Probing the evolution of Influenza at high resolution

From the Bloom Lab, Basic Sciences Division

Viruses by definition are obligate parasites: they require a host organism to complete their life cycle and replicate their genomes.  virus like influenza can quickly mutate into genetically diverse populations so much that a new flu vaccine is needed each year. The Bloom Laboratory in the Basic Sciences Division studies the evolutionary dynamics of viral populations, with a special focus on influenza.

The lab uses a combination of computational and experimental approaches to study how viruses such as influenza evolve in the face of different selection pressures, and to understand the public-health consequences of viral genetic variation. In previous work, they showed that two different influenza viruses can grow better when grown together than individually in a laboratory setting. Since the mutation responsible for cooperation is often observed when human samples of influenza virus are grown in the lab before sequencing, it was unclear whether the mutation also exists in human infections or is exclusively the result of lab passage. A follow-up study from the lab using unpassaged human samples found no evidence of such cooperation, suggesting that the cooperation arises primarily under laboratory conditions. Former graduate student in the Bloom lab, Katherine Xue, led both studies.

Influenza viruses evolve rapidly from year to year across the globe, with immense consequences for public health. This rapid evolution at the global scale begins with mutations that arise as viruses replicate within infected individuals. As such, the virus evolves within and between hosts. Noting that the same within-host mutations are only rarely observed in different individuals, and mutations that reach detectable frequencies at the global scale are not notably more common than other mutations within hosts, Xue and Bloom wondered how within-host mutations fare at the between-host scale. A better understanding of the within- and between host mutation dynamics of influenza can help elucidate the mechanisms driving the global evolution of influenza virus.

Schematic shows how viral mutations that arise within hosts can transmit from person to person and eventually contribute to global viral evolution.
Schematic shows how viral mutations that arise within hosts can transmit from person to person and eventually contribute to global viral evolution. Image Courtesy of Katherine Xue.

In a new study, published in a recent issue of Virus Evolution, Xue and Bloom compared the genetic variation of H3N2 influenza within and between hosts to link viral evolutionary dynamics across scales by analyzing genomic data from three deep-sequencing datasets. “We systematically compared genetic diversity within hosts and on a global evolutionary scale using several large sequencing datasets,” said Xue. “This work would not have been possible without the original authors' dedication to making their data publicly available,” she added.

The authors calculated the rates of evolution within and between hosts to determine how selection and genetic drift shape viral evolution. “Powerful new sequencing methods have made it possible for us to track viral genetic diversity within clinical influenza infections, but it hasn't been clear how that genetic diversity contributes to flu's rapid global evolution,” Xue explained.

Evolution can be explained at the most fundamental level as a process driven by two major opposing forces; variation and competition. For a system to evolve, it must undergo change. In biological systems, mutations are the source of variation. A mutation can be as simple as a change in a single nucleotide, or a point mutation, such that a sequence of bases that encoded a particular amino acid may now encode another. The prevailing conditions are the source of selective pressures and therefore competition. As such some variant offspring may, by chance, be better suited for survival under certain prevailing conditions than their biological parent. 

Due to the redundancy of the genetic code, a change in the DNA sequence may not lead to a change in the protein sequence. This kind of mutation is known as a synonymous mutation. In contrast, nonsynonymous mutations result from changes in the DNA code that alter the protein sequence. Xue and Bloom compared the prevalence of synonymous vs. nonsynonymous mutations between and within hosts. They found that synonymous mutations accumulate at similar rates within and between hosts. This was expected for near neutral non-disruptive genetic changes. “There is some debate over whether all synonymous mutations are neutral for RNA viruses, since synonymous mutations can still affect RNA structure”, explained Xue. On the other hand, nonsynonymous mutations were depleted between hosts compared to within hosts. These observations suggest that many nonsynonymous mutations that reach detectable frequencies within hosts are later purged as these variants circulate at the global scale. Interestingly, nonsynonymous mutations that occurred at antigenic sites, i.e, sites that are potentially susceptible to the host immune system, accumulated more rapidly between hosts than they did within hosts. 

Xue reflects on their findings: “On a global scale, flu quickly acquires antigenic mutations that affect how it's recognized by the immune system, but these mutations don't seem to be enriched within typical flu infections.” So, when is natural selection taking place? She wonders. Xue suspects that viruses that carry antigenic mutations may be favored in transmission, since they might be more likely to start new infections in hosts who have immunity against existing strains of flu. “Other groups are tracking how flu transmits within households, and I'm excited to see if they see this natural selection in action.” 

In summary, the authors were able to use a deep sequencing approach to probe influenza evolution at high resolution. They concluded that purifying selection against deleterious mutations and selection for antigenic change, potentially useful for immune evasion, are the main forces that act on within-host variants of influenza virus as they transmit and circulate between hosts.

Xue KS, Bloom JD. 2020. Linking influenza virus evolution within and between human hosts. Virus Evolution. doi: 10.1093/ve/veaa010

This work was supported by a Hertz Foundation Myhrvold Family Fellowship, the National Institutes of Health and the Howard Hughes Medical Institute.