2950 P2A
b) A colleague who studies hedgehog behavior noticed that infected hedgehogs stop eating and become lethargic, spending much of their time alone in their dens. What does this suggest to you about how this new, virulent virus might evolve? Why might you expect it to become less virulent, or why not? [10 points]
According to the Virulence Evolution theory, the transmission of a pathogen can be limited by high virulence. Infection with the virus has shown to cause a host behavior change which decreases interaction with other potential hosts and thus transmission. If the hedgehogs are sick to the extent where they remain alone and isolated in their dens, indicative of high virulence, this means they will not interact with other hedgehogs enough to transmit the pathogen. Similarly, the virus may be so virulent that it kills the host relatively quickly, decreasing its chances of transmitting to other hosts. If the virus evolves to become less virulent, this will increase the transmission of the virus because the hedgehog behavior will be more reminiscent of normal, more social behavior without high degrees of isolation, and hedgehogs will more rapidly transmit the virus via interaction. The concept that viruses are under selection pressure to be less virulent so that they can be transmitted more rapidly is referred to as the "virulence-transmission tradeoff".
8. We have seen examples of antigenic diversity in viruses (HA and NA in Influenza A virus) and Plasmodium falciparum (monoallelic expression of var genes). a) In general, what benefits do pathogens gain from antigenic diversity? [5 points]
Antigenic diversity makes it difficult for the host to form immunity to the pathogen, allowing this pathogen to bypass the immune system. In doing so, the pathogen can continue to survive within the host and use its machinery to replicate and spread to other hosts. For example, with diverse antigens, P. falciparum can "switch" to a new var gene that the host may not be familiar with, and therefore avoid the immune response.
b) What evolutionary process(es) can lead to these changes? [10 points]
Changes in HA receptor specificity can occur via antigenic drift or shift. Antigenic drift, which is where small mutations during RNA replication accumulate as the virus continues to replicate, can result in many mutations until it results in an HA that binds to the human SA. Antigenic shift is also likely to occur, which is where influenza strains from multiple hosts co-infect and recombine within one host, thus producing a new influenza strain. An avian influenza strain and a human influenza strain can co-infect a pig host, which contains both types of SA receptors. Within that host, the two strains can swap genetic material until a novel virus is created that has avian strain features but is able to infect humans due to being able to bind the α2,6-linked SA receptor. There is no way for the virus to control genetic drift or shift to increase virulence to humans, but selection allows viruses that have made the appropriate switch from α2,3-linked SA to α2,6-linked SA receptors to survive and spread amongst human hosts.
b) Describe how antigenic variation works in P. falciparum. [5 points]
Different lineages of Plasmodium can have different var genes, which can make it difficult for a host to develop immunity. Also, P. falciparum can switch var gene expression within a host to one that is not visible to the host's immune system, which makes it difficult for the host to track the parasite within the body. P. falciparum express one var gene variant of PfEMP1 when initially growing within RBCs, which causes RBCs to stick together and hide within the body. While this prevents infected RBCs from being cleared, this structure is displayed on the surface of the infected red blood cell, which exposes an infected cell to the immune system. When growth is nearly done, the parasites stop expression of the var gene epigenetically, but a portion of the parasite population switches to a new var gene between cycles. The domains of PfEMP1 are variable because they are coded by 60 different var genes, so the chances of being reinfected with the same malarial gene are quite low, which prevents the development of immunological memory.
ii. Surveillance for pandemic spread
For both influenza and coronaviruses, it would be important to track which strain is most abundant in the population. Determining the R0 would allow researchers to see how quickly the virus is spreading and if it is becoming increasingly infectious. For example, the delta variant of SARS-CoV-2 showed an increase in R0 from the initial variant and is spreading even more quickly. Since an R0 below 1 is ideal, this data would inform public health measures such as isolating infected individuals or travel restrictions. Additionally, the incubation period, or the time between infection and when you have symptoms, and the length of illness are both shorter for the flu than they are for COVID-19. This means it is easier to identify cases of the flu than coronavirus cases. Because of this, contact tracing, while important for both viruses, is increasingly important for tracking coronavirus transmission, as individuals are more likely to find out they are infected after they have already spread the virus to others. Because there are seasonal outbreaks of influenza every year, there are already surveillance systems in place that can be magnified for pandemic scenarios to keep track of cases and deaths.
5. The paper by Herfst et al. (2012) focused on the potential for airborne transmission of avian influenza A/H5N1 virus. Humans can become infected with wildtype strains of this virus if they are in contact with infected birds, but typically the virus does not spread between people.a) What kind of changes to the A/H5N1 virus might occur to allow human-to-human transmission? [5 points]
Hemagglutinin (HA) is a viral surface protein that binds to sialic acid (SA) on host cell receptors. Influenza viruses in birds bind to α2,3-linked SA receptors, while human influenza viruses recognize α2,6-linked SA receptors. A switch from receptor specificity from α2,3-linked SA to α2,6-linked SA is expected to be necessary for an avian virus to transmit to humans AND become human transmissible and cause a pandemic. Increased virus production in the upper respiratory tract and efficient release of viral particles from the URT to yield an airborne virus may also be required to allow spread via airborne transmission.
a) Explain how such changes in host range can occur for influenza, and why viruses that undergo such a host shift can result in pandemics. [5 points]
If a host acquires multiple genetically different strains of influenza A, reassortment of genetic segments of each strain can occur, thus resulting in a new virus with novel combinations of surface proteins that have not been encountered by hosts. With no prior exposure to this new strain of the virus, populations have no built-up immunity to this strain. This leaves the entire population susceptible, thus resulting in a pandemic. This is known as antigenic shift, and it often requires an intermediate host between certain animals and humans, often in an animal more genetically similar to humans than the other involved animal.
ii. Host cell receptors and tissue tropism (for Influenza A and SARS-CoV-2)
Influenza A contains hemagglutinin (HA) surface proteins that are able to bind to sialic acid (SA) receptors on host cells. If the virus's HA is able to bind to the human SA receptor, α2,6-linked SA receptors, the virus will be able to infect humans. Furthermore, if the virus contains an HA and NA surface protein combination that humans have not previously been exposed to, that strain would be able to cause a pandemic. SARS-CoV-2 contains spike protein on its surface that binds to the host cell receptor, ACE2. Enzymes on the host cell cleave spike protein, changing its conformation to lead to tighter binding, which makes SARS-CoV-2 better at infecting the upper respiratory tract than other viruses. Since ACE2 receptors are widespread in human tissues, SARS-CoV-2 is able to cause respiratory infection, which is good for transmission as the virus can spread via aerosols, but can also affect other tissues. This accounts for the diversity in COVID symptoms, including the loss of taste and smell.
b) Explain why influenza strains like the one that caused the 1918 flu don't continue to cause devastating pandemics indefinitely. [5 points]
Influenza strains like the one that caused the 1918 flu don't continue to cause devastating pandemics indefinitely as these strains, such as the H1N1 strain from 1918, mutate to be less virulent; while these strains continue to circulate, this diminished virulence allowed these strains to replace the seasonal flu strains, as opposed to continuing to cause pandemic-scale damage. Mutations that lessen virulence could occur through antigenic drift, where small mutations during RNA replication accumulate over time.
c) Using examples of the biology of each pathogen, why was it easier to develop vaccines for the Influenza virus than for Plasmodium? [10 points]
It has been difficult to develop a malaria vaccine because Plasmodium has so much variation in the antigens that the body would use to recognize the pathogen. P. falciparum can "switch" to a new var gene that the host may not be familiar with, and therefore avoid the immune response. Influenza, on the other hand, only has one type of antigen per strain, so it is easier to isolate that antigen and put it into a vaccine. Additionally, the Plasmodium parasite spends much of its time in the human body hidden in RBCs, making it less exposed to the immune system. This makes it difficult for the immune system to develop immunity to the parasite, which is the main purpose of the vaccine. Influenza, however, does not have any mechanisms to evade the immune system; it simply invades cells to use their machinery to replicate the viral genome
b) What are the consequences of this cycling for virulence to humans and interactions with the human immune system? [10 points]
Overarchingly, as more RBCs are being increasingly infected by merozoites, severe malaria symptoms begin to manifest, specifically the characteristic high fever. When merozoites develop into gametocytes, that means P. falciparum is able to be taken up by a mosquito vector when it feeds on the infected host. The vector can then inject the parasite into a new host, indicating that the cycling of parasite levels in the initial host allows for a higher virulence in humans. Additionally, the bursting of RBCs allows for a continuous increase in merozoite levels to spread throughout the host's body. This means that the continuous cycle of hiding and bursting that leads to high and low levels allows for a high virulence in human hosts. However, the bursting also means that the parasite is no longer hidden from the host's immune system. Increased interaction with the host's immune system means that P. falciparum can be destroyed or cleared from the host.
b) For both Influenza A viruses and Coronaviruses, consider how you would design approaches for pandemic preparedness. Compare and contrast how your approaches might be different or similar based on the biology for the viruses. Describe your respective approaches to: [10 points]
Predicting pandemic emergence Both Influenza A and Coronaviruses are able to jump from other species into humans. For influenza, it would be important to track if any strains are jumping from animal hosts into human hosts, which would likely be evidence of genetic shift and a significant novel strain. It would also be important to compare phylogenies of different influenza strains to look for evidence of genetic drift; long branches would indicate more evolution, and therefore a strain that humans are less likely to have immunity to. Unlike influenza, coronaviruses are not prone to antigenic shift or drift, but rather evolve very slowly. Despite this, coronaviruses undergo host shifts fairly often so it would still be critical to track if any strains are jumping into humans. It would also be important to keep track of mutations or cases that indicate the ability of a specific virus to infect the upper respiratory tract. This would indicate that the virus can spread between droplet and/or airborne transmission and could spread through the human population very quickly.
Influenza A viruses and coronaviruses can both cause serious emerging pandemics a) For the following aspects of each virus's biology, explain a feature that contributes to their respective pandemic potential or potential to damage hosts: [10 points] i. Natural host range (for all influenza and coronaviruses)
The ability of both of these viruses to infect many host species leaves these viruses open to antigenic shift, and thus, gives these viruses strong pandemic potential. Both influenza and coronaviruses infect multiple hosts, and if genetically diverse strains from different hosts co-infect one host, recombination events can occur that yield new strains of the virus to which populations hold no immunity to, causing a pandemic.
c) How does this cycling complicate our ability to develop vaccines for malaria? [5 points]
The cycling complicates our ability to develop malaria vaccines because it is so difficult for the immune system to recognize that it is infected with malaria, as it spends a lot of time in the cells. The binding protein that is put on the surface of the red blood cell (PfEMP1) is also very variable, making it even harder for the immune system to recognize. Vaccines that target the blood stages have been unsuccessful due to the hidden nature of the pathogen. It has been said that targeting the sporozoite stage where it is moving into the liver (pre-red blood cell stage), could be more beneficial because there are fewer of these to target and eliminate.
8) The Casadevall (2012) reading discussed a hypothesis that mammals are relatively more protected from fungal pathogens than other animals, and that fungi could contribute significantly to the success of mammals compared to some other animals (like the dinosaurs!). a) Explain this hypothesis and two types of evidence that you think provide the most support for this hypothesis.
The fungal-mammalian emergence hypothesis posits that fungi selected for the emergence of mammals. The hypothesis suggests an explanation for how the highly energy-intensive mammalian lifestyle was selected and for the relative resistance of immuno- logically intact mammals to fungal diseases. Recent developments with amphibian chrytridmycosis and the white nose syndrome in bats provide strong circumstantial evidence for the notion that fungal diseases could have provided strong selection pressures and driven some species to extinction. In addition, there is now considerable evidence that fungi are potential threats to entire ecosystems. The second piece of evidence is that [immunologically intact mammals are highly resistant to fungal diseases, such that most human systemic fungal are considered ''opportunistic''
c) What is the significance of airborne transmission of A/H5N1 among humans? If one were interested in managing influenza, why is the mode of transmission important? [5 points]
The pandemic and epidemic influenza viruses throughout the past century were all transmitted via airborne transmission. This means that while A/H5N1 might be contained in birds, if the virus spreads to humans and acquires airborne transmission, it can cause a pandemic. The mode of transmission determines how quickly the virus might spread through a population, as well as what preventive measures might be necessary. For example, if the virus was spread through fomites, wiping surfaces and washing hands would be key, whereas if the virus is spreading via airborne transmission, wearing masks and social distancing would be important.
HedHOG a) Your first question is which viruses these hedgehog coronaviruses keep evolving from. Why is this an important question and how would you go about answering it? [10 points]
The question of where the hedgehog coronaviruses are evolving from is important because hedgehogs are kept in captivity and thus have frequent and close interactions with humans. As domestic animals, hedgehogs are likely serving as intermediate hosts. It is important to know where the virus is evolving from in order to determine the natural host. To determine this, scientists should study the viral phylogeny. If there are similarities between the novel virus and the pangolin or bat sequences known to be able to undergo host-shifts to humans, this will raise further concerns. Since hedgehogs are mammals, the coronavirus must be of either of the alpha or beta group.It would be helpful to know which viruses they are evolving from because then researchers would be able to identify where the viruses are originating. Then, if researchers are able to identify where the hedgehog coronaviruses are specifically evolving from, they would be able to identify the reservoir. This would allow researchers to monitor for future species jumps and be better prepared for future hedgehog outbreaks. Additionally, knowing which viruses they are evolving from would allow researchers to better determine characteristics, specifically differences, between the original virus and the outbreak virus. Knowing these characteristics would allow researchers to predict how the virus spreads among the hedgehog population. For example, they may be able to determine if the R0 of the hedgehog coronavirus is greater than the original virus, which would indicate an increase in infectiousness. To determine where the virus is originating from, it would be important to establish a phylogeny showing the evolution of the various coronavirus strains. Longer branches would indicate a high degree of evolution, while shorter branches would indicate a high degree of similarity between the two viruses. To obtain the biological data for the phylogeny, researchers could isolate coronaviruses from as many hedgehog cases as possible, as well as the most common reservoirs that result in species jumps.
d) For one of these examples above, discuss how this attachment mechanism can have a potential cost for the pathogen. [5 points]
While PfEMP1 allows P. falciparum to recruit RBCs and hide within the body, the protein also exposes an infected cell to the immune system. The human immune system is able to recognize any PfEMP1 that is not hidden via rosetting as foreign, and is therefore able to target those infected cells for clearance or destruction.
10. The number of Plasmodium falciparum merozoites circulating in the blood of an infected human host typically cycles repeatedly between high and low levels.
a) Based on your knowledge of the Plasmodium-host interaction, explain the cause of this cycling. [5 points] A Plasmodium infected mosquito injects sporozoite into the subcutaneous tissue, which then migrate to the liver where they can pass through Kupffer cells and invade hepatocytes. Inside the hepatocyte, each sporozoite develops into tens of thousands of merozoites which can each invade an RBC on release from the liver. In the bloodstream, the merozoites invade RBCs and multiply within the cells until they burst, each merozoite now infecting more RBCs. This cycle repeats and more merozoites infect more RBCs, leading to an increase in malaria symptoms in the host. However, some of these infected blood cells leave this cycle of asexual multiplication and develop into sexual forms of the parasite, gametocytes, that circulate the blood stream. Thus, the number of merozoites circulating the blood of an infected human host cycles between high and low levels as some of these merozoites end up developing into gametocytes which are ingested by mosquitoes when they bite an infected human. Furthermore, since there is a burst of merozoites that rupture from infected RBC every 48 hours, this means that they are no longer "hidden" from the immune system within the cell, indicating high levels. When the merozoites are within RBCs and hidden from the immune system via rosetting, P. falciparum levels appear to be low
9. The pathogens that cause influenza, cholera, and malaria all require attachment to host tissues at some stage during their interactions with their hosts. Hemagglutinin (HA) of influenza A virus binds to sialic acid receptors in the respiratory or digestive tract; toxin coregulated pili (TCP) in Vibrio cholerae bind to the villi in small intestines; and PfEMP1 in Plasmodium falciparum binds to various receptors (CD36, ICAM-1, CSA, etc.) on endothelial cells. For each of these three pathogens, explain how attachment is essential in the disease cycle, i.e., explain how attachment benefits the pathogen. [5 points each]
a. Influenza virus: Hemagglutinin (HA) on the surface of an influenza virus binds to the host receptor, SA (sialic acid), on the surface of host cells. This allows the virus to enter host cells and utilize their machinery to replicate its viral genome and spread to other hosts. b. Vibrio cholerae: Vibrio cholerae uses its toxin coregulated pilus to attach to and enter target cells. If cholera attaches to cells in the intestinal lumen, it allows cholera to enter the gut and colonize more effectively. When attached, cholera is then able to make changes in the cell's pore, causing water and nutrients to leave the cell and be more accessible to the pathogen. c. Plasmodium falciparum: P. falciparum secretes the antigen PfEMP1 to the surface of the RBC it has infected. Receptors for PfEMP1 on endothelial cells allow for binding of infected red blood cells to those epithelial cells, which in turn prevents parasite clearance. This attachment mechanism also allows infected red blood cells to bind to uninfected red blood cells, which is called rosetting. This allows the infected red blood cells to hide from the host immune system.
