Javaney Thomas
ENGL 21003
Michael Grove
March 23, 2018
Literature Review Draft
Commentary
This paper is one of the first of many stressful papers I wrote in trying to understand the direction of my argument and thesis, and how to satisfy the requirements of a Literature Review Paper. I left the title the way it is as a testament to the confusion I encountered in the first interactions with this type of paper and frame of writing. In all honesty a Lit. Review sounds simple but is much more complicated than simply compiling sources and information.

A Study of How Viruses Evolve and How they cause Pandemics
Pandemics escalate and spread much more rapidly today than it did centuries ago, due to our developments in travel. Before the onset of the agricultural evolution, humans were hunters, which forced them to follow game which constantly allowed free movement and small groups. At the very beginning of the agricultural revolution, settlements were small and relatively genetically homogeneous, so if outbreak of an illness occurred and the immune system of the people were not accustomed to the virus, all would most likely perish. It was not until international travel and trade occurred that outbreaks would be pandemic. Popular pandemics such as the Black Death that peaked in Europe from 1347-1351, the Yellow Fever and more modern diseases such as HIV/AIDS have all progressed as quickly as they did due to improvements in travel. However, it is to be considered that the factors such as lack of hygiene and medical knowledge, incompetence in the disposal of waste, handling and sterilization of diseased corpses, lack of understanding in the concept of bacterium, it’s replication and how it spreads and the lack of governing health official bodies to vet, teach and treat the public, made it much easier for viruses and diseases to transmit and change in animal and human hosts.
At first, when a new wave of viral infection occurs, it is considered an epidemic. These only last for a few weeks at best in a region, however a virus graduates to pandemic, when it spreads to whole countries and regions in the world. What causes a virus such as the flu to always spread? Shouldn’t the immune system be accustomed to influenza by now? Furthermore, the Center for Disease Control (CDC) along with the World Health Organization (WHO), tracks the development of viruses, so why do pandemics still occur? We shall look at the causes of pandemics and how efficient our governing bodies are at preventing and countering these pandemics.
A virus is a microscopic infective agent that can only replicate inside the living cells of a host. The most common known virus in western countries is influenza, in other words the flu. According to the CDC, Influenza is an “acute and infectious disease of the respiratory system caused by a virus and characterized by fever, muscle pain, headache, and inflammation of the mucous membranes in the respiratory tract”. When a virus is introduced to a region it may become rampant depending on the immune system of the people and the strain of the virus introduced. If the antibodies cannot attack the virus, the virus harms the body.
A notable virus that caused a pandemic is the 2009 H1N1 influenza virus. Popularly known as the “Swine Flu” because it is endemic in pigs, the H1N1 Influenza can invade both humans and birds as well. There are three types of influenza, types A, B and C. Influenza A is most common in humans and are broken up into subtypes by the representation H#N#, therefore H1N1 is an influenza A virus . For the focus of how viruses develop and cause pandemics, we will not focus on the less rampant, types B and C. The H1N1 virus was identified before the 2009-2010 outbreak, in fact it has been recorded for over 80 years . In 1998, it was noticed that the strain mutated through a combination of the original H1N1, North American avian, and the human H3N2 strains. This is referred to as the triple-reassortant H3N2. This was then further circulated with the already present H1N1 and H1N2 strains, eventually it outpaced the original H1N1 strain and created an entirely new form of swine originated influenza virus (S-OIV). This continual evolution of the virus is the reason for the outbreak occurrence in 2009. How it deceives the immune system lies in its evolution. Firstly, when a virus enters the body through infection or vaccination, the antigens on the surface of the virus triggers an immune response, this is the creation of specific antibodies against the antigen of the influenza virus. However, in the scenario of the yearly flu season, where new generations of the influenza are introduced to the immune system, people get sick and therefore the H1N1 virus became a pandemic. The mortality rates as counted for people who sought medical assistance or were confirmed to die from the virus were estimated around 60.8 million cases (range: 43.3-89.3 million), 274,304 hospitalizations (195,086-402,719), and 12,469 deaths (8868-18,306) from April 12, 2009 to April 10, 2010 .
In recent news, the fall of 2017 to early 2018 experienced the onset of new flu outbreaks with the surprising outcome of claiming lives even though some of these victims sought out a physician and or received a flu shot for the season. Some cases, both fatal and non-fatal, described that they caught the flu twice. According to North Jersey news, “Hudson county has had more than 900 cases since October 7th, 2017, the start of the flu season” . Additionally, a North Bergen student “died from flu like symptoms”, another case was that of a 4-year-old child who also died of flu symptoms much earlier as the first suspected fatal case of the season.
These cases support the premise that the influenza virus has evolved again. The CDC describes this pattern as antigenic drift which is the process where viruses makes small genetic changes overtime. Then there is antigenic shift which is “an abrupt, major change in the influenza A viruses, resulting in new hemagglutinin and/or new hemagglutinin and neuraminidase proteins in influenza viruses that infect humans”. “Shift results in a new influenza A subtype or a virus with a hemagglutinin or a hemagglutinin and neuraminidase combination that has emerged from an animal population that is different from the same subtype in humans” . This produces a new generation resistant to the current antibodies in the immune system, thus, people may catch the flu frequently. The CDC and WHO continually tracks viruses because of these shifts and drifts which give birth to viruses much different from their ancestors. Genetic characterization and genome sequencing is used to map out and compare the new viruses with ones prior, then vaccines are developed for the most threatening.
However, if the CDC is producing vaccines to counter the virus, why are people still getting sick? The only solutions to this inquiry could be A) The CDC are not making effective vaccines due to inefficient and lack of thorough work or B) The vaccines are not the true solution to influenza. Well, further research into vaccines show that they are not 100% effective, factors such as age and health, and the “match between the flu viruses the flu vaccine” are things that do not guarantee a person’s safety if they get a flu shot. The CDC states “flu vaccination reduces the risk of flu illness by between 40% and 60% among the overall population during seasons when most circulating flu viruses are well-matched to the flu vaccine”. Also, “flu vaccination has been associated with reduced hospitalizations among people with diabetes (79%) and chronic lung disease (52%)” , according to the CDC.
While the age and health factors are uncontrollable, why is it that the flu vaccine would not match the flu virus. The CDC states that this is a result of the antigenic drift, which apparently is very aggressive in its progression of strains in the phylogenetic tree. Stated by the CDC, it claims that when the vaccine is well-matched, it greatly raises the probability of protection against the flu, particularly H1N1 and types A and B influenza but not strain H3N2, due to its incompatible genome sequence. Therefore, one has to argue that vaccines to counter the H3N2 strains must be developed immediately. It seems that having a 100 percent compatible vaccine is out of reach as the CDC argues that when a vaccine is developed and by the time it is implemented, the virus has already changed, so then we are stuck with a 60 percent maximum vaccine compatibility, which seems good enough since many people benefit yearly form vaccinations.
With these odds, the efficiency of governing bodies in the way they study and share data and the aggression of viruses on a daily basis, it is astonishing to that humans are not extinct. The WHO and CDC collect, study and share data with GENBANK, a health body stores all genetic data on viruses, data such as genome sequence, their family strain, origin etc. The CDC’s shortcomings stem from lack of future planning. Their solution may be the development of vaccines for possible influenza strains. Furthermore, they could place institutions that screen test for possible new strains that may have potential for an epidemic. “Target areas” such as schools, popular tourist locations, popular cities, etc., should be zoned for random testing. At risk age groups should also be targeted for strains of influenza, this way we better understand which strains affect particular age groups and which strains have the most success of infiltration and or fatality to allow us to target the most dangerous viruses.

Works Cited
“CDC Estimates of 2009 H1N1 Influenza Cases, Hospitalizations and Deaths in the United States, April – October 17, 2009.” Centers for Disease Control and Prevention, Centers for Disease Control and Prevention, www.cdc.gov/h1n1flu/estimates/April_October_17.htm.
Duda, Kristina, and Sanja Jelic. “Influenza: Making Sense of the Flu.” Verywell Health, www.verywell.com/what-is-influenza-a-770484.
“H1N1 Flu | H1N1 | Swine Flu | MedlinePlus.” MedlinePlus Trusted Health Information for You, medlineplus.gov/h1n1fluswineflu.html.
“Influenza (Flu).” Centers for Disease Control and Prevention, Centers for Disease Control and Prevention, 27 Sept. 2017, www.cdc.gov/flu/professionals/laboratory/antigenic.htm.
“Influenza (Flu).” Centers for Disease Control and Prevention, Centers for Disease Control and Prevention, 3 Oct. 2017, www.cdc.gov/flu/about/qa/vaccineeffect.htm#why_flu_vax_less_effective_against_H3N2.
Jongsma, Joshua. “North Bergen Student Dies of Flu-like Symptoms.” North Jersey, NorthJersey, 13 Feb. 2018, www.northjersey.com/story/news/hudson/north-bergen/2018/02/12/north-bergen-student-dies-flu-like-symptoms/331830002/.
Smith, Gavin J. D., et al. “Origins and Evolutionary Genomics of the 2009 Swine-Origin H1N1 Influenza A Epidemic.” Nature News, Nature Publishing Group, 11 June 2009, www.nature.com/articles/nature08182.
“What Is a Pandemic?” WHO, World Health Organization, www.who.int/csr/disease/swineflu/frequently_asked_questions/pandemic/en/.