virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.

Deadly New Virus Strikes European Farm Animals

Imagine the shock and dismay of a farmer who sees that his prized ewe just gave birth to a horribly deformed, stillborn lamb. This is exactly what some farmers in several European countries experienced in 2012 as a newly discovered virus spread from farm to farm.

Disease caused by Schmallenberg virus (SBV) was first detected in adult animals in November 2011, when dairy cows in Schmallenberg, Germany, became ill. The cows had a fever, but the most striking symptom was drastically reduced milk production, an obvious loss of income for farmers.

Unfortunately, this was just the tip of the iceberg. Within about a month, the first deformed lambs were born, indicating that the virus not only had spread from cows to sheep but also transmitted vertically from cows and ewes to their offspring.
Goats were the next animals to be attacked.

During 2012, increasing numbers of adult animals were infected, and more and more of their offspring affected. For farmers, this virus is a two-pronged threat: decreased milk production from adult animals and loss of progeny from infected females.

The emergence of the Schmallenberg virus should not come as a surprise. Over the last several decades, several new viruses or virus strains have been discovered—consider HIV, SARS and MERS coronaviruses, Ebola virus, and new influenza viruses. The ongoing discovery of new viruses is a reminder of the diversity of viruses.

Virus Phylogeny Is Difficult to Establish

In 1971 the International Committee on Taxonomy of Viruses (ICTV) developed a uniform classification system for viruses.

Since then the number of viruses and taxa has continued to expand. In its ninth report, the ICTV describes over 2,000 virus species and places them in 6 orders, 87 families, 19 subfamilies, and 349 genera. (See the table Characteristics of Some Virus Families posted to Connect.)

The committee considers many viral characteristics but places the greatest weight on the following properties to define families: nucleic acid type, presence or absence of an envelope, symmetry of the capsid, and dimensions of the virion and capsid. Virus order names end in -virales; virus

Virus Taxonomy

Because of the difficulty in establishing evolutionary relationships, most virus families have not been placed into an order.

The taxa names are derived from various aspects of the biology and history of the members of the taxa, including features of their structure, diseases they cause, and locations where they were first identified or recognized. The suffixes used for each type of taxon (e.g., order, family) are underlined.

family names in -viridae; subfamily names in -virinae; and genus names in -virus. An example of this nomenclature scheme is shown in figure

Virion structure is defined by capsid symmetry and presence or absence of an envelope

As we discuss in chapter 19, the goal of taxonomy is to classify organisms based on their evolutionary history. To piece together the phylogenetic relationships of viruses, virologists are increasingly using two major approaches: comparisons of genome sequences and comparisons of protein folds observed in their major capsid proteins.

Both approaches are challenging, in part because horizontal gene transfer among unrelated viruses and between viruses and their host cells is clearly evident. Despite this, evidence suggests that retroviruses (section 27.7) and reverse transcribing DNA viruses (section 27.8) share a common evolutionary history.

All of these viruses use an enzyme called reverse transcriptase in their life cycles. Evidence also suggests that double-stranded (ds) DNA viruses can be divided into two lineages based on folding of their capsid proteins.

These viruses include nucleocytoplasmic large DNA (NCLD) viruses (section 27.2), which have garnered considerable interest in part because they seem to blur the distinctions between cells and viruses.

Although ICTV reports are the official authority on viral taxonomy, many virologists find it useful to group viruses using a scheme devised by Nobel laureate David Baltimore.

The Baltimore system complements the ICTV system but focuses on the viral genome and the process used to synthesize viral mRNA. Recall from chapter 6 that all four nucleic acid types can be found in viruses: dsDNA, single-stranded (ss) DNA, dsRNA, and ssRNA.

The characterization of the genome of a ssRNA virus is further differentiated by the sense of the ssRNA—that is, whether the genome is identical to or complementary to the mRNA produced by the virus.

ssRNA viruses with an RNA genome that is identical in base sequence to that of the mRNA it produces are said to have plus-strand or positive-strand RNA genomes (figure). Other ssRNA viruses have genomes that are complementary to the mRNA they produce. These viruses are said to have minus-strand or negative-strand RNA.

Viral mRNA5­…GAC UCG AGC…3­
Plus-strand RNA5­…GAC UCG AGC…3­
Negative-strand RNA3­…CUG AGC UCG…5­
Plus-strand DNA5­…GAC TCG AGC…3­
Negative-strand DNA3­…CTG AGC TCG…5­
Plus-Strand and Negative-Strand Viral Genomes

The genomes and replication intermediates of viral genomes can be either plus strand or negative strand. This designation is relative to the sequence of nucleotides in the mRNA of the virus. Plus-strand genomes have the same sequence as the mRNA, either using DNA nucleotides if a DNA genome or RNA nucleotides if an RNA genome. Negative-strand genomes are complementary to the viral mRNA.

The Baltimore System
The Baltimore System

Key Concepts

Virus Phylogeny Is Difficult to Establish

■  Currently viruses are classified with a taxonomic system placing primary emphasis on the type and strandedness of viral nucleic acids, and on the presence or absence of an envelope (figure)

■  Increasingly, comparisons of viral genome sequences and the folding patterns of viral capsid proteins are being used to establish phylogenetic relationships among viruses.

■  The Baltimore system is used by many virologists to organize viruses based on their genome type and the mechanisms used to synthesize mRNA and replicate their genomes (table).

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