A cross-species view on viruses

Abstract

We describe the creative ways that virologists are leveraging experimental cross-species infections to study the interactions between viruses and hosts. While viruses are usually well adapted to their hosts, cross-species approaches involve pairing viruses with species that they do not naturally infect. These cross-species infections pit viruses against animals, cell lines, or even single genes from foreign species. We highlight examples where cross-species infections have yielded insights into mechanisms of host innate immunity, viral countermeasures, and the evolutionary interplay between viruses and hosts.

Figure 1. A cross-species view on viruses and hosts

Different types of virus-host dynamics are illustrated. The hypothetical phylogenetic trees depict class-specific genetic divergence of viruses (left) and species-specific genetic divergence of hosts (right). Not shown are additional genetic differences that exist within host and viral populations. All of these genetic differences have the potential to contribute to viral host range, which may be broad or narrow (colored triangles), and may make some viruses more likely to evolve to expand their host range (dotted line). This dynamic interplay between hosts and viruses is difficult to recapitulate in laboratory-based studies that employ a single viral clone infecting an isogenic host population.

Figure 2. A heterologous gene approach for identifying and characterizing viral immunity proteins

A) Observations of susceptible and resistant cell lines are common in virological research, and often these cells represent different species. In cases where resistance is conveyed by a dominant genetic factor, as would be the case with a cellular restriction factor or other immunity protein, the genetic basis for resistance can be uncovered by performing the illustrated screen. A cDNA library prepared from the resistant cell line is introduced into the susceptible cell line. The resulting cells are screened for a cDNA clone that conveys resistance. This scheme was used to identify the HIV restriction factor, TRIM5α [5]. B) Once cellular immunity proteins have been identified, heterologous gene studies can also be used to finely map the genetic determinants of viral recognition. In this case, multiple orthologs of the gene of interest (here, “gene X”) from related species will be required. These orthologous genes are introduced into a common cell background, and these cells are then tested for susceptibility or resistance to the virus of interest. Phenotypic differences can be compared to the genotypes of each ortholog as shown on the top right, where black tick marks indicate mutational differences compared to the top blue ortholog of species 1. By comparing unique mutations in the resistant (red) versus susceptible (blue and green) orthologs, the genetic determinants of viral detection can be identified (orange arrows). Of these, the best candidate protein regions or residues (dark orange arrows) will be those with signatures of positive selection over the evolution of these species (bottom right, positions under positive selection indicated with asterisks). This scheme was used to identify the region of TRIM5α that conveys HIV/SIV recognition [6].

Figure 3. Cross-species infections at the level of organisms, cells, and genes

A) Cross-species infections in nature form the basis for the emergence of new diseases. Experimental cross-species infections are commonly used in the laboratory for viral attenuation and evolution studies, and sometimes out of necessity. For instance, most research on the human hepatitis C virus was historically performed in chimpanzees, because this virus was not easily studied in tissue culture. B) Sometimes cell lines from heterologous species are used in tissue culture-based virology experiments. In cases where incompatibility is observed between a virus and a cell line of a heterologous species, this presents an opportunity to identify cellular barriers to infection in a genetically tractable system (see Figure 2). C) It is becoming more common to express single genes from one species in cell lines derived from a second species. This allows one to study the significance of genetic divergence at a single host locus with regards to viral replication. Also, in such systems viral evolution experiments elucidate how a virus can escape specific cellular blocks.

Figure 4. The process of virus host-switching

New diseases arise when existing viruses acquire novel hosts. This diagram illustrates the steps by which a virus is transmitted from its original host to a new host species. While all organisms are continuously exposed to the viruses of other species, infection resulting in virus replication and potentially illness (step 1) is thought to be a relatively rare event. Rarer still will be infections that are successful enough to transmit between individuals in the new host species (step 2). Of these, only some will progress to the point of epidemic or pandemic spread through the new host species (step 3). In theory, each of these steps may or may not require the acquisition of novel mutations in the viral genome, although existing evidence suggests that additional mutations usually do accumulate in viral genomes as viruses become more and more adapted to a particular host. Virus mutations can be acquired through point mutation, insertion, deletion, recombination, or reassortment. The acquisition of combinations of mutations may be required for viruses to advance through this process. Figure adapted in part from [55].