CHAPTER 1
DEFINING THE ECOLOGY OF VIRUSES*

CHRISTON J. HURST1,2

1 Consulting Microbiologist, Cincinnati, OH, USA

2 Engineering Faculty, Universidad del Valle, Ciudad Universitaria Meléndez, Santiago de Cali, Valle, Colombia

CONTENTS

1. 1.1 Introduction
   1. 1.1.1 What is a Virus?
   2. 1.1.2 What is Viral Ecology?
   3. 1.1.3 Why Study Viral Ecology
2. 1.2 Surviving the Game: The Virus and it's Host
   1. 1.2.1 Cell Sweet Cell, and Struggles at Home
   2. 1.2.2 I Want a Niche, Just Like the Niche, That Nurtured Dear Old Mom and Dad
   3. 1.2.3 Being Societal
3. 1.3 Steppin' Out and Taking The A Train: Reaching Out and Touching Someone by Vector or Vehicle
   1. 1.3.1 "Down and Dirty" (Just Between Us Hosts)
   2. 1.3.2 "The Hitchhiker" (Finding a Vector)
   3. 1.3.3 "In a Dirty Glass" (Going There by Vehicle)
   4. 1.3.4 Bringing Concepts Together
   5. 1.3.5 Is There No Hope?
4. 1.4 Why Things Are the Way They Are
   1. 1.4.1 To Kill or Not to Kill - A Question of Virulence
   2. 1.4.2 Genetic Equilibrium (versus Disequilibrium)
   3. 1.4.3 Evolution
5. 1.5 Summary (Can There be Conclusions?)

   Acknowledgement

   A Remembrance of Ricardo Flores

   References

1.1 INTRODUCTION

The goal of virology is to understand the viruses and their behavior. Virology is an interesting subject and even has contributed to the concepts of what we consider to represent dieties and art. Sekhmet, an ancient Egyptian goddess, was for a time considered to be the source of both causation and cure for many of the diseases that we now know to be caused by viruses (Figure 1.1). Influenza, a viral-induced disease of vertebrates, was once assumed to be caused by the influence of the stars, and that is represented by the origin of it's name which is derived from Italian. The following was a rhyme which children in the United Sates sang while skipping rope during the influenza pandemic of 1918-1919:

FIGURE 1.1 Image of Sekhmet, "Bust Fragment from a colossal statue of Sekhmet," Cincinnati Art Museum, John J. Emery Fund, Accession #1945.65 Cincinnati, Ohio. Originally the warrior goddess of Upper Egypt, Sekhmet was for a time believed to be the bringer of disease. She would inflict pestilence if not properly appeased, and if appeased could cure such illness.

I had a little bird

And its name was Enza

I opened the door

And in-flew-Enza.

(Source: The flu of 1918, by Eileen A Lynch, The Pennsylvania Gazette November/December 1998 (http://www.upenn.edu/gazette/1198/lynch.html).

And a bit more recently an interesting poem was written about viruses (Source: Michael Newman, 1984):

"The Virus"

Observe this virus: think how small

Its arsenal, and yet how loud its call;

It took my cell, now takes your cell,

And when it leaves will take our genes as well.

Genes that are master keys to growth

That turn it on, or turn it off, or both;

Should it return to me or you

It will own the skeleton keys to do

A number on our tumblers; stage a coup.

But would you kill the us in it,

The sequence that it carries, bit by bit?

The virus was the first to live,

Or lean in that direction; now we give

Attention to its way with locks,

And how its tickings influence our clocks;

Its gears fit in our clockworking,

Its habits of expression have a ring

That makes our carburetors start to ping.

This happens when cells start to choke

As red cells must in monoxidic smoke,

Where membranes get the guest-list wrong

And single-file becomes a teeming throng,

And growth exists for its own sake;

Then soon enough the healthy genes must break;

If we permit this with our cells,

With molecules abet the clanging bells;

Lend our particular tone to our death knells.

The purpose of this book is to define the ecology of viruses and, in so doing, try to approach the question of what life is like from a "virocentric" (as opposed to our normal anthropocentric) point of view. Ecology is defined as the branch of science which addresses the relationships between an organism of interest and the other organisms with which it interacts, the interactions between the organism of interest and its environment, and the geographic distribution of the organism of interest. The objective of this chapter is to introduce the main concepts of viral ecology. The remaining chapters of this book will then address those concepts in greater detail and illustrate the way in which those concepts apply to various host systems.

1.1.1 What is a Virus?

Viruses are biological entities which possess a genome composed of either ribonucleic acid (RNA) or deoxyribonucleic acid (DNA). Some virus groups produce single stranded genomes, and other virus groups produce either fully or partially double stranded genomes. Viruses are infectious agents which do not possess a cellular structure of their own, and hence they are "acellular infectious agents." In 2000, (Hurst, 2000) I proposed a biological domain that would represent the acellular infectious agents which possess nucleic acid genomes (termed "genomic acellular infectious agents"), and its constituent members would be the infectious agents commonly termed to be either viruses, satellite viruses, virusoids or viroids. The proposed domain title was Akamara (a?aµa?a), whose derivation from Greek (a?+??aµa?a) would translate as meaning "without chamber" or "without vault," and I suggested that name as describing the fact that these agents lack a cellular structure of their own. I feel honored by the recognition that my suggestion has received https://es.wikipedia.org/wiki/Akamara; https://prezi.com/accqbr5jjusj/christon-j-hurst/; https://www.timetoast.com/timelines/historia-de-la-clasificacion-de-los-seres-vivos-2b8474a8-2d53-45ba-8516-5338c25fd224.

Furthermore, the viruses are obligate intracellular parasites, meaning that they live (if that can be said of viruses) and replicate within living host cells at the expense of those host cells. Viruses accomplish their replication by usurping control of the host cell's biomolecular machinery. Those which are termed "classical viruses" will form a physical structure termed a "virion" or viral particle that consists of their RNA or DNA genome surrounded by a layer of proteins (termed "capsid proteins") which form a shell or "capsid" that protects the genomic material. Together, this capsid structure and its enclosed genomic material are often referred to as being a "nucleocapsid". If the question becomes one of "Which came first, the virus or the capisd proteins?," then Jalasvuori and coauthors (2015) have suggested that capsid proteins came first as a means of facilitating horizontal gene transfer.

Two of the most basic categories of capsid structures are those described as being helical versus icosahedral. The genetic coding for the capsid proteins generally is carried by the viral genome. Most of the presently known virus types code for their own capsid proteins. However, there are some viruses which are termed as being "satellite viruses." The satellite viruses encapsidate with proteins that are coded for by the genome of another virus which coinfects (simultaneously infects) that same host cell. That virus which loans its help by giving its capsid proteins to the satellite virus is termed as being a "helper virus." The capsid or nucleocapsid is, in the case of some groups of viruses, surrounded in turn by one or more concentric lipid bilayer membranes which are obtained from the host cell. Viruses are grouped taxonomically from the levels of species and genus, on upward through to higher taxonomic levels. The basis for those taxonomic designations includes viral morphology, host range, and replication strategy. Viral taxonomic designations historically incorporated distinctions that were based upon viral antigenic cross reactivity. The usage of antigenic cross reactivity has largely been replaced by taxonomic designations that reflect viral genomic analysis.

Figure 1.2 is a drawing of a helical nucleocapsid structure showing how the capsid proteins attach to the helical coil of the viral nucleic acid genome. Presumably, all of the capsid proteins are identical to one another in a helical structure. Those viruses that possess helical capsid structures generally have single stranded RNA genomes. Some of the virus families which possess single stranded RNA genomes have a genome that is positive sense, which means that their genome has the coding of a messenger RNA molecule and can be translated. There also are virus families that have negative sense single stranded RNA genomes, which means that their genome must be copied to produce complimentary strands, and those...