most recent technological advances used for virus and host characterization. Additionally, the cornerstone discoveries that have defined the pathway for viral characterization are presented and the importance of implementing advanced HCV molecular surveillance is highlighted.

Show MeSH
Related in: MedlinePlus