Periodic Reporting for period 1 - GIVIREVOL (Host range and genome adaptation of giant viruses)
Periodo di rendicontazione: 2021-04-01 al 2023-03-31
Viruses infect organisms across all domains of life. As human pathogens they are a major public health concern. In the environment they shape microbial communities and affect ecosystem functioning and biogeochemical cycles. For more than a century, viruses were considered tiny particles, fully dependent on their host cells to replicate. The recent discovery of giant viruses, containing unusually large genomes, challenged this assumption and blurred the sharp division between viruses and cellular life. Translation is what separates viruses from cells, as in general viruses lack translation-related genes and thus depend on the hosts’ translation system. However, many of the giant virus genomes encode a high number of translation-related genes, indicating that they are presumably more independent –in terms of translation– as compared to other viruses. This also indicates that giant viruses potentially infect and replicate in a broad range of hosts. Nonetheless, for most of the giant viruses, the precise host range and natural host species remain to be investigated.
In this project we investigate the host range and genome adaptation of giant viruses by combining in silico and wet-lab strategies. The project is based on the idea that, besides the number of translation-related genes, codon usage is a principal factor in the adaptation of viruses to their hosts, where well-adapted codon usage provides for superior viral fitness. Under this assumption this project has four main objectives: (i) examine whether giant virus codon usage preferences are evolutionary conserved, (ii) assess whether we can computationally predict giant virus host range, (iii) evaluate the in-silico predictions with laboratory experiments, and (iv) investigate the rate of giant virus genome adaptation through experimental evolution.
So far, the results of this project suggest that the number of translation related genes and codon usage preferences alone are not an accurate predictor for giant virus host range nor the rate of genome adaptation. The experimental data that we already have and that we are currently generating will aid us in defining the additional factors that we need to consider to be able to make more accurate predictions. By investigating the evolutionary relationships between giant viruses and their hosts in the context of codon usage preferences, we contribute to a better understanding of the factors determining host range and the evolutionary processes shaping giant virus genomes. Disentangling the connection between genomic content and host range will provide important knowledge in virology, evolutionary biology, genomics, and virus-host interactions.
In this project we investigate the host range and genome adaptation of giant viruses by combining in silico and wet-lab strategies. The project is based on the idea that, besides the number of translation-related genes, codon usage is a principal factor in the adaptation of viruses to their hosts, where well-adapted codon usage provides for superior viral fitness. Under this assumption this project has four main objectives: (i) examine whether giant virus codon usage preferences are evolutionary conserved, (ii) assess whether we can computationally predict giant virus host range, (iii) evaluate the in-silico predictions with laboratory experiments, and (iv) investigate the rate of giant virus genome adaptation through experimental evolution.
So far, the results of this project suggest that the number of translation related genes and codon usage preferences alone are not an accurate predictor for giant virus host range nor the rate of genome adaptation. The experimental data that we already have and that we are currently generating will aid us in defining the additional factors that we need to consider to be able to make more accurate predictions. By investigating the evolutionary relationships between giant viruses and their hosts in the context of codon usage preferences, we contribute to a better understanding of the factors determining host range and the evolutionary processes shaping giant virus genomes. Disentangling the connection between genomic content and host range will provide important knowledge in virology, evolutionary biology, genomics, and virus-host interactions.
Giant viruses infect protists. To be able to calculate codon usage preferences, high quality genomes are essential. The availability of these in the public databases is limited to very few protist species. We therefore sequenced six selected protists to subsequently generate high quality genome assemblies, that were contained in a small number of fragments with high completeness scores. The codon usage patterns of these protists show to be highly distinct at the genus level. When comparing giant virus genomes, we found that they also have markedly different codon usage patterns at both the family and genus levels. We then performed direct comparisons of the codon usage preferences of giant viruses and hosts. This analysis gave surprising results as not all giant viruses have close codon usage preferences, and some even opposite, to their best-known hosts. Interestingly, this analysis also revealed a potential novel host in which certain giant viruses might perform better. Our experimental results suggest that the cultivation conditions for obtaining high viral fitness in alternative hosts are closer to those of a natural environment. Nonetheless, the results of this study also suggest that tRNA content and codon usage preferences alone are not an accurate predictor of giant virus host range. The experimental data that we already have and that we are currently generating will aid us in defining the additional factors to be considered for making more accurate predictions at the genomic level.
To better understand the factors that drive the evolution of large viral genomes with a wide range of codon usage preferences, we used experimental evolution. For this we used three different giant viruses and three different hosts. We performed weekly passages of these viruses in their hosts for a total duration of half a year. For Tupanvirus, that has a wide host range, we included additional setups with (i) one host-switch at half of the experiment, (ii) a monthly host switch, (iii) and a weekly host switch. For the three viruses, we observed three different outcomes: (i) a decrease in cytopathic effects (CPE) and viral copy number, (ii) no change in CPE and viral copy number, and (iii) an increase in CPE and viral copy number. Although we have not completely finalized analyzing the genome sequences of the ancestral and evolved viruses, the timing of the increase in the number of mutations correlates well with the observed increase in CPE as well as viral copy number. In line with our initial hypothesis, frequent host switches generate viral variants that are able to perform well in different host species. However, lower viral replication success appears to be an important trade-off for maintaining a mixed viral population that works well in multiple hosts.
To be able to answer our original question on whether codon usage preferences define the rate of genome adaptation of giant viruses, we need to finalize the analysis of the viral genome sequencing along the evolution experiment, and potentially perform additional experiments. Like many other projects, this project was affected by the COVID-19 pandemic. Therefore, we were unfortunately not able disseminate the results at international conferences or at events targeting the general public within the project period. We recently presented our results for the first time at two international conferences: Viruses of Microbes and the IX European Congress of Protistology & Annual Congress of the International Society of Protistologists joint meeting.
To better understand the factors that drive the evolution of large viral genomes with a wide range of codon usage preferences, we used experimental evolution. For this we used three different giant viruses and three different hosts. We performed weekly passages of these viruses in their hosts for a total duration of half a year. For Tupanvirus, that has a wide host range, we included additional setups with (i) one host-switch at half of the experiment, (ii) a monthly host switch, (iii) and a weekly host switch. For the three viruses, we observed three different outcomes: (i) a decrease in cytopathic effects (CPE) and viral copy number, (ii) no change in CPE and viral copy number, and (iii) an increase in CPE and viral copy number. Although we have not completely finalized analyzing the genome sequences of the ancestral and evolved viruses, the timing of the increase in the number of mutations correlates well with the observed increase in CPE as well as viral copy number. In line with our initial hypothesis, frequent host switches generate viral variants that are able to perform well in different host species. However, lower viral replication success appears to be an important trade-off for maintaining a mixed viral population that works well in multiple hosts.
To be able to answer our original question on whether codon usage preferences define the rate of genome adaptation of giant viruses, we need to finalize the analysis of the viral genome sequencing along the evolution experiment, and potentially perform additional experiments. Like many other projects, this project was affected by the COVID-19 pandemic. Therefore, we were unfortunately not able disseminate the results at international conferences or at events targeting the general public within the project period. We recently presented our results for the first time at two international conferences: Viruses of Microbes and the IX European Congress of Protistology & Annual Congress of the International Society of Protistologists joint meeting.
The 7-month early termination of the MSCA grant is the main reason why the project is not completely finalized. The reason for early termination is that the researcher of the MSCA grant obtained an ERC StG grant and was able to secure an assistant professor position. Therefore, her work on giant viruses will not terminate here, and ongoing work of this project will be finalised.
A significant number of protists are the causative agents of human disease, including the almost always fatal primary amebic meningoencephalitis, eye infections, malaria, sleeping sickness, and waterborne gastroenteritis. Better understanding protist evolution as well as giant virus host range and genome adaptation will aid us to design studies in which we can use giant viruses as biocontrol agents, where giant viruses can be used to lyse the cells of these pathogenic protists. This can either serve as giant virus therapy to cure protist infected patients or to decrease the chance of infection by aiming to remove pathogenic protists from their natural environment.
A significant number of protists are the causative agents of human disease, including the almost always fatal primary amebic meningoencephalitis, eye infections, malaria, sleeping sickness, and waterborne gastroenteritis. Better understanding protist evolution as well as giant virus host range and genome adaptation will aid us to design studies in which we can use giant viruses as biocontrol agents, where giant viruses can be used to lyse the cells of these pathogenic protists. This can either serve as giant virus therapy to cure protist infected patients or to decrease the chance of infection by aiming to remove pathogenic protists from their natural environment.