Raw sewage provides a perfect ecosystem for studying the diversity of viral populations that remain uncharacterized. This is one of the principal conclusions of a study published in the journal mBio by a team comprising experts from the UB’s Laboratory of Water and Food Viral Pollution, Washington University and the University of Pittsburgh, under the direction of James Pipas (Department of Biological Sciences, University of Pittsburgh). The pioneering study, which applies metagenomics to the analysis of viral populations present in sewage, reveals that the viral universe is far larger than previously thought.
Some 3000 different viruses are currently recognized, but it is believed that this represents only a small proportion of the real number of viruses in nature. This new study analyses viral diversity through the examination of nucleic acid sequences from sewage samples from Pittsburgh (USA), Barcelona (Spain) and Addis Ababa (Ethiopia). According to the lecturer Rosina Gironès, co-author of the study and head of the Laboratory of Water and Food Viral Pollution at the University of Barcelona, “this is the greatest diversity of viral populations revealed in any research study, many of which infect humans. We have also seen that current databases are not always fully correct: you have to be extremely thorough when analysing these new sequences to make sure that homologies with known virus groups are in fact reliable.”
Metagenomics: opening new ground in virology
Metagenomics is a powerful new technique that enables scientists to study the genetic diversity of microorganisms in different environmental surroundings. The metagenomic approach, initially used to study viral diversity in oceans, arctic lakes, faecal matter and other environments, is broadening the scope of research to discover a level of viral diversity unknown to scientists. The article describes the identification of 234 known viruses belonging to 26 taxonomic families, 17 of which infect humans. However, the majority of the viral genomes detected bear little or no resemblance to known viruses.
According to the experts behind the study, the most abundant types are plant viruses and bacteriophages (which infect bacteria). “People may not be aware of the large proportion of viruses that are founds in plants,” says Rosina Gironès. “In fact, we can transmit viral plant pathogens via sewage.” The study also reveals the presence of skin-tropic viral species that can be excreted, such as the human papillomavirus 112 and the recently described human polyomavirus 6.
The paper published in mBio establish a new framework for improving our knowledge of viral diversity and the origin of emerging pathogens. The team now intends to conduct further study of the newly detected viruses and their pathogenicity and fine-tune the metagenomic approach to improve sequence analyses. “We know there are viruses that we have been unable to detect, but we will be able to identify them with the right techniques. By using the novel metagenomic approach, which is generating a substantial volume of data on specific viral genome segments, we will be able to refine results on newly detected viruses, the diversity of the families observed and their impact on human health,” explains Rosina Gironès.
Viruses: more than infectious agents
The Laboratory on Water and Food Viral Pollutants, coordinated by Rosina Gironès, is an authority on the study of pathogens (hepatitis A and E), enteroviruses, adenoviruses, emerging human viruses, prions and various viruses indicative of faecal contamination. The projects carried out by the laboratory team have contributed to the discovery of new viruses with a bearing on human health and have reshaped the accepted paradigm of viral infection. “We have confirmed that human viruses are always present in sewage from human populations.
In other words, we excrete viruses regularly, not simply during periods of widespread infection. The concept of what viruses are has changed. We no longer consider them simply as pathogenic agents; viruses form part of the microbiome of the human body, of nature in general, and can also have positive effects on the body, as recent studies have shown. I am sure that once we have definitively identified the role of viruses in the human microbiome we will obtain a clearer picture of their effects and benefits,” concludes Gironès.
- Gantalupo, Paul G.; Calgua, Byron; Zhao, Guoyan; Hundesa, Ayalkibet; Wier, Adam D.; Katz, Josh P.; Grabe, Micahle; Hendrix, Roger W.; Gironès, Rosina; Wang, David; Pipas, James M. Raw Sewage Harbors Diverse Viral Populations. mBio, 2011, vol. 2, núm. 3, e00180-11 DOI: 10.1128/mBio.00180-11
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