The metagenomic approach and causality in virology

Castrignano, Silvana Beres; Nagasse-Sugahara, Teresa Keico

h chronic active infections, may be devoid of pathogenicity (they can be components of the normal human microflora), and can be found in the central nervous system, blood, and several other body fluids. 15 The viruses can also be detected by metagenomic approaches in chronic diseases; however, the causal association can be even more difficult, 27 as can be observed in a large amount of data on the Merkel cell polyomavirus (MCV). This virus was identified in human Merkel cell carcinoma (MCC) samples, 8 and the investigation of the causal association between MCV and the disease began with the investigation of 10 MCC samples from different patients; of these, the viral genome was detected in eight samples. In 75.0% of these samples, viral DNA was integrated into the tumor genome in a clonal pattern, suggesting that the infection and integration process preceded the clonal expansion of the tumor cells. Control tissue samples tested positive for the MCV genome in expressively lower percentage, and there was evidence that the number of copies of the viral genome in these positive samples was lower than that in the MCC samples. 8 A high incidence of MCV among MCC cases has been confirmed in several countries, except in Australia. 21 It is known that human infection with MCV occurs early, considering that the seroprevalence is 50.0% among individuals aged below 15 years. 21 Studies with RNA interference and on the genetic changes of the viral genome integrated into MCC cells have indicated that MCV may contribute to the onset of MCC. 21 When a new virus is detected in the blood of a patient with a disease that is probably infectious, only the identification of a new agent is also not proof of its causal relationship with the disease, as can be exemplified by the discovery of a new bunyavirus in China, which was named Henan fever (HNF) virus 30 or severe fever with thrombocytopenia syndrome virus (SFTSV). 31 This virus was detected almost simultaneously by two research groups using a metagenomic approach in serum 30 and blood leucocytes; 31 samples were obtained during the acute phase of the disease, which is characterized by fever, thrombocytopenia, and leukopenia. An extensive epidemiological, clinical, and laboratory investigation was conducted along with this discovery. In the laboratory, the evidence for this association included viral isolation, followed by visualization of the viral particles by electron microscopy, detection of the viral genome, and positive serology in patient samples. 30, 31 The investigation by both research groups also included analysis of the control groups. When discussing the causal association between the HNF virus and the severe fever with thrombocytopenia syndrome, both the groups concluded that, although they could not completely fulfill Koch's postulates, there was a strong evidence indicative of this association. 30, 31 The fact that independent researchers confirmed these results 25, 30, 31 corroborates this potential association, as stated in Lipkin's guidelines. 13