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Fix dms-view link and expand on dms-view caption
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huddlej committed Oct 1, 2020
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Expand Up @@ -31,7 +31,7 @@ For flu's primary surface proteins, hemagglutinin (HA) and neuraminidase (NA), s
These mutations increase a virus's fitness by allowing the virus to escape existing antibodies in a process called antigenic drift ([@fig:beneficial-and-deleterious-mutations]).
HA and NA experience fitness trade-offs, as they acquire beneficial mutations associated with antigenic drift against a background of deleterious mutations.

![HA accumulates beneficial mutations in its head domain that enable escape from antibody binding and deleterious mutations in its stalk domain that reduce its ability to infect new host cells. [Explore this figure interactively with dms-view.](https://dms-view.github.io/?markdown-url=https%3A%2F%2Fdms-view.github.io%2Fdata%2FIAV%2Flee2019mapping.md&data-url=https%3A%2F%2Fdms-view.github.io%2Fdata%2FIAV%2Fflu-dms-view.csv&condition=2009-age-53&site-metric=site-Positive+Differential+Selection&mutation-metric=mut-Positive+Differential+Selection&selected-sites=52%2C53%2C54%2C55%2C56%2C57%2C58%2C59%2C60%2C61%2C62%2C63%2C64%2C65%2C66%2C67%2C68%2C69%2C70%2C71%2C72%2C73%2C74%2C75%2C76%2C77%2C78%2C79%2C80%2C81%2C82%2C83%2C84%2C85%2C86%2C87%2C88%2C89%2C90%2C91%2C92%2C93%2C94%2C95%2C96%2C97%2C98%2C99%2C100%2C101%2C102%2C103%2C104%2C105%2C106%2C107%2C108%2C109%2C110%2C111%2C112%2C113%2C114%2C115%2C116%2C117%2C118%2C119%2C120%2C121%2C122%2C123%2C124%2C125%2C126%2C127%2C128%2C129%2C130%2C131%2C132%2C133%2C134%2C135%2C136%2C137%2C138%2C139%2C140%2C141%2C142%2C143%2C144%2C145%2C146%2C147%2C148%2C149%2C150%2C151%2C152%2C153%2C154%2C155%2C156%2C157%2C158%2C159%2C160%2C161%2C162%2C163%2C164%2C165%2C166%2C167%2C168%2C169%2C170%2C171%2C172%2C173%2C174%2C175%2C176%2C177%2C178%2C179%2C180%2C181%2C182%2C183%2C184%2C185%2C186%2C187%2C188%2C189%2C190%2C191%2C192%2C193%2C194%2C195%2C196%2C197%2C198%2C199%2C200%2C201%2C202%2C203%2C204%2C205%2C206%2C207%2C208%2C209%2C210%2C211%2C212%2C213%2C214%2C215%2C216%2C217%2C218%2C219%2C220%2C221%2C222%2C223%2C224%2C225%2C226%2C227%2C228%2C229%2C230%2C231%2C232%2C233%2C234%2C235%2C236%2C237%2C238%2C239%2C240%2C241%2C242%2C243%2C244%2C245%2C246%2C247%2C248%2C249%2C250%2C251%2C252%2C253%2C254%2C255%2C256%2C257%2C258%2C259%2C260%2C261%2C262%2C263%2C264%2C265%2C266%2C267%2C268%2C269%2C270%2C271%2C272%2C273%2C274%2C275%2C276&protein-data-color=&protein-other-color=&pdb-url=https%3A%2F%2Fdms-view.github.io%2Fdata%2FIAV%2F4O5N-trimer.pdb)](images/beneficial-and-deleterious-mutations-in-ha.png){#fig:beneficial-and-deleterious-mutations}
![HA accumulates beneficial mutations in its head domain (sites with color) that enable escape from antibody binding and deleterious mutations in its stalk domain (sites in gray) that reduce its ability to infect new host cells. The one-dimensional genome view on the left shows how sites from HA's head domain map to the three-dimensional structure of an HA trimer. The site highlighted in yellow reveals where different amino acid mutations allowed a flu virus to escape binding from existing antibodies in a human's polyclonal sera [@lee-mapping-2019]. [Explore this figure interactively with dms-view.](https://dms-view.github.io/?markdown-url=https%3A%2F%2Fdms-view.github.io%2Fdata%2FIAV%2Flee2019mapping.md&data-url=https%3A%2F%2Fdms-view.github.io%2Fdata%2FIAV%2Fflu_dms-view.csv&condition=2009-age-53&site_metric=site-Positive+Differential+Selection&mutation_metric=mut-Positive+Differential+Selection&selected_sites=52%2C53%2C54%2C55%2C56%2C57%2C58%2C59%2C60%2C61%2C62%2C63%2C64%2C65%2C66%2C67%2C68%2C69%2C70%2C71%2C72%2C73%2C74%2C75%2C76%2C77%2C78%2C79%2C80%2C81%2C82%2C83%2C84%2C85%2C86%2C87%2C88%2C89%2C90%2C91%2C92%2C93%2C94%2C95%2C96%2C97%2C98%2C99%2C100%2C101%2C102%2C103%2C104%2C105%2C106%2C107%2C108%2C109%2C110%2C111%2C112%2C113%2C114%2C115%2C116%2C117%2C118%2C119%2C120%2C121%2C122%2C123%2C124%2C125%2C126%2C127%2C128%2C129%2C130%2C131%2C132%2C133%2C134%2C135%2C136%2C137%2C138%2C139%2C140%2C141%2C142%2C143%2C144%2C145%2C146%2C147%2C148%2C149%2C150%2C151%2C152%2C153%2C154%2C155%2C156%2C157%2C158%2C159%2C160%2C161%2C162%2C163%2C164%2C165%2C166%2C167%2C168%2C169%2C170%2C171%2C172%2C173%2C174%2C175%2C176%2C177%2C178%2C179%2C180%2C181%2C182%2C183%2C184%2C185%2C186%2C187%2C188%2C189%2C190%2C191%2C192%2C193%2C194%2C195%2C196%2C197%2C198%2C199%2C200%2C201%2C202%2C203%2C204%2C205%2C206%2C207%2C208%2C209%2C210%2C211%2C212%2C213%2C214%2C215%2C216%2C217%2C218%2C219%2C220%2C221%2C222%2C223%2C224%2C225%2C226%2C227%2C228%2C229%2C230%2C231%2C232%2C233%2C234%2C235%2C236%2C237%2C238%2C239%2C240%2C241%2C242%2C243%2C244%2C245%2C246%2C247%2C248%2C249%2C250%2C251%2C252%2C253%2C254%2C255%2C256%2C257%2C258%2C259%2C260%2C261%2C262%2C263%2C264%2C265%2C266%2C267%2C268%2C269%2C270%2C271%2C272%2C273%2C274%2C275%2C276&protein-data-color=&protein-other-color=&pdb-url=https%3A%2F%2Fdms-view.github.io%2Fdata%2FIAV%2F4O5N_trimer.pdb)](images/beneficial-and-deleterious-mutations-in-ha.png){#fig:beneficial-and-deleterious-mutations}

Viruses carrying beneficial mutations should grow exponentially relative to viruses lacking those mutations ([@fig:exponential-growth-with-clonal-interference]A).
If beneficial mutations have large effects on fitness, viruses with different beneficial mutations will compete with each other for hosts in a process known as clonal interference ([@fig:exponential-growth-with-clonal-interference]B).
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