Over the last decade, discoveries of extremely large and complex viruses have challenged our concepts of what viruses are and how they evolved. These giant viruses are often comparable in dimension and genome size to small bacteria, even prompting some to postulate that they should be classed as a new kind of life form. Now, a novel giant virus named Samba (SMBV) has been found within amoebae of the Negro River in the Amazonian basin. Jônatas Santos Abrahão from the Federal University of Minas Gerais, Brazil, Bernard La Scola, from Aix-Marseille University, France, and colleagues, who discovered the virus, conducted a phylogenetic analysis of SMBV, the results of which are presented in their recent study in Virology Journal.
Their analysis showed that SMBV is most closely affiliated with Acanthamoeba polyphaga mimivirus (APMV), and falls within group A of the putative order Megavirales. SMBV virus has an average particle diameter of 574 nm and a genome containing 938 ORFs (that is, putative protein-coding genes). This contrasts with APMV, which is around 750 nm in diameter and has 911 predicted ORFs. Indeed, SMBV has one of the largest genomes of any group A Mimivirus known to date. They found that, although around 91 percent of SMBV’s ORFs are shared with APMV, and are largely in the same genome locus, many of SMBV’s ORFs are inverted when compared to APMV. SMBV also shares many ORFs that are known only from the Mimiviridae family, including those that putatively encode proteins with roles in protein translation or DNA repair.
Analysing the SMBV-infected amoeba further using electron microscopy revealed the presence of a small, parasitic virus infecting SMBV’s viral factories. This virophage, named Rio Negro (RNV), shared high gene identity with Sputnik virus, the virophage associated with a strain of APMV. SMBV particles in those amoebas also containing RNV, were atypical in appearance, some presented with defective capsids (protein coats) wrapped around small particles, whilst others were lemon-shaped and had defective spiral capsids. RNV also caused decreased infectivity of SMBV – and, interestingly, of APMV.
This study expands our knowledge of viral distribution, diversity and evolution, and presents the first record of a giant virus in the Amazon rainforest – an environment already known for its striking diversity of flora and fauna, but with a poorly understood microbial ecology. Genome sequencing of SMBV sheds light on the relationships between different giant viruses, and also adds further data to the evolving story of why giant viruses appear to contain genes relating to translation when they rely on their host’s machinery for this process.