Reference no: EM133334266

Case Study SARS (Severe Acute Respiratory Syndrome), a viral respiratory illness, was first reported in February 2003. SARS was caused by a novel coronavirus and was the first major new disease outbreak of the 21st century. Before it could be contained, the illness spread to over two dozen countries with the largest number of SARS cases in North America being in Toronto. The global outbreak was successfully contained, and no new cases were reported by the end of 2004. In 2019 another novel coronavirus causing respiratory illness was identified. The virus was named Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), and now the coronavirus that caused the 2003 outbreaks is often referred to as SARS-CoV-1. SARS-CoV-2 is the pathogen that causes coronavirus disease 2019 (COVID-19). Acute COVID-19 is characterized by a broad range of clinical severity, from asymptomatic to fatal. As of September 2022, the COVID-19 pandemic has caused more than 6.5 million deaths worldwide. Introducing Ami Ami had joined a Toronto based research center, the Respiratory Infectious Disease Research Unit (RIDRU), as a Research Associate just before the 2003 SARS outbreak. One of Ami's first projects at the RIDRU was tracking SARS survivors and they were part of the group that showed many survivors still suffered from symptoms over 1 year after infection. Ami continued to work at the RIDRU, and is now one of the unit's lead researchers overseeing a team of scientists and clinicians. On January 30, 2020 the World Health Organization (WHO) declared the novel coronavirus behind COVID-19 was a "public health emergency of international concern (PHEIC)", the virus would be named SARS-CoV-2. Ami was put in charge of the team studying COVID-19 at the RIDRU. One of the many projects Ami oversees is one studying the immune response to SARS-CoV-2 infection. Ami's previous work on SARS led them to push for research protocols that supported long-term (postacute) follow up of COVID-19 survivors. Results of these first post-acute studies are now being published.

The Three Phases of SARS-CoV-2 Infection with SARS-CoV-2 can be broken down into three phases. The first phase is the incubation period is the time between getting infected and when symptoms appear. The incubation period varies (usually 2-14 days) and we now know the infection can be transmitted to others even during this incubation period. The second phase - acute COVID-19 - is when symptoms (eg., cough, fever, shortness of breath/dyspnea) appear. Active illness lasts on average between one to four weeks, but severe cases may last longer than a month. Some people are asymptomatic, meaning they never have the typical COVID-19 symptoms marking the acute phase. The third phase is the post-acute phase. After surviving the acute infection phase those who were infected with SARS-CoV-2 can still suffer from a complex array of clinical sequelae*, up to and beyond 7 months post-acute-infection. This has been described as "long COVID" or "Post-Acute Sequelae of COVID-19" (PASC). * Note: sequelae = a condition which is the consequence of a previous disease Long COVID is not restricted to those who suffered from severe symptoms during the initial stage of infection and may develop following even mild acute illness (i.e., illness that did not require medical intervention) or even in those who remained asymptotic through the acute period. Acute Phase

The first published data out of Ami's group looked at immunophenotype in hospitalized patients during the acute phase of infection. Blood was collected from patients hospitalized for COVID-19 at the time of hospital admission. All patients used in the study were unvaccinated and had no evidence of previous exposure to SARS-CoV-2 (i.e., hospitalization was result of first infection). Cytokines with proinflammatory, anti-inflammatory and anti-viral activities, as well as antibody responses to SARS-CoV-2 antigens were measured. Ami's group found they could sort COVID-patients into three groups based on antibody and cytokine levels at time of hospital admission. Compared to other patients those in Group 1 had the lowest average pro- and anti-inflammatory cytokine levels, while those in Group 2 had the highest average pro-inflammatory cytokine levels. Those in Group 3 differed from the other two groups by having muted/low antibody responses even when follow up tests were run 10 days past symptom onset. While those in Groups 1 and 2 had early and robust IgM, IgG, and IgA antibody responses to SARS CoV-2 antigens. When admitted to hospital, those in Group 2 had the highest mean COVID-19 severity classification score (severity score takes into account multiple factors such as age, blood oxygen level, respiratory rate, blood pressure, etc.). Days since symptom onset, at the time of hospitalization, did not differ between groups. In other words, how long you had symptoms before you were hospitalized could not explain any differences present at the time of hospitalization. This suggests that higher proinflammatory cytokine levels, and therefore the inflammatory response itself, may be contributing to the severity of symptoms.

Question 1 Thinking of immune responses against pathogens, what is the purpose of inflammation (i.e., how does it help)? Why might having a greater inflammatory response be detrimental? Note: broad terminology is fine, no molecular detail necessary; you also don't need to explain how COVID symptoms are generated. Those in Group 2 and Group 3 had the highest peak COVID-19 severity scores. The peak severity score was the maximum severity a patient reached anytime throughout their hospital stay (not just at time of admission). This means while patients in Group 3 (the low antibody response group) had COVID-19 severity scores lower than those in Group 2 when they were initially hospitalized, those in Group 3 eventually had similarly severe outcomes.

Question 2 Why might the effect of extent of inflammation on severity be noticed before the effect of low antibody levels (inflammation from day of hospitalization, effect of antibodies seen a few days to weeks later in time)? Ami's group also looked at T-cell responses throughout the acute period in a broader group of COVID-19 patients. These patients had confirmed infection with SARS-CoV-2, were all unvaccinated and had no evidence of previous exposure to SARS-CoV-2 (i.e., hospitalization was result of first infection) but not all were hospitalized. Ami's study found that mild cases of COVID-19 were characterized by strong and early CD4+ and CD8+ T-cell responses. A result that has since been found by other research groups. Despite the role of T-cell responses in controlling COVID-19, vaccines design focused on eliciting a neutralizing antibody response. SARS-CoV-2 mutates readily, and variants of concern (mutated variants of SARS-CoV-2) have the potential to escape neutralizing antibodies that are generated through vaccination with antigens derived from previous variants. This has led to vaccines becoming less effective as new variants of concern arise. Variants of concern have not had as much of an effect on T-cell responses (in other words the T-cell epitopes aren't mutating as quickly in a way that allows them to escape the previous responses). Therefore, vaccines designed to elicit strong T-cell responses may help control disease even when VOCs are able to escape neutralizing antibody responses to vaccine antigens. Ami wants to redo the RIDRU study of T-cell responses using patients that were previously vaccinated against COVID-19 but had breakthrough infections (infections despite vaccination).

Question 3 Think of someone who has never been exposed to SARS-CoV-2 but has been vaccinated. They successfully generate neutralizing antibodies to SARS-CoV-2. While they still have a protective level of neutralizing antibodies to SARS-CoV-2 they are exposed to the virus naturally (assume the strain they are exposed to has identical antigens variants as the vaccine). Would you expect these individuals to have CD4+ and CD8+ T-cell responses as strong as those with a natural infection and no history of vaccination (i.e., no neutralizing antibodies present)? Why or why not? Hint: think about what neutralizing antibodies do (how they work). Post-Acute Phase Studies out of RIDRU and other groups have found 20-30% of COVID-19 survivors experience Post-Acute Sequelae of COVID-19 (PASC). The most common post-acute sequelae are fatigue, shortness of breath and neurological symptoms such as issues with memory and executive functioning. Some COVID-19 survivors still experience symptoms that interfere with their quality of life two years past acutesymptom onset. Changes to the immune system caused by COVID-19 have been proposed as a potential factor contributing to PASC. Ami's group has been able to perform long-term follow-up on COVID-19 patients infected since early 2020. The patients are recruited after presenting to one of the RIDRU affiliated hospitals with acute symptoms, and confirmation of infection with SARS-CoV-2 through real-time PCR. To help monitor changes in the immune response over time blood was collected from patients both during the acute phase and at multiple time points in the post-acute phase: 3-, 6-, 8- and 12-months post infection. Ami's group found COVID-19 survivors had increases in the number of granulocytes that persist up to 12 months post-infection when compared to controls (controls were those who had been infected with other respiratory viruses, including seasonal coronaviruses). These differences were most prominent in COVID-19 survivors who had post-acute respiratory symptoms (e.g., shortness of breath). Ami's data supports other studies that suggest post-acute lung pathology (and associated post-acute respiratory symptoms) is driven by a persistent inflammatory response that continues months or more beyond symptom onset.

Question 4 How do the granulocyte results support the idea that a persist inflammatory response underlies postacute lung pathology? Hint: you don't need to know how inflammation damages the lungs Ami's group also found significant differences within T-cell populations in COVID-19 survivors. Most strikingly, in those with PASC the level of naive CD8+ T-cells was reduced and the number of "exhausted" effector CD8+ T-cells was increased in COVID-19 survivors compared to controls (controls were those who had been infected with other respiratory viruses, including seasonal coronaviruses). The T-cell differences were most striking in the first 8 months post-infection but in some survivors the differences persisted even 12 months post-infection. • T-cell "exhaustion" is a response of T-cells to chronic antigen stimulation, usually caused by chronic viral exposure or chronic exposure to tumour antigens. "Exhausted" T-cells produce lower immune response proteins such as cytokines and are generally less able to kill virally infected cells or tumor cells. Ami's group is very concerned that the changes to T-cell populations caused by SARS-CoV-2 infection have the potential to weaken immunity. As more and more people are infected (i.e., as there are more COVID-19 survivors) this may raise the overall burden of new viral illnesses and cancer.

Question 5 Why would the changes to CD8+ T-cells noted by Ami's group make COVID-19 survivors more susceptible to new viral infections and tumours? Note: "new" in this context is viruses the individual is exposed to for the first time; make sure your answer is touching on the link between Ami's data and both "new" infections and tumours. Conclusion The results out of Ami's RIDRU group and other research groups led Public Health Ontario to include the following statement in their risk assessment report issued on July 8th, 2022: There is increasing evidence that SARS-CoV-2 infection can cause immune dysregulation. Although all outcomes and the scale of immune dysregulation remain unclear, a potential increase in acquired impaired immunity in the Ontario population could have significant impact on the incidence and associated burden of infectious diseases (e.g., high viral loads, increased antibiotic use and resistance) and other conditions in the longer-term.1 1. Ontario Agency for Health Protection and Promotion (Public Health Ontario). SARS-CoV-2 Omicron variant sub-lineages BA.4 and BA.5: evidence and risk assessment (up to date as of June 23, 2022). Toronto, ON: Queen's Printer for Ontario; 2022.