Exam 2 Flashcards
All viruses have envelopes, and some have capsids.
-False
-True
False
All DNA viruses replicate in the host cell’s genome, where they utilize host RNA-dependent, RNA-polymerase.
-True
-False
False
HIV utilizes which two receptors to enter host cells?
Sialic acid receptor
CD4 receptor
ACE2 receptor
USB receptor
CCR5 receptor
CCR5 receptor
CD4 receptor
The most common viral capsid shape is:
Filamentous
Cubic
Ovoid
Coronal
Icosahedron
Icosahedron
The standard steps of a viral lifecycle within a host cell include:
Penetration
Uncoating
Genome replication
Virion assembly
Release
All of the above are correct
RNA virus genomes are typically smaller than DNA virus genomes.
True
False
True
Acute infections typically involve a period of rapid virus replication followed by a long (months/years) period of slow virus replication during which symptoms accumulate.
True
False
False
In contrast to the innate immune response to infection, the adaptive immune response is (choose all that are correct):
Slower
Specific
General
Rapid
Memory-less
Slower and specific
For ssRNA+ viruses, translation (i.e., production of protein) occurs before transcription (i.e., production of nucleic acid).
True
False
True
Which of the following divisions are used to classify viruses? (Choose all that are correct.)
RNA vs DNA
Positive- vs. Negative-sense
Segmented vs. Unsegmented
Double- vs. Single-stranded
Chronic vs. Slow
RNA vs DNA
Positive- vs. Negative-sense
Segmented vs. Unsegmented
Double- vs. Single-stranded
The concept of the ‘quasi-species’, first postulated by Domingo et al. in 1978 and explained by Geoghegan & Holmes, is related to what trait of RNA virus evolution?
The high mutation rate of RNA viruses
The small population size of RNA viruses
The stranded-ness of RNA viruses
The low mutation rate of RNA viruses
The difference between segmented and non-segmented genomes
The high mutation rate of RNA viruses
(Crawford Chapter 1) Dmitry Ivanonsky, a Russian biologist, thought that the material making it through his filters to cause disease in plants was:
mould
bacteria
small plants
bacterial toxins
virus particles
bacterial toxins
(Crawford Chapter 2) Cholera epidemics occur during wet seasons due to:
the growth of crustaceans in tidal pools
the migration of seals carrying cholera
the dilution of phage in cholera infested waters
the start of grilling (i.e., under-cooking meat) season
hygienic neglect during the NCAA basketball tournaments
the dilution of phage in cholera infested waters
(Crawford Chapter 1) The enzyme that integrates viral from retroviruses DNA into the host cell’s genome is called:
reverse transcriptase
RNA-dependent-RNA-polymerase
protease
DNA-dependent-RNA-polymerase
integrase
integrase
According to Geoghegan & Holmes, another term for experimental evolution is:
population level evolution
long-term evolution
adaptive evolution
progressive evolution
intrahost evolution
intrahost evolution
(Crawford Chapter 2) Cyanophages play an important role in global ecology because they:
spread photosynthesis genes in bacteria
are a pretty blue-green color
infect only blue-green bacteria
are found in marine environments
create cyanide that pollutes marine environments
spread photosynthesis genes in bacteria
Geoghegan & Holmes say the main conceptual tool used in the study of viruses at the macro- or comparative-level is:
the recombination graph
the phylogenetic tree
the polymerase chain reaction
the quasispecies
the model organism
the phylogenetic tree
(Crawford Chapter 2) The marine ‘viral shunt’ enriches microbial communities whilst simultaneously releasing vast amounts of carbon dioxide - in fact, more than burning fossil fuels.
True
False
True
Crawford Chapter 1) The molecular clock is used to date the origins of viruses.
True
False
True
According to Crawford (Chapter 1), viruses lack which of the following structures (you may choose more than one):
nucleus
mitochondria
cell membrane
capsids
ribosomes
nucleus
mitochondria
cell membrane
ribosomes
As described in Smith et al. 2009, the 2009 swine-origin H1N1 pandemic influenza A virus was a triple-reassortment of which pre-existing influenza A viruses? (You may choose multiple viruses.)
H1N1 classical swine virus
H3N2 seasonal human virus
H1N1 avian virus
H1N1 Eurasian ‘avian-like’ swine virus
SARS-CoV-1
H1N1 classical swine virus
H3N2 seasonal human virus
H1N1 avian virus
According to Pepin 2011, of the three main HIV-1 groups (M, N, and O), viruses which group did not cluster (or were not closely related to) with SIV viruses from common chimpanzee samples?
HIV-1 M
HIV-1 N
HIV-1 O
HIV-1 O
What two observations made early in the HIV epidemic led researchers to suspect that the epidemic originated in Africa? (Please choose two of the possible answers.)
-Full genome sequences of HIV generated in the late 1980s
-High prevalence of HIV infections in sub-populations within Central/West Africa
-Retrospective diagnoses of immunodeficiencies amongst people from Central/West Africa
-The presence of HIV-like viruses in gorillas from Central Africa
-Identification of HIV in contaminated oral polio vaccines from Central Africa
-High prevalence of HIV infections in sub-populations within Central/West Africa
- Retrospective diagnoses of immunodeficiencies amongst people from Central/West Africa
The DRC60 sample of HIV, which was isolated from lymph node biopsies taken in Kinshasa in 1960 (when the city was called Leopoldville), provides significant information about the origins of HIV (Sharp & Hahn 2008). This virus genome belongs to which group of HIV-1 viruses, which is common in Eastern/Central Africa?
HIV-1 A
HIV-1 O
HIV-1 P
HIV-1 D
HIV-1 B
HIV-1 D
According to Sharp & Hahn by the mid- to late-1950s HIV-1 had been circulating in humans in Africa for years, which was long enough for it to differentiate into multiple lineages through the accumulation of mutations/substitution over time.
True
False
True
Smith et al. inferred that the reassortment events occurred between 9 and 17 years ago and the present, meaning that the triple reassortment virus may have been circulating for some time in pigs before host-jumping into humans.
True
False
True
Peppin argues (in the Introduction) that a major source of HIV transmission OF WHICH HE WAS PART was:
Illicit intravenous drug use
Vaccine development from cell culture
Healthcare
The bushmeat trade
Ostrich farming
Healthcare
According to Peppin 2011 (chapter 1), the earliest evidence for HIV in East Africa was found in:
in 1980 in Nairobi STD patients and sex workers
in 1990 in South African truckers
in 1989 in Ethiopian soliders
in 1970 in Kinshasan bushmeat traders
in 1976 in Zaire amongst Ebola patients
in 1980 in Nairobi STD patients and sex workers
Scientists compare the genomes of viruses to construct this model of evolutionary history, which resembles a genealogy:
network
venn diagram
principal component plot
box-plot
phylogenetic tree
phylogenetic tree
The species Pan troglodytes troglodytes is also know by the common name of bonobo.
True
False
False
In addition to intravenous drug uses (IDUs) and homosexual men (MSM), what other community was particularly at risk for HIV infection during the early stages of the epidemic in the United States?
Professional basketball players
Hollywood actors
Hemophiliacs
Journalists
Healthcare workers
Hemophiliacs
The causative agent of AIDS (Acquired Immuno-Deficiency Syndrome) was identified in 1983, but clusters of patients with compromised immune systems (i.e., with AIDS) were first recognized in 1981. How did health professionals identify these individuals as being immuno-deficient, and how was it recognized that a national epidemic was occurring?
There was a dramatic increase in lung cancer
Clusters of patients with opportunistic infections, such as Kaposi’s sarcoma, began to appear
Clusters of patiences with bleeding disorders
A marked increase in the number of intravenous drug users in the US
The first use of DNA sequencing to find virus genomes
Clusters of patients with opportunistic infections, such as Kaposi’s sarcoma, began to appear
Life on Earth seems to be governed by a law that relates what two features of an organism, both of which are particularly important for the evolution of viruses?
Recombination rate and multi-cellularity
Virulence and transmission
Mutation rate and recombination
Genome size and polymerase size
Genome size and mutation rate
Genome size and mutation rate
HIV is prone to recombination because of what feature of the virus?
The virus has an envelope
The virus nucleocapsid contains two capsid proteins
The virus genome is double-stranded RNA
Two copies of the genome are packaged into every virion
The virus uses RNA-dependent RNA polymerase (RdRp)
Two copies of the genome are packaged into every virion
How have people been cured of HIV infection?
Bone marrow transplant with homozygous recessive CCR5-delta32 donor
Kidney transplant
HIV PrEP medication
Drug cocktail including AZT
There is no cure for HIV
Bone marrow transplant with homozygous recessive CCR5-delta32 donor
Recombination combines genetic information from two different viral genomes into one descendent genome. This is a type of recombination that occurs only between segmented viruses.
Lateral gene transfer
Segmented recombination
Passive recombination
Specific budding
Reassortment
Reassortment