Virus that infects pigs in China is found in human patient in Brazil

Discovered in the feces of a child with gastroenteritis, the virus was sequenced, but the study was unable to prove it was brought from China to Brazil or even that it caused the disease.

By José Tadeu Arantes  |  Agência FAPESP – A virus that infects the large pig roundworm Ascaris suum found in the stomachs of pigs in China has been identified in Brazil. The virus was discovered in the feces of a two-year-old female child with acute gastroenteritis and described by researchers from various institutions in Brazil and the United States. An article on the discovery has been published in the journal Virus Genes.

The research findings do not prove that the virus in question – named WLPRV/human/BRA/TO-34/201 – was brought from China to Brazil by someone who ate infected pork or that this virus caused the child’s gastroenteritis.

“When we analyzed a fecal sample from a child with diarrhea in which the pathogenic agent hadn’t been identified, we discovered a virus that had been sequenced only once before, in China. However, it’s too soon to say whether the virus was brought from China to Brazil. Our description was published only recently, and it’s highly likely that the virus will be found elsewhere, so that it will be possible to establish a propagation route. Meanwhile, we don’t know if the virus came from China. All we have are two similar genome sequences,” Ester Cerdeira Sabino, who led the study, told Agência FAPESP. Sabino heads the University of São Paulo’s Institute of Tropical Medicine (IMT-USP) and is a professor in the Department of Infectious Diseases at the same university’s Medical School (FM-USP).

The research was supported by FAPESP via the projects “Investigating the evolution of animal rotavirus strains infecting humans” and “Viral metagenomics to track, explain and predict the transmission and spatiotemporal spread of dengue, chikungunya and Zika viruses in Brazil”.

According to Antonio Charlys da Costa, a coauthor of the study, there are large numbers of active viruses in the world that have not yet been described.

“In light of the number of eukaryotes on Earth, it’s estimated that some 87 million viruses have yet to be described. The International Committee on Taxonomy of Viruses (ICTV) currently recognizes 4,404 species of virus in eukaryotes, so more than 99.99% of the estimated total number of viruses remain unknown or unclassified. Although it’s an estimate, we’re confident about the number given the considerable viral diversity found in samples sequenced to date,” said Costa, a postdoctoral researcher at IMT-USP with a scholarship from FAPESP.

The aims of Costa’s research include identifying and sequencing viruses that have not yet been fully described. An epidemiological study covering the distribution of viruses, the frequency of their occurrence in the population, the associated diseases, etc., will follow.

“We analyzed samples of human feces taken during the occurrence of gastroenteritis caused by unidentified pathogens,” Sabino explained. “We found many pathogens to be present, and we’re now describing these findings. The methodology used is viral metagenomics, which can identify any infectious agent. That doesn’t mean the pathogens identified were responsible for gastroenteritis, but the analysis enables us to indicate initial correlations for future research.”

Because viruses are the focus of this study, it has to be conducted in several stages. The first is to filter each sample on the micrometric scale to block and discard cells, parasites, fungi and bacteria.

Nevertheless, pieces of free DNA and RNA manage to pass through the filter and must be eliminated. This elimination is done with nucleases, enzymes that digest DNA and RNA. The virus’s nucleic acid (DNA or RNA) is not digested, since it is protected inside the viral capsid. Only free nucleic acid is digested. Next, the viral particle is submitted to cell lysis (destruction or dissolution of the cell by rupture of the plasma membrane). Finally, the genetic material is released and sequenced.

“This produces billions of small sequences, which must be aligned in an attempt to reconstruct the viral genomes,” Sabino said. “Once the larger sequences are obtained, the next step is to use bioinformatics to look for similar sequences in the database. This usually requires a great deal of processing time and computer power. We sequence all possible viruses in the samples. We then try to see whether the sequences obtained match those of known viruses.”

New viral agents

According to the authors of the study, rotaviruses continue to be the main viral agents of diarrhea in Brazil, but it is possible that other viral agents may be causing gastroenteritis as vaccination takes effect in preventing infection by rotaviruses.

According to Sabino, nonpathogenic viruses may produce a pathogenic virus via recombination, for example. In recombination, a piece of one virus is spliced to a piece of a second virus to form a third.

“The etiologies of many human diseases are unknown. For example, the cause of diarrhea is unknown in more than 50% of cases. Many agents have yet to be discovered. Previously, we were unable to look for these agents because sequencing was very difficult and costly. It’s easy with the next-generation sequencers available now, but there’s still a considerable distance between finding an agent and proving it causes a disease,” Sabino said.

The other coauthors of the article are Adriana Luchs, Elcio de Souza Leal, Shirley Vasconcelos Komninakis, Flavio Augusto de Padua Milagres, Rafael Brustulin, Maria da Aparecida Rodrigues Teles, Danielle Elise Gill, Xutao Deng and Eric Delwart.

The article “Wuhan large pig roundworm virus identified in human feces in Brazil” (doi: https://doi.org/10.1007/s11262-018-1557-0) can be retrieved from link.springer.com/article/10.1007%2Fs11262-018-1557-0.