Genomics Revolution

Guest Hosts: Matthew Hecker & Miranda Mordue

Episode 54: MERS Coronavirus- Middle East Respiratory Syndrome-related coronavirus

Hello, and welcome to Genomics Revolution.  This is Matthew Hecker, and this is Miranda Mordue, bringing you in from the Hiram College Genetics course of 2020. 

As we stand in April 2020, the world is currently in a state of flux with COVID-19, a novel coronavirus that is taking the world by storm, and not in a good way.  In light of COVID-19, our topic for today is another variety of novel coronavirus, MERS-Coronavirus.  This stands for Middle East Respiratory syndrome coronavirus, but we’ll be calling it MERS from here on out.

MERS was first reported in 2012 in Saudi Arabia in the respiratory tract of a businessman who had died from viral pneumonia.  It was the first highly pathogenic coronavirus since the SARS coronavirus in 2003.  This virus had a very high mortality rate of greater than 35%. 

The MERS genome is single stranded RNA and is made up of about 30,000 bases.  Though sometimes it is difficult to think about the scale of genetics, this is a relatively small genome size that contains only 10 Open Reading Frames, or ORFs.  Each of these ORFS is a section in which transcription can occur.  One of these ORFs encodes for a “polyprotein.”  This is a large encoded structure that can be cleaved in order to serve different purposes, basically a conglomeration of different proteins that can be broken up and used as necessary.  In the case of MERS, this polyprotein encodes viral replicase and the methods of interaction with ribosomes.  Basically, this polyprotein is what allows for the infection and takeover of host cells to replicate itself, while the rest of the ORFs translate to structural and functional proteins.  These other proteins are responsible for getting the polyprotein into host cells. 

Knowing this, what else can genetics tell us about MERS?  Based on genomic comparison, it is very likely that the strain of MERS that eventually came to affect humans began development in the dromedary camel.  With MERS, the evidence of human to human transmission is differing based on location the virus was found.  In Riyadh, there were cases of human transmission, but in other places, it was not observed.  This means that some of the infections of humans beyond the initial case are a result of contact with livestock. 

Because of this discreet infection from various sources, it was actually discover that that are many different strains of MERS.  In a study from 2013, 21 samples of MERS were examined from different patients, and 10 different genomes were produced for the virus.  This means that MERS infections are not limited to human contact and this will obviously affect the manner in which the virus must be addressed.

MERS has also shown some resistance to the innate immune response of the body.  The codon selectivity in MERS is variable in three genetic clusters, which have developed a codon bias to survive inside the host.  By using different codon sequences, the immune system is not able to recognize the virus as effectively.  In different strains, this leads to adaptation to resist the human immune system, making MERS a more dangerous virus. 

As of now, there is no specific “cure” for MERS, but levels of infection remain relatively low due to low human to human transmission in strains, as well as potentially lethal symptoms from the onset which cause quarantining very quickly.

I’d hate to end on too negative a note, so let me just say this: Scientists all over the world are very capable at what they do, and they will be able to figure out a way to defeat MERS, as well as the current COVID-19.  Just remember to continue listening and learning!  Thank you all for listening!  This has been Genomics Revolution.

Sources:

1)     Cotten et al., 2013. The Lancet Vol 382, pp 1993-2002. Transmission and  evolution of the Middle East Respiratory syndrome coronavirus in Saudi Arabia: A descriptive Genomics Study.

2)     Alnazawi et al., 2017. Biol. Pharm. Bull. Vol 40 pp 1289-1298. Comparative Genomic Analysis MERS CoV Isolated from Humans and Camels with Special Reference to Virus Encoded Helicase. 

3)     Shapiro et al., 2016. Disaster and Military Medicine 2:9. Middle EAst Respiratory Syndrome Coronavirus: A Review of the Current Situation in the World.

4)     Chafekar, A., & Fielding, B. C., 2018. Viruses vol. 10,2 93. MERS-CoV: Understanding the Latest Human Coronavirus Threat. 

Genomics Revolution

Guest Hosts: Denise Hart & Madyson Morris

Episode 53: SARS Coronavirus

     Welcome to Genomics Revolution. This is Denise Hart and Madyson Morris from the 2020 Hiram College Genetics course hosting this episode on the SARS coronavirus. The acronym SARS stands for Severe Acute Respiratory System.1 To distinguish between the virus and the disease it causes, we will call the virus the SARS coronavirus and the disease SARS from here on out. Today, we will discuss the SARS coronavirus genome, as well as the outbreak that occurred across the globe from 2002 to 2003. 

Did you know that SARS coronavirus was once the largest RNA virus genome? This genome is also single-stranded and it has 29,751 RNA molecules. The genome has 14 genes and 29 mature proteins. The largest gene found within the SARS coronavirus genome encodes a polyprotein. This polyprotein gets cut into 16 mature proteins. In addition to these mature proteins, the genome also shows that hypothetical proteins, unique to SARS-coronavirus, exist. Researchers used BLAST, along with other function prediction programs, to determine the function of these proteins.3Their research concluded that the genome has carbon-oxygen lyase, oxidoreductases that act on CH-OH groups, an ATP-binding cassette transporter, structural proteins, and a voltage-gated ion channel.3

So, why should we care about SARS coronavirus and the disease it causes? The outbreak started almost 20 years ago!2 We should care about understanding this virus because it causes most patients to develop pneumonia, hence the “Severe Acute Respiratory System” title. Pneumonia can be a very deadly disease if not treated right away. We should also care about educating ourselves on SARS coronavirus because during the outbreak, 8,098 people suffered from SARS as well as pneumonia or respiratory distress syndrome. 774 of those people died.1,2 If contracted, SARS coronavirus can have detrimental side effects, and having a good understanding of this virus could potentially prevent future outbreaks and pandemics caused by it.

SARS coronavirus originally started out in bat species, but is able to be contracted by humans. The symptoms of SARS coronavirus in humans include fever, dry cough, headache, muscle aches, and difficulty breathing. These symptoms are very typical of Coronavirus- and true for most of the 36 types of coronaviruses.6 While it is good to be aware of these symptoms, 1 symptom really sets SARS coronavirus apart from other strains: urinary abnormalities. For the first patients with SARS, they were diagnosed with other ailments due to these unique symptoms. It wasn’t until the genome was sequenced that researchers learned that SARS not only turns cells along the respiratory tract into host cells, but also cells in the intestines, liver, heart, vascular endothelium, testis, and the kidneys!6

Not only did some of the patients with SARS get treated for other ailments due to having urinary abnormalities, some of the patients with SARS received treatment but nothing happened!6,8 These were patients with the common symptoms. They received treatment but they did not get better. This was because the SARS coronavirus had mutated 14 times.6,7 Some patients had the original strain and others had one of the mutated strains. The treatment of the original strain did not help patients with a mutant strain. Researchers used high density sequencing arrays to find the places in the SARS coronavirus genome that had mutated.5,6 The scientists found that in mutant strains, 5-6 nucleotides were inserted or deleted. 5,6 This small change caused the virus to be harder to treat because of the variations between each mutation. 

As these mutations were being discovered, the need to understand this virus was vital because of the global outbreak. Although there were not enough cases to consider it a pandemic, a virus causing a global outbreak still needs to be understood to prevent the outbreak from turning into a pandemic! In order for a disease to be considered a pandemic, it must affect several countries and a very large amount of people. The CDC does not define how many countries or people, but a pandemic does affect more people than an outbreak.4 

It’s about time to wrap up. Today we learned about the SARS coronavirus and the global outbreak of SARS from 2002 to 2003. What we want you to take away from this episode of Genomics Revolution are four things:

       Number 1: SARS coronavirus was one of the largest RNA virus genomes at the time. The size of the genome increased the amount of time needed for geneticists to understand the virus to create presentation education and control measures for the public. 

       Number 2: Whenever the SARS coronavirus genome experiences a mutation, the mutation is an insertion or deletion of 5 or 6 nucleotides. 

       Number 3: While SARS is an acronym for Severe Acute Respiratory System, the virus targets not just the respiratory tract, but also other organs such as the kidney and heart.

       Number 4: Understanding viruses like this one is important to the future of science so that when a new strain of virus arises, we may be able to fight it quicker than the last one!

Thanks for listening to Genomics Revolution. Bye guys! Bye!

References:

1.     SARS. Centers for Disease Control and Prevention. 2017 Dec 6 [accessed 2020 Apr 9]. https://www.cdc.gov/sars/about/fs-sars.html

2.     SARS (Severe Acute Respiratory Syndrome). World Health Organization. 2012 Apr 26 [accessed 2020 Apr 9]. https://www.who.int/ith/diseases/sars/en/

3.     Cai CZ, Han LY, Chen X, Cao ZW, Chen YZ. Prediction of Functional Class of the SARS Coronavirus Proteins by a Statistical Learning Method. Journal of Proteome. 2005 Aug 10 [accessed 2020 Mar 28]. https://doi.org/10.1021/pr050110a

4.     Caceres V. What's the Difference Between an Epidemic and Pandemic? U.S. News & World Report. [accessed 2020 Apr 9]. https://health.usnews.com/conditions/articles/whats-the-difference-between-an-epidemic-and-pandemic

5.     Wong CW. Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays. Genome Research. 2004;14(3):398–405. doi:10.1101/gr.2141004

6.     Cheng VC, Lau SK, Woo PC, Yuen KY. Severe Acute Respiratory Syndrome Coronavirus as an Agent of Emerging and Reemerging Infection. American society for microbiology. 2007;20(4):660–694.

7.     Graham RL, Sparks Jifr S, Eckerie LD, Sims AC, Denison MR. SARS Coronavirus replicas proteins in pathogenesis. Virus Res. 2008;133(1):88–100.

8.     Hung LS. The SARS epidemic in Hong Kong: what lessons have we learned? Jrsm. 2003;96(8):374–378. doi:10.1258/jrsm.96.8.374

Genomics Revolution

Guest Hosts: Keegan Rankin and Torey Coward

Episode 52: Zika

Script:

Keegan: Hello welcome to the podcast!  I'm Keegan!

Torey: And I’m Torey Coward!

Keegan: And we are here today to talk to you about the Zika Virus.  I’ll start us off with some general information.  The Zika Virus belongs to a group of viruses known as flaviviruses.  Flaviviruses are single-stranded RNA viruses encapsulated by a protein coat.  Some of Zika Virus’ closest relatives include Yellow Fever Virus and West Nile Virus.  They replicate in the cytoplasm of host cells.  All zoonotic flaviviruses are rely on arthropods as vectors.  In the case of Zika, its two primary vectors are Aedes aegypti (Yellow Fever Mosquito) and Aedes albopictus (Asian Tiger Mosquito).  The reservoir of the virus are primates, including humans.  This virus is usually spread to a host through the bite of a mosquito, but it can also be transmitted by coming into contact with infected blood and saliva.  Common symptoms include fever, headache, rash, joint and muscle pain and conjunctivitis.  Symptoms usually last for several days to a week.

Torey: I’ll speak briefly about the genome of the Zika Virus.  As Keegan stated before, the Zika Virus is a single-stranded RNA, and since it has been sequenced, we know today that it consists of nearly 10.8 thousand bases.  There are 3424 amino acids that generate the polyprotein that the virus encodes for.  The polyprotein is made up of 10 proteins, one capsid, a precursor membrane protein, an envelope protein, and 7 non-structural proteins.

Keegan: The Zika Virus was first isolated from a Macaque in 1947 obtained from the forest of Uganda.  Though 80% of those infected are asymptomatic and 20% of patients contract mild, non-lethal symptoms, the real danger arises when the infected patient is pregnant.  Getting Zika Virus while pregnant puts the child at risk of lethal birth defects such as microcephaly.  Microcephaly is a genetic defect that causes an infant’s brain and head to be smaller than normal, healthy infants.  This can result in seizures, intellectual impairment, hearing loss, visual problems, and even infant mortality.  Prevention of the spread and contraction of Zika Virus is imperative to prevent infant mortality. 

Studying Zika Virus and other flaviviruses on a genetic level has given use crucial revelations as to how Zika works and can spread.  One such revelation is that many of its genes can be successfully targeted, which brings about the possibility of new treatments and vaccines.  Another revelation is that certain mRNAs coding for viral replication have been isolated and can be targeted, yielding the possibility of developing treatments that suppress the virus further, stopping its growth.  Another discovery in researching Zika virus is that it also can use other organisms as reservoirs.  Research suggests that Zika Virus can possibly be transmitted by birds, horses, goats, cattle, and bats. 

Torey:  Hopefully the information that we have provided for you today had been insightful and helped to foster a greater understanding of the Zika Virus. From the genus and sequence, to the pathway and effects of this intriguing virus.

Keegan: And that concludes our talk for today! Thank you so much for listening to us and stay safe out there!

Works Cited:

Facts about Microcephaly. Centers for Disease Control and Prevention. 2020 Feb 18 [accessed 2020 Apr 9].

Flavivirus. Flavivirus - an overview | ScienceDirect Topics. [accessed 2020 Apr 9]. 

Malone RW, Homan J, Callahan MV, Glasspool-Malone J, Damodaran L, Schneider ADB, Zimler R, Talton J, Cobb RR, Ruzic I, et al. Zika Virus: Medical Countermeasure Development Challenges. PLoS neglected tropical diseases. 2016 Mar 2 [accessed 2020 Apr 9].

Zika Virus. Centers for Disease Control and Prevention. 2019 Nov 20 [accessed 2020 Apr 9].

Molecular cloning and characterization of the genes encoding the proteins of Zika virus. NCBI-PubMed. [Accessed 2020 April 9]

Genomic Revolution

Guest Hosts: Alexus Acton & Rachna Prasad

Episode 51: Ebola

Script:

Rachna: Welcome to Genomics Revolution. This is Alexus Acton and Rachna Prasad from the 2020 Hiram College Genetics course hosting this episode on the Zaire Ebolavirus. This virus causes the disease ebola that originated from human animal contact, most likely from a bat (1). The Ebola Virus Disease, or EVD for short, was first discovered in 1976 with 2 consecutive outbreaks of fatal hemorrhagic fever in Central Africa. The first outbreak was in the Democratic Republic of Congo, which was formerly called Zaire, in à village near the Ebola river, which accounted for nearly 2700 deaths. The second outbreak was in South Sudan. Originally scientists believed it was spread by à single infected person travelling between the two areas, but it was later discovered they were two genetically distinct viruses - the Zaire ebolavirus and the Sudan ebolavirus.(4) The most recent, and familiar Ebola outbreak occurred in 2014-2016, originating in Southeastern Guinea. It rapidly spread to urban populations within weeks, and soon turned into à global epidemic. (4)

Lexi: With this virus going many months without detection we should care about knowing about this virus because  the human-human transmission chain was growing exponentially. Before the World health Organization declared it an outbreak, it had already spread over country borders infecting thousands of people (1). Ebola virus is a negative- sense single strand RNA ((-)ssRNA) that has a 19 kilobase genome (1). There are several encoded proteins from EVD which are nucleoprotein (NP), viral proteins (VP) as well as RNA polymerase (L), and Glycoprotein (GP) (2). VP24 is a membrane associated protein, VP30 and VP35 are polymerase matrix proteins, and VP40 is a matrix protein (2). VP40 is the primary EVD matrix protein and regulated assembly and progress of infectious particles (2). It assembles on the inner leaflet of the plasma membrane in human cells to regulate viral budding.  Each of these genes encodes for a single protein product with the exception of GP. Gp encodes three proteins of different sizes with a full length of 676  residues. Glycoprotein 1 and 2, mediates viral-host cell attachment and fusion (2). Like other RNA viruses ebola quickly generates mutations through error prone replication. The various glycoproteins are produced from frameshift as a result of mRNA editing (1). 

Rachna: Ebolavirus belongs to à group of viruses called filoviruses. A phylogenetic analysis revealed that the Sudan Ebola virus diverged early from the other strains, showing that the  Bundibugyo and Tai Forest were closely related to Zaire Ebola Virus (2). EBOV is à single stranded RNA virus. This gives it a higher likelihood of acquiring meaningful genetic adaptations and evolving into different strains, when compared to other DNA viruses. (5) À 2017 study, by Tao Li et al., conducted on 514 different EBOV genome sequences from patients with confirmed EVD cases showed that 11 different lineages of EBOV arose from one outbreak in Sierra Leone alone. It also showed that different lineages of EBOV had different fatality rates and certain strains with specific SNPs correlated with higher fatality rates.  Variation in nucleotide sequences can help target each Ebolavirus strain from one another, ultimately leading to better diagnosis and therapeutics. This is important to note as the divergence of diseases from other common viruses could potentially be headway in targeting vaccines and treatments to those infected. 

Lexi: Evidence  demonstrates cooperative dimeric binding of  double stranded RNA by ebolavirus VP35. The C-terminal domain of viral protein 35 dimerizes upon binding to double stranded RNA, showing coppertivity (3). Reston ebolavirus is named to show where it was derived from, which has  previously been shown to be critical for RNA binding, but is also important for VP35 dimeric interface binding (3). These researches mutated R312/301 which likely abolished dsRNA binding which disrupted the formation of the viral protein dimer leaving it in unstable formation (3). This is important as the binding mechanism permits the ebola virus from avoiding the innate immune response and enhancing harmfulness to human cells. (3). This alone can help researchers target the structure based conformational states or protein targeting drugs for  drug development and biodefense mechanisms. 

Rachna: One study showed that multi sequence alignment generated several conserved sequences from each protein mentioned above. Using an Ebola strain from 1976 and a recent strain of 2014, the two sequences were 100% identical (6). The conservation allowed for detection of B and T cell epitopes which covered between 25.37 and 61.51% of the population (6). B cell epitope is the portion of the antigen which interacts with B lymphocytes to trigger immune responses (6). The importance of this is to understand the efficacy in eliciting immunity through humoral and cell-mediated immune responses. T cell immune response usually promises long lasting immunity, and here the prediction of T and B cell epitopes provides two alternative but effective immune response mechanisms. 

Lexi: Thank you for tuning in on this podcast of Genomics Revolution. We hope you enjoyed your time and learned something new about Ebola.

References:

1.     Holmes, Edward C., et al. “The Evolution of Ebola Virus: Insights from the 2013–2016 Epidemic.” Nature, vol. 538, no. 7624, 13 Oct. 2016, pp. 193–200., doi:10.1038/nature19790.

2.     Jun, Se-Ran et al. “Ebolavirus comparative genomics.” FEMS microbiology reviews vol. 39,5 (2015): 764-78. doi:10.1093/femsre/fuv031

3.     Kimberlin, C. R., et al. “Ebolavirus VP35 Uses a Bimodal Strategy to Bind DsRNA for Innate Immune Suppression.” Proceedings of the National Academy of Sciences, vol. 107, no. 1, 14 Sept. 2009, pp. 314–319., doi:10.1073/pnas.0910547107.

4.     Li T, Yao HW, Liu D, et al. Mapping the clinical outcomes and genetic evolution of Ebola virus in Sierra Leone. JCI Insight. 2017;2(15):e88333. Published 2017 Aug 3. doi:10.1172/jci.insight.88333

5.     Regnery, RL., Johnson, KM., and Kiley, MP. Virion nucleic acid of Ebola virus. J. Virol. 1980; 36(2): 465-469.

6.     Yasmin, T., and A. H. M. Nurun Nabi. “B And T Cell Epitope-Based Peptides Predicted from Evolutionarily Conserved and Whole Protein Sequences of Ebola Virus as Vaccine Targets.” Scandinavian Journal of Immunology, vol. 83, no. 5, 2016, pp. 321–337., doi:10.1111/sji.12425.

Genomics Revolution

Guest Hosts: Alysa Giudici & Rachel Jerkins

Episode 50: West Nile Fever

Script:

Rachel: Hey everybody, and welcome to another episode of Genomics Revolution. This is Rachel Jerkins and Alysa Giudici (Guh-Dee-Cee), here to talk about the West Nile Virus. 

Rachel: The West Nile Virus comes from the flavivirus genus and the family flaviviridae. In 1937, the virus was first discovered in the West Nile area of Uganda in Africa. It is a single-stranded RNA virus around 11kbp in size with stem loops on the 5’ and 3’ ends. The genome codes for 10 proteins— 3 for structure in the coding region, plus seven not in the new virus structure from the non-coding region. 

Rachel: The West Nile Virus causes a disease called West Nile fever (Richter et al. 2017). It is believed to spread when a mosquito bites an infected bird and then bites a person. It wasn’t until 1999 that the virus made its first appearance in the western hemisphere (White et al., 2001). It is crucial to study the disease because it can be a fatal neurological disease and has now spread across a majority of the globe.It is believed to be the main cause of viral encephalitis around the world (Chancey et al. 2015) 

Alysa: Thanks Rachel, Since the sequencing of the genome, there are many key findings that have emerged. The virus thrives utilizing a vector-virus relationship. The entry of the WNV is through receptor mediated endocytosis once the virus attaches to the cell surface (Colpitts et al.) Interestingly, the virus was able to be tracked through an enzootic cycle involving Culicidae mosquitoes and birds. The birds act as a form of host reservoirs allowing the virus is amplified through the bird – mosquito – bird cycle, until the fall when female mosquitoes begin to “bite” humans. Although many external factors can contribute to the amplification cycle, the disease does exist in multiple habitats (Peterson, 2002). This form of transmission causes the virus to transmit quickly and effectively. 

Alysa: The apparent symptoms appear to be anorexia, nausea, vomiting, eye pain, headache, etc. that last roughly 3-6 days (Peterson, 2002). These symptoms eventually, if untreated became neurological and possibly deadly. After research, it was determined that there are, however, two lineages of the West Nile Virus. The 1st lineage is the one that is known to affect humans. Not only is the West Nile Virus detrimental to humans, but it is also a leading neurologic disease in many animals such as the equine population. Further sequencing of this genome and Reverse transcription-PCR has further educated the veterinary world as well. Recent evidence acquired by Venter et al. in horses suggests that the lineage 2 strains are highly neuroinvasive in humans and mice. A disease that we continue to fight in humans is also a disease we will continue to fight in animals as well. Who would have guessed that? Thanks for listening.

Works Cited:

Richter, J., C. Tryfonos, A. Tourvas, D. Floridou, N. Paphitou, and C. Christidoulou (2017).

Complete genome sequence of West Nile virus (WNV) from the first human case of neuroinvasive WNV infection in Cyprus. Amer. Soc. for Microbio. 5(43) 1-2. Doi: 10.1128/genomeA.01110-17

Chancey, C., A. Grinev, E. Volkova, and M. Rios. (2015). The global ecology and epidemiology of West Nile virus. BioMed Res. Int. 376230. Doi: 10.1155/2015/376230

White, D. J., Kramer, L. D., Backenson, P. B., Lukacik, G., Johnson, G., Oliver, J., … Campbell, S. (2001). Mosquito Surveillance and Polymerase Chain Reaction Detection of West Nile Virus, New York State. Emerging Infectious Diseases, 7(4), 643–649. doi: 10.3201/eid0704.017407 

Petersen, L. R., & Marfin, A. A. (2002). West Nile Virus: A Primer for the Clinician. Annals of Internal Medicine, 137(3), 173. doi: 10.7326/0003-4819-137-3-200208060-00009

Colpitts, T. M., Conway, M. J., Montgomery, R. R., & Fikrig, E. (2012). West Nile Virus: Biology, Transmission, and Human Infection. Clinical Microbiology Reviews, 25(4), 635–648. doi: 10.1128/cmr.00045-12 

Venter, M., Human, S., Zaayman, D., Gerdes, G. H., Williams, J., Steyl, J., Leman, P. A., Paweska, J. T., Setzkorn, H., Rous, G., Murray, S., Parker, R., Donnellan, C., & Swanepoel, R. (2009). Lineage 2 west nile virus as cause of fatal neurologic disease in horses, South Africa. Emerging infectious diseases, 15(6), 877–884. https://doi.org/10.3201/eid1506.081515

Genomics Revolution

Guest Hosts: Giselle Bahena & Diamond Johnson 

Episode 49 – Rabies Lyssavirus

Script:

      Welcome to Genomics Revolution.  This is Giselle Bahena and Diamond Johnson from the 2020 Hiram College Genetics course hosting this episode covering the Rabies lyssavirus.  As the scientific name of this virus implies, the disease that results from such infection is commonly known as Rabies.  This disease has been around since antiquity and the earliest writings about it was found in 300BC in Mesopotamia.2  It was discovered through the infectious bite from one animal to the other.  The biggest red flag that indicated a rabid animal was excessive salivation which then required preventative actions to take place in order to protect against the virus being transmitted elsewhere.  It is important to understand the virus as transmission does not only occur between one animal and the other, rather humans are also at risk from such infectious bites as well.  Thousands of people in third would countries continue to die of Rabies and if one is not educated nor treated for the disease, its impact on the central nervous system will take place and result in death. 

The Rabies virus genome is a single stranded, antisense, non-segmented, negative stranded RNA of approximately 12kb.1. There is a 50 nucleotide leader sequence that is followed by the the five genes in the genome.  The proteins encoded by these five genes are nucleoprotein(N), phosphoprotein(P), matrix protein(M), glycoprotein(G) and polymerase(L), all of which make up the structure of the bullet-shaped virion.1  Fusion of the rabies virus envelope to the host cell membrane initiates the infection process and from this point the bullet-shaped virion, with 10nm spike-like glycoprotein peplomers covering its surface, penetrates and enters the host cell cytoplasm via pinocytosis.1  Next, the viral RNA is uncoated and the transcription process of producing messengers RNAs(mRNAs) begins.  Since the lyssavirus is a negative single stranded RNA genome, these mRNAs must be transcribed as they are needed to permit virus replication later on in its cycle of infection and replication.1  Now, the synthesized mRNAs are translated into the genomes structural proteins.  As G protein glycosylation is processing, the first step in viral replication occurs by synthesizing full length positively stranded copies of the genome that serve as templates for the final synthesis of the negatively stranded genome.1  When this switch to replication occurs, RNA transcription then becomes non-stop as stop codons are ignored.  Finally, the assembly process of the bullet-shaped virion takes place and proceeds to its budding formation. 

There has been an unrecognized member of the lyssavirus genus found in bats that is similar to the one found in dogs, both of which have been seen to be transmitted in humans.3  This is important because with the genome sequence of the lyssavirus, another member in the family was able to be identified along with other animals who would not be typically associated with caring the such virus.  On a similar note, sixty nine rabies virus isolates from various parts of the world were partially sequenced and compared to thirteen representative isolates of the six lyssavirus genotypes in order to analyze their genetic diversity.4  The analysis was performed on each of their complete nucleoprotein coding gene and it was discovered that all of the rabies virus isolated belonged to genotype 1, most likely diverging by the accumulation of synonymous mutations.4  With this being said, having the knowledge that the nucleoprotein is highly conserved among all the isolates is important as it can be used as a potential target for preventing the viral Rabies infection.  For example, a complementary RNA can can be created to hybridize with the nucleoprotein mRNA and prevent its translation by targeting it for degradation.  This would ultimately prevent one of the key structural proteins of the bullet-shaped virion to be made and prevent the virus from being transmitted.  It has also been discovered that the human monoclonal antibody (HuMAbs) may serve as an alternative treatment against less affordable treatments.   HuMAbs was found to be the best monoclonal antibody as it neutralized all the rabies viruses it was tested against, it recognized both minor site A and antigenic site III and was able to protect hamsters from the most lethal dose of the virus.5  This is another important finding as even if an individual is infected, HuMAbs can be applied for post-exposure protection against the viral genome. 

Thank you for listening to this episode of Genomics Revolution, we hope you enjoyed your time and were able to learn something new from this talk. 

References: 

1.     What is Rabies? Centers for Disease Control and Prevention. 2019 Jun 11 https://www.cdc.gov/rabies/about.html

2.      A brief history of rabies: Microbiology. 2017 Apr 12 https://www.labroots.com/trending/microbiology/5761/brief-history-rabies

3.      A brief history of rabies: Microbiology. 2017 Apr 12 https://www.labroots.com/trending/microbiology/5761/brief-history-rabies

4.     Kissi B, Tordo N, Bourhy H. Genetic Polymorphism in the Rabies Virus Nucleoprotein Gene. Virology. 1995;209(2):526–537.

5.     Sloan SE, Hanlon C, Weldon W, Niezgoda M, Blanton J, Self J, Rowley KJ, Mandell RB, Babcock GJ, Thomas WD, et al. Identification and characterization of a human monoclonal antibody that potently neutralizes a broad panel of rabies virus isolates. Vaccine. 2007;25(15):2800–2810. 

Some More Information on How HIV Causes AIDS & on New Drugs:

https://m.youtube.com/watch?v=BADDj82oces (Battle between HIV & Immune System video from Nature Reviews)

https://www.npr.org/sections/health-shots/2019/05/30/727731380/old-fight-new-front-aids-activists-want-lower-drug-prices-now (National Public Radio (NPR) segment “AIDS Activists Take Aim at Gilead to Lower Price of HIV Drug PrEP”

https://www.npr.org/sections/health-shots/2019/06/11/731350223/expert-panel-recommends-wider-use-of-daily-pill-to-prevent-hiv (NPR segment “Expert Panel Recommends Wider Use of Daily Pill to Prevent HIV”

https://www.npr.org/sections/health-shots/2019/12/04/784733337/hiv-prevention-drugs-are-available-for-free-how-do-you-get-them (NPR segment “HIV Prevention Drugs are Available for Free: How Do You Get Them”

Genomics Revolution 

Guest Hosts: Emily Harris & Tim Murton

Episode 48: HIV & AIDS

Script:

     Welcome to Genomics Revolution! This is Emily Harris and this is Tim Murton. We are from the 2020 Hiram College Genetics course, and we are hosting this episode on the genome of Human Immunodeficiency Virus, or HIV. HIV targets a host’s immune system and causes it to fail. This complication is referred to as HIV infection, and can eventually develop into acquired immunodeficiency syndrome, or AIDS, which is the most advanced stage of HIV infection (1). 

This virus is in the genus lentivirus, the family of Retrovirdae, and the subfamily Orthoretrovirinae (1). HIV is typically divided into two types, HIV-1 and HIV-2, and each type can be subdivided into several smaller groups based on differences in viral antigens, and from where each strain evolved (3). HIV was recognized on a wide scale during an outbreak in the 1980s, but was actually first discovered in humans between 1920 and 1940 (1). After years of studying the virus, it was discovered that it is spread through contact with infected bodily fluids like blood, semen, breast milk, or several others. It was also discovered that the virus was very similar, genetically, to simian immunodeficiency-deficiency virus, or SIV, which is a non-human primate immunodeficiency virus (1). HIV-1 appears to have evolved from SIV strains in chimpanzees in Central Africa, and HIV-2 likely evolved from a strain in West African mangabeys (1). So it is believed that the virus was transmitted to humans when these primates were hunted for meat and their infected blood was ingested. The virus then mutated and evolved in humans into HIV (3). 

Now let’s talk about the HIV genome. The genome of this virus consists of two single stranded RNA molecules and is roughly 9,200 bases in size (2). After sequencing the genome, it was found that it contains 9 genes and encodes 15 viral proteins, which is relatively small when we consider how powerful of a virus it is (3). HIV is also classified as an enveloped retrovirus (1). This means the virus uses a special enzyme called  reverse transcriptase, which turns its RNA into DNA, then uses that DNA to infect a host (1). They literally insert a copy of their own genome into a host’s genome!    

So this virus works in a very intelligent way making treatment for infection extremely difficult, especially before the virus was understood. This is why it was so important to sequence the HIV genome. By learning more about the genetic makeup of HIV, it became easier to understand how the virus operates, how it evolves and what it evolved from, how to prevent possible outbreaks, and what types of treatment may work. Sequencing the genome even opened the door to possible gene therapy that can be used to treat or hopefully even cure the disease someday!

Sequencing the HIV genome told us a lot about the virus, so let’s highlight a few of the key findings. Sequencing the genome is how we found out that HIV is closely related to SIV (5). This information was crucial because then we were able to use our understanding of SIV to help come up with a better treatment for HIV.  

Another finding was that there are subtypes of HIV-1 such as the CG-0018a-01 HIV-1 genome (7).  This subtype-L was found in the Democratic Republic of the Congo. The research showed that this subtype-L was found to be transmitting in the DRC and that there could be more strains circulating (7). Knowing this was extremely important because it shows the dangers of mutations, and how easily the virus can evolve and create new strains. This let scientists know to look out for new strains of HIV that could be more easily transmitted and harder to combat than the original strain.

Sequencing the HIV genome also showed us that HIV-1 genetic material is damaged by hypermutation (6).  G-to-A hypermutation, for example, damages the virus by producing abnormal amounts of transitions from guanine to adenine. These mutations are thought to be caused by HIV’s reverse transcriptase enzyme, which has the ability to hypermutate in the presence of unbalanced nucleotide pools during the cell cycle (6).  This is important because it shows that the virus has a weakness that is possibly being caused by a host mechanism that can decrease virus replication. This finding implies that if we can promote hypermutation states in HIV, we may be able to induce non-reversible mutagenesis of the viral DNA. This strategy may pave the way to discovering a cure for HIV! Thanks for listening!

References:

[1]    Arbeitskreis Blut, Untergruppe ‘Bewertung Blut- assoziierter Krankheitserreger’: Human 

immuno- deficiency virus (HIV). Transfus Med Hemother 2004;31:102–114.

[2]    Feinberg Mark B, Greene Warner C (1992). "Molecular Insights into human immunodeficiency virus type1 pathogenesis". Current Opinion in Immunology. 4 (4): 466–474. doi:10.1016/s0952-7915(06)80041-5. PMID 1356348.

[3]    Li G, Piampongsant S, Faria NR, Voet A, Pineda-Peña AC, Khouri R, Lemey P, Vandamme AM, 

Theys K (February 2015). "An integrated map of HIV genome-wide variation from a population 

perspective". Retrovirology. 12 (1): 18. doi:10.1186/s12977-015-0148-6. PMC 4358901. PMID 25808207.

[4]    German Advisory Committee Blood (Arbeitskreis Blut), Subgroup ‘Assessment of Pathogens Transmissible by Blood’ (2016). Human Immunodeficiency Virus (HIV). Transfusion medicine and hemotherapy : offizielles Organ der Deutschen Gesellschaft fur Transfusionsmedizin und Immunhamatologie, 43(3), 203–222.

[5]    Janini, M., Rogers, M., Birx, D. R., & McCutchan, F. E. (2001). Human immunodeficiency virus type 1 DNA sequences genetically damaged by hypermutation are often abundant in patient peripheral blood mononuclear cells and may be generated during near-simultaneous infection and activation of CD4(+) T cells. Journal of virology, 75(17), 7973–7986.

[6]    Williams, K. C., & Burdo, T. H. (2009). HIV and SIV infection: the role of cellular restriction and immune responses in viral replication and pathogenesis. APMIS : acta pathologica, microbiologica, et immunologica Scandinavica, 117(5-6), 400–412.

[7]    Yamaguchi, Julie BS; Vallari, Ana MS; McArthur, Carole MD, PhD; Sthreshley, Larry PhD; Cloherty, Gavin A. PhD; Berg, Michael G. PhD; Rodgers, Mary A. PhD. (2020) Complete Genome Sequence of CG-0018a-01 Establishes HIV-1 Subtype L. JAIDS Journal of Acquired Immune Deficiency Syndromes: Volume 83 - Issue 3 - p 319-322

Genomics Revolution

Guest Hosts: Sheree Nobles & Joshua Gregory

Episode 47: Human Papillomavirus (HPV)

Script:

Josh- Hello everyone, and welcome to this episode of Genomics Revolution! We’re your guests hosts 

today, Sheree Nobles and Joshua Gregory. Today we’ll be talking about Human Papillomavirus, 

or HPV as it’s commonly known. This is a sexually transmitted infection, and to keep on topic with this year’s theme, it’s a virus.

Sheree- There isn’t a scientific name for it, so much as a bunch of scientific names, as there are over 100 

different human papillomaviruses. These viruses can cause not only genital warts, but warts 

elsewhere, and have even been linked to cervical cancers.

Josh- Five types of HPV were found prior to 1983, but most of those HPVs were present in animals, not 

humans. HPV 6 was found by German virologist Harold zur Hausen shortly before HPV 11 was 

found by the same man in 1983. Shortly after that, he found HPVs 16 and 18, which together are 

present in roughly 70% of cervical cancers.

Sheree- zur Hausen was originally studying cervical cancer, and the only reason he thought to look for 

viruses was because the cancer seemed to be “infectious” despite cancer not behaving the way 

the should . It was when his friend, a U.S. researcher named Richard Shope, told him about a 

virus in rabbits  that would cause warts and cervical cancer did he think about the possibility of a 

virus causing the disease.

Josh- It’s important to note that most HPVs don’t cause cancer, or any symptoms at all. More often 

enough, HPV is present in a human, but does not cause any symptoms before the immune 

system removes it. It’s only a few types of the virus that can stay around long enough to induce 

cancer, like HPV 16 or 18. This is because the virus affects a cell’s growth cycle while trying to 

reproduce, causing the cells to grow rapidly and for warts to form, and sometimes causing 

tumors as well.

Sheree- This is why it’s important to understand the virus. Cervical cancer only has a 66% survival rate, 

so if it can be avoided, it should be. Because HPV is so closely related to the cancer, it makes 

sense that we should try to understand it completely to try and stay safe from deadly diseases. 

It’s also important to realize that someone can be carrying the virus without showing any 

symptoms, and could possibly transfer it to another person, spreading the virus and its 

dangerous symptoms.

Josh- Not only should we understand the virus, but everyone should also get tested regularly to make 

sure whether or not they’re carrying HPV. Now the virus itself isn’t too complicated. Its genome is made of double-stranded DNA in a circular formation, with a singular DNA molecule. It is roughly 7916 base pairs in length with 8 ORFs, though this data is subject to slight change between different types of HPV.

Sheree- There were three findings that we thought were really important. One, HPVs are separated into 

two unofficial classifications: low and high risk. Most human papillomaviruses never cause any 

symptoms, let alone serious diseases, but even still, they can be transferred between people. If 

someone has a compromised immune system, an HPV that doesn’t hurt one person could hurt 

them. Two, certain HPVs are much more likely to cause cervical cancer.

Josh- HPVs 16 and 18 are some of the more dangerous types of the virus you can get. Together they are 

present in approximately 70% of all cervical cancer cases. This is due to their ability to target 

retinoblastoma (Rb) protein families and p53 in our cells. This can induce telomerase 

production, causing the cell to be unable to repair damaged DNA, a crucial task for cancer cells 

to continue to survive. And last but not least, HPV is total is present in around 99.7% of cervical 

cancer samples, as found in 1999 by a group of scientists including U.K. Researcher Professor 

Julian Peto.

Sheree- These findings are important for several reasons. They tell us that anyone could be carrying HPV 

at any time and not know it. This is a common trend among some viruses, much like the corona 

virus that is currently causing an uproar. They also tell us that cervical cancer, which only has a 66% survival rate, is so closely linked to HPV that we should take every care to avoid contracting HPV. Lastly, knowing the mechanism of HPV causing cancer brings us a step closer towards finding an actual cure for existing HPV infection, not just prevention, a vaccine, or surgery.

Josh- This has been an episode of Genomics Revolution, and we thank you all for listening to us ramble 

about a virus.

Sheree- We’ve had some fun recording this for you, and we hope you’ll take away from this the 

importance of understanding viruses and the diseases they can cause.

Josh- This has been Josh,

Sheree- and Sheree,

Josh- and we hope you have a great day, take care!

References:

IARC Working Group on the Evaluation of Carcinogenic Risk to Humans. “Human Papillomavirus (HPV) 

Infection.” Human Papillomaviruses., U.S. National Library of Medicine, 1 Jan. 1970, www.ncbi.nlm.nih.gov/books/NBK321770/.

“HPV: the Whole Story, Warts and All.” Cancer Research UK - Science Blog, 

scienceblog.cancerresearchuk.org/2014/09/16/hpv-the-whole-story-warts-and-all/.

Burk, Robert D., et al. “Human Papillomavirus Genome Variants.” Virology, Academic Press, 31 Aug. 

2013, www.sciencedirect.com/science/article/pii/S0042682213004388.

Liu, Ying, et al. “Whole-Genome Analysis of Human Papillomavirus Types 16, 18, and 58 Isolated from 

Cervical Precancer and Cancer Samples in Chinese Women.” Scientific Reports, Nature Publishing Group UK, 21 Mar. 2017, www.ncbi.nlm.nih.gov/pmc/articles/PMC5428204/#!po=25.0000.