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
The adaptive immune response of humans is specific (i.e., it acts in response to individual pathogens), has memory, and is generally slower than the the innate immune response.
True
False
True
Which proposal for virus origins posits an important role for the ‘RNA world’ hypothesis of the evolution of life on Earth?
*The ‘Pre-Cellular Life’ theory
The ‘Escaped Gene’ theory
The ‘Escaped Cell with Proliferation’ theory
The ‘Regressive’ theory
The ‘Midichlorians’ theory
The ‘Pre-Cellular Life’ theory
He was erroneously labeled as ‘Patient Zero’ in the US media:
Ryan White
Rock Hudson
Gaetan Dugas
Pat Buchanan
Elizabeth Glaser
Gaetan Dugas
Since the mid-1990s, in the US most new HIV infections are in the heterosexual community, whereas in Africa it is in the homosexual male (MSM) community.
True
False
False
The Oral Polio Vaccine (OPV) theory for the origin of HIV in humans hinges upon which of the following being true?
-The common ancestor of HIVs date to the 1950s/1960s, when the OPV was first distributed in Africa
-The OPV was contaminated by SIV
-Kidneys from chimpanzees living in the eastern DRC were used to develop and produce the OPV
- HIV is most closely related to SIV that infects chimpanzees in the eastern DRC
-All of these things must be true to support the OPV
All of these things must be true to support the OPV
The 1918 Flu, the most destructive human pandemic of the 20th century, was caused by a virus with which combination of hemagglutinin and neuraminidase?
H3N2
H5N1
H2N2
H1N1
H7N9
H1N1
In influenza viruses, antigenic drift is caused by _______, and antigenic shift is caused by ________.
reassortment, genetic drift
genetic drift, natural selection
recombination, natural selection
recombination, reassortment
natural selection, reassortment
natural selection, reassortment
Most cases of polio over the past 20 years are due to wild type (i.e., natural circulating endemic) viruses and not viruses used in vaccines. This is true of infections today, too.
True
False
False
The historical spread of HIV-1 from Africa into North America went through which Caribbean nation?
Venezuela
Suriname
Barbados
Cuba
Haiti
Haiti
The 2009 H1N1 ‘swine’ flu pandemic virus was a triple reassortment between which three strains of virus? (Please choose three.)
Correct Answer
H1N1 ‘Classical’ swine flu
H1N1 avian flu
H3N2 seasonal human flu
H7N2 ‘Classical’ avian flu
H5N1 avian flu
H1N1 ‘Classical’ swine flu
H1N1 avian flu
H3N2 seasonal human flu
In what two countries is wild-type poliovirus (Enterovirus C) still endemic? (Please choose two.)
Congo
South Africa
Pakistan
Afghanistan
India
Pakistan
Afghanistan
The host specificity of influenza viruses is determined by sialic acid receptors and the virulence is determined by viral protein motifs recognized by host protease enzymes.
True
False
True
Viral RNA sequenced from patient tissue sampled in 1959 and 1960 and fixed in paraffin wax blocks found in Congo indicated what about HIV in Africa?
-HIV circulating in 1959 & 1960 was from orangutans
-HIV circulating in 1959 & 1960 was of a different type than HIV circulating today
- That by 1959, HIV had already spread widely and diversified within the human population of central Africa
-Early HIV was not a sexually transmitted virus - it was a respiratory infection
-HIV did not cause AIDS prior to the 1980s
That by 1959, HIV had already spread widely and diversified within the human population of central Africa
The most closely related virus to Measles virus (MeV) is:
Human rhinovirus 1
Rinderpest virus
Human Enterovirus B
Canine distemper virus
Professor distemper virus 2
Rinderpest virus
By 2003, up to how many children were saved from vaccine-preventable-deaths by vaccines and how many children died from vaccine-preventable-deaths each year (Ehreth 2003)?
200,000 and 3,000,000
3,000,000 and 200,000
Not many, and a lot
1,000,000 and 1,000,000
3,000,000 and 3,000,000
3,000,000 and 3,000,000
Which polio vaccine was a live-attenuated vaccine, and why does the United States (as of 2000; Blume & Geesink 2000) no longer use this vaccine?
Sabin vaccine; because it leads to sporadic cases of polio
Sabin vaccine; because it is not cost effective
Salk vaccine; because it does not require boosters
Salk vaccine; because polio has been eradicated
Sabin vaccine: because it can be administered only through injection
Sabin vaccine; because it leads to sporadic cases of polio
All states in the US require childhood vaccinations for some public benefits such as school, but many also include broad exemptions for religious purposes. According to Paumgarten 2019, as measles infections increase nationally and vaccination rates for preventable childhood diseases decrease, some states are thinking about removing these exemptions as possibly too broad and permissive.
True
False
True
According to Holmes et al. 2021, what lines of evidence DO NOT SUPPORT a natural origin for SARS-CoV-2 (i.e., a host-jump from a currently unknown animal reservoir into humans)?
-High seropositive rates of Chinese citizens in areas where coronaviruses are common
-Viruses closely related to SARS-CoV-2 have been identified in bats and pangolins from places in East and Southeast Asia
-None of the coronaviruses most closely related to SARS-CoV-2 were collected by the Wuhan Institute of Virology
- SARS-CoV-2 is actively adapting to replicate and transmit more efficiently in humans
-The furin cleavage site is sub-optimal relative to other human coronaviruses
-All of the above support a natural origin of SARS-CoV-2
All of the above support a natural origin of SARS-CoV-2
According to Morens et al. 2020, coronaviruses have been a well-documented threat to human populations since the emergence of SARS in the early 21st century. Which of the following is NOT a coronavirus that has host-jumped to cause an epidemic of disease in a new host in the last 20 years?
SARS-CoV
SADS-CoV
MERS-CoV
Lassa-CoV
None - they are all coronaviruses that have emerged from bats in the 21st century
Lassa-CoV
Dengue virus (DENV) has 4 serotypes (DENV-1 to DENV-4) that are all important pathogenic viruses of humans. When did Holmes & Twiddy (2003) estimate the most recent common ancestor (MRCA) of all four DENV serotypes exist?
10 years-ago
100 years-ago
1,000 years-ago
10,000 years-ago
It was too far in the past to estimate
1,000 years-ago
In their phylogenetic analysis of Yellow fever virus (YFV), Bryant et al. (2007) inferred that the current geographic distribution of the virus was due to which large event in human history?
The Spanish-American War
The Bolivarian Wars of Independence
The Trans-Atlantic Slave Trade
The American Revolutionary War
The Louisiana Purchase
The Trans-Atlantic Slave Trade
According to Wasik & Murphy, what was the tell-tale sign to the 4th Duke of Richmond (and Governor-General of Canada), Charles Lennox, that made him realize he had rabies?
His shoulder hurt
He had insomnia
He was fatigued
He had a fever
He could not drink or be around water or liquid
He could not drink or be around water or liquid
Which of the following is not an arbovirus described by Crawford (2018) that is vectored by mosquitoes?
Yellow fever virus
Dengue virus
Zika virus
West Nile virus
Bluetongue virus
None - all of the viruses listed are vectored by mosquitoes
Bluetongue virus
As explained by Specter (2012), Oxitec’s plan to use transgenic mosquitoes involves first injecting mosquito eggs with genes that stop mosquito development in the absence of tetracycline (an antibiotic) and then releasing the females into the wild to mate with natural (“wild-type”) males. The fertilized offspring of these crosses will not develop into adults, thus reducing the overall levels of mosquitoes.
True
False
False
The single largest risk factor for developing dengue hemorrhagic fever (DHF) is what?
Host genetics
Host age
Infection from a tick
Infection with a second type of dengue virus
Host sex
Infection with a second type of dengue virus
We may never know the intermediate host through which SARS-CoV-2 likely moved from bats and into human. What non-bat animal is host to coronaviruses most closely related to SARS-CoV-2?
Civets
Camels
Pangolins
Raccoon dogs
Dogs
Pangolins
The polybasic cleavage site found in the spike protein of SARS-CoV-2 has been of much interest, with some commentators suggesting that it is so unusual as to be evidence of genome engineering. However, other coronaviruses also have polybasic cleavage site motifs, indicating that the most likely origin of the SARS-CoV-2 spike protein is natural.
True
False
True
Case fatality rates for SARS-CoV-2 are difficult to estimate because:
-Asymptomatic cases make it difficult to count the true number of cases
-Mortality rates differ by race/ethnicity
-There are significant differences in mortality by age
-There is significant geographic variation in case fatality rate
-All of the above are issues that make case fatality rates difficult to estimate
All of the above are issues that make case fatality rates difficult to estimate
MERS-CoV and SARS-CoV both emerged prior to SARS-CoV-2. We know that coronaviruses circulate primarily in bats. We think what animals served as intermediate hosts that facilitated the emergence of these coronaviruses in humans? (choose two)
Pangolins
Dogs
Civets
Sheep
Camels
Civets
Camels
How many different serotypes of dengue virus (DENV) are there?
1 (trick question - good try, Professor Kitchen!)
2
3
4
5
4
Unlike Yellow fever, dengue virus circulates primarily in what type of cycle?
Urban
Sylvatic
Carbon
Equatorial
Baseball
Urban
The initial reports of a potential emerging coronavirus in China were shared across social media, email, and text networks by:
November 2019
December 2019
March 2020
April 2020
May 2020
December 2019
One of the main differences between SARS-CoV and SARS-CoV-2 that partially explains why SARS-CoV was ultimately controlled but SARS-CoV-2 was not is that so few patients infected with SARS-CoV were symptomatic, whereas all of SARS-CoV-2 infections are symptomatic.
True
False
False
Unlike dengue virus, Yellow fever virus exists primarily in an urban cycle.
True
False
False
As described by Anne Gibbons, the DNA from Variola virus genome is the oldest ever sequenced from a human pathogen.
True
False
False
DNA from Lithuanian mummies, dating to the 17th century (1600s C.E.), has provided insight into the evolution of Variola virus (VARV; the causative agent of smallpox disease). Specifically, Duggan et al. suggest that modern strains of VARV emerged only in the 17th century on the basis of molecular clock analysis. What other, non-genetic information suggests that highly virulent smallpox disease might have emerged in the 1600s in Europe?
-Pock-mark scars on Egyptian mummies
- Reports of a postule-causing disease from 4th C.E. China
-A strain of virulent VARV from West Africa (P-II) is also found in Native Americans probably due to the trans-Atlantic slave trade
- Bills of mortality from London (England) show the first documented evidence for high-mortality smallpox disease starting in 1632 C.E.
-None of the above suggest smallpox disease was ever less virulent or changed during the 17th century
Bills of mortality from London (England) show the first documented evidence for high-mortality smallpox disease starting in 1632 C.E.
Carl Zimmer, senior science writer for The New York Times, interviewed several evolutionary biologists/virologists about the West African Ebola virus (EBOV) epidemic in 2014. What was their opinion about why the 2014 EBOV epidemic was so much larger than any previous outbreak?
-The virus had evolved to spread via airborne transmission
-It is essentially the same as previous EBOV, but it emerged in the wrong place (i.e., a city)
-The virus emerged from rodents, which make it more adapted to humans
-It has acquired many genetic mutations that make it more transmissible in humans, for the first time
- It was spread, by accident, as part of a polio vaccine drive
It is essentially the same as previous EBOV, but it emerged in the wrong place (i.e., a city)
Which of the following viruses does not belong to the Ebolavirus genus of Filoviridae?
MARV
RESTOV
TAFV
SUDV
BDBV
MARV
As summarized in de La Vega (2015), Ebolavirus (EBOV) was the first virus of the family Filoviridae to be discovered.
True
False
False
The study of virus-host phylogeographic vicariance is also called the study of, following Holmes 2004:
co-divergence
dispersal
adaptation
drift
co-divergence
HPV vaccines are usually multivalent (i.e., against multiple types/species) and have proven to reduce disease in both women and men, despite unfounded concerns of severe side effects in some countries.
True
False
True
HPV associated cancers in men outnumber HPV associated cervical cancers in women in the US.
True
False
True
The geographic associations of P-II clade of Variola virus are linked, following Duggan et al. 2016, to what from human history?
The Carthage Wars with Rome
World War II
The Atlantic Slave Trade
The Bolivarian Revolutions
The Spanish-American War
The Atlantic Slave Trade
The supposed natural reservoir host of viruses from the genus Ebolavirus are:
vampire bats
primates
rodents
dogs
fruit bats
fruit bats
Which of the following Ebolaviruses EBOV is associated with the lowest case fatality rates in humans?
EBOV-Zaire
EBOV-Cote de Ivoire
EBOV-Sudan
EBOV-Marburg
EBOV-Reston
EBOV-Reston
Ebolaviruses and Marburg viruses tend to occupy different geographic areas. It is hypothesized that this is because:
-One group of viruses is found in bats and the other infects mostly birds
-Human interventions have eliminated Marburg viruses (MARV) from their natural reservoir
-Public health efforts to vaccinate possible reservoir species have limited the spread of Ebolaviruses
-There is likely some cross-immunity by Ebola and Marburg viruses that leads to competitive exclusion between them
There is likely some cross-immunity by Ebola and Marburg viruses that leads to competitive exclusion between them
The Ebolaviruses are spread by:
Droplets in the air
Intravenous drug use
Contact with contaminated body fluids
Primarily respiratory transmission
Contact with contaminated body fluids
Rabies virus does not circulate in humans (every human infection is a spillover) because (you may choose multiple answers):
Humans don’t tend to bite each other as a form of aggression
We have vaccinated dogs against rabies
We can vaccinate humans against rabies
We no longer keep bats as pets, which was common in the US prior to the 1980s
Humans don’t tend to bite each other as a form of aggression
We have vaccinated dogs against rabies
We can vaccinate humans against rabies
The main source of rabies virus infections in humans (globally) are:
Skunks
Raccoons
Bats
Dogs
Raccoon Dogs
Dogs
Rabies virus infections are almost invariably fatal. The only known humans to have survived symptomatic infection underwent a procedure called the ___________ protocol.
Milwaukee
Madison
Chicago
Minnesota
Duluth
Milwaukee
We think the natural reservoir species for the filoviruses and lyssaviruses are:
Raccoons
Bats
Primates
Birds
Rodents of unusual size
Bats
The most notable/unusual symptom of Zika virus infection is:
Deep muscle & bone pain (why it is called ‘break bone fever’)
The severe fever and malaise
The associated mosquito bites
It’s extremely high mortality amongst the middle aged (CFR > 50%)
Developmental microcephaly
Developmental microcephaly
Public health departments have begun to use transgenic mosquitoes whose offspring cannot complete their development without tetracycline to control local mosquito populations - and it works and is evolution proof and reversible (but expensive)!
True
False
True
Dengue exists largely in a ________ cycle whilst Yellow fever circulates in a ___________ cycle.
sylvatic; urban
terminal; peripheral
spin; wash
human; plant
urban; sylvatic
urban; sylvatic
