Pandemic Threats and COVID-19

Potential Pandemic Threats: Bird Flu

• Focus on subtypes H5N1 and H7N9.
• Reservoir: Aquatic birds (ducks, swans). They often migrate.
• Transmission to domestic poultry (chickens, turkeys, quail) due to shared water sources and free-range environments.
• Bird flu starts as Low Pathogenic Avian Influenza (LPAI):
  • Minor or no symptoms in birds (e.g., snotty beak).
  • Reduced weight gain, impacting the poultry sector.
• Mutation to High Pathogenic Avian Influenza (HPAI):
  • Systemic, hemorrhagic, highly virulent infection.
  • Can wipe out entire flocks in days.
  • Control: Culling the infected flock.
• Historically, HPAI outbreaks were rare (about a dozen in the last century).
• Early 2000s: Increased reports of HPAI outbreaks in domestic poultry, particularly in Southeast Asia and China.
• Spread via migratory bird fly zones to Europe, Africa, and Indonesia.
• HPAI has become endemic in some regions, causing economic impact.
• Human infections reported via direct transmission of bird flu to humans.
• Relatively old data indicates approximately 800 confirmed human cases with a 50% mortality rate. This is extremely concerning.
• H7N9 virus emerged more recently (starting about ten years ago).
• Outbreaks of human infection via direct transmission from birds. No intermediate host needed.
• Approximately 800 confirmed cases with about 300 deaths, mainly in China and Southeast Asia.
• Transition from LPAI to HPAI is associated with insertion of basic amino acids (arginines and lysines) into the cleavage site of hemagglutinin.
• This changes the breadth of proteases that can cleave it, leading to systemic infection.
• Instead of being localized by a lung-specific protease, it can be cleaved by more systemic proteases such as plasmodium furan.
• Direct transmission from birds to humans removes the need for an intermediate host (like pigs).
• H5N1 infection is no longer sporadic, becoming endemic in wild aquatic bird populations, leading to continued outbreaks and viral evolution.
• These viruses have not yet acquired the ability to spread from person to person.
• The species barrier (alpha 2-3 to alpha 2-6 linkage) makes human infection difficult, requiring high doses due to the location of alpha 2-3 receptors in the lower respiratory tract.
• Persistence and repeated spillover events increase the chance of adaptation for human-to-human transmission.
• Recent HPAI outbreaks are associated with human infection, increasing the likelihood of spillover events.
• A recent paper showed molecular signatures of mammalian adaptation in a South American sample.
• Mass kill of seals (aquatic mammals) in Chile by H5N1.
• Concern due to the potential impact, modeled after the 1918 Spanish flu:
  • The Spanish flu killed 30 to 50 million people.
  • Applying similar impact to current population and travel conditions.
  • Modeling shows a potential for up to 10 million deaths in six months from an H5N1 high-path epidemic due to non-existent pre-existing immunity.

SARS CoV-2 Pandemic (COVID-19)

• Movie "Contagion" as a scientifically accurate depiction of a global pandemic response to an emerging paramyxovirus.
• Touches on virus identification, therapy development, and public response (including conspiracy theories).

Basic Virology of Coronaviruses

• Enveloped virus with positive-sense, linear RNA genome.
• Spike proteins on the outside act as the attachment receptor.
• Named coronaviruses due to the crown-like appearance (corona) of the spikes.
• Two major families: alpha and beta coronaviruses.
• Prior to SARS and SARS-CoV-2, circulating human coronaviruses caused mild cold-like symptoms.
• Limited research on these viruses due to their mild impact.
• Beta coronaviruses (SARS, MERS, SARS-CoV-2) cause more severe disease.
• SARS and MERS served as warnings of potential animal-to-human transmission.

Coronavirus Genome

• Positive-sense RNA genome that is linear.
• Encodes multiple proteins. $pp1a$ and $pp1b$ (or $ORF1a$ and $ORF1b$) encode polymerase subunits (replication machinery).
• Polymerase subunits are highly conserved.
• The Spike protein and accessory proteins have are areas of genetic variation.
• Viral particle includes spike protein, viral genome associated with nucleocapsid protein, and matrix protein.
• Matrix protein helps initiate viral replication through pH drops.

Viral Replication Cycle

• Spike protein binds to host cell receptor (e.g., CKM in mouse coronavirus).
• Internalization and uncoating release the positive-sense RNA genome.
• Translation of $ORF1A$ and $ORF1B$ sections.
• Proteolytic cleavage generates RNA-dependent RNA polymerase.
• RNA polymerase generates copies of the genome.
• Translation of mRNA transcripts encodes structural and accessory proteins.
• Combination of genome copies with structural proteins.
• Egress and release.
• Proteolytic cleavage is crucial for initiating replication via the RNA-dependent RNA polymerase.

Origins of Circulating Coronaviruses

• Spillover events from animal reservoirs.
• Alpha coronaviruses (229E and NL63) originate from bats; 229E may have spilled over into camelids (alpacas) before infecting humans.
• Beta coronaviruses (OC43 and HKU1) originate from rodents; OC43 came via cows; the intermediate host for HKU1 is unknown.
• SARS and MERS: natural reservoir in bats; intermediate hosts are civet cats (SARS) and camels (MERS).
• SARS, MERS, and SARS-CoV-2 are beta coronaviruses.

Warnings from SARS and MERS

• Early 2000s: SARS outbreak in Hong Kong spread to other regions.
• Unusual symptoms distinguished it from influenza.
• Approximately 8,000 cases and 774 deaths (9-10% case fatality rate).
• Transmission occurred after symptoms appeared, unlike flu.
• Patient zero in Hong Kong led to super-spreader events.
• Local epidemics due to close contact (e.g., healthcare workers).
• MERS emerged in 2012 in the Middle East.
• Fewer cases (2,400) but higher case fatality rate (35-40%).
• Limited spread likely due to camels being the intermediate host.
• Outbreaks occur where camels are exported from the Middle East.
• Ongoing bubbling outbreaks, with travel advisories in the Middle East.
• Clear evidence of spillover events from bats into intermediate hosts (civet cats for SARS, camels for MERS).
• Wet animal markets and close contact facilitated transmission.

SARS CoV-2 Emergence

• Late 2019: Reports from Wuhan, China, of severe acute respiratory syndrome cases and viral pneumonia.
• Progression to respiratory failure requiring ICU admission.
• By the end of 2020, approximately 2,700 cases and 80 deaths, mainly in China.
• WHO declared a public health emergency of international concern.
• February 2020: WHO raised the risk assessment to very high.
• March 2020: WHO declared a pandemic.
• Update: almost 676 million cases and close to 7 million deaths worldwide (noted it is likely still a pandemic).
• Fatality rate: Ranges from 1-4% depending on jurisdiction.
• Case fatality rate is lower than MERS and SARS but higher than flu.
• Continuous mutation and evolution due to the lack of proofreading capacity of the RNA-dependent RNA polymerase.
• Emergence of new strains that dominate circulation (Alpha, Delta, Omicron).
• Omicron is now the predominant variant globally.

Origins of SARS CoV-2 and Conspiracy Theories

• Conspiracy theories emerged due to the presence of the Wuhan Institute of Virology, which was researching SARS coronaviruses.
• Suggestion of accidental lab leak with little to no evidence.
• Epidemiological and molecular evidence suggests a spillover event.
• Primary cases linked to the Huanan Seafood Wholesale Market.
• Sick individuals were linked to visiting this market.
• Molecular signals and viral fragments were identified within the market.
• The likely outbreak started from the store selling specific animals.
• Strong molecular and epidemiological evidence indicates a spillover event via intermediate hosts.
• Chinese New Year migration concentrated people in Wuhan.
• Infected individuals then traveled globally, spreading SARS-CoV-2.

Natural Host Reservoir of SARS CoV-2

• Virus called RATG13, isolated from bats, is genetically similar to SARS-CoV-2.
• Early studies of SARS-CoV, allowed for quick data comparisons of samples of information available in data banks.
• RATG13 has the most similarity in the SARS group.
• Human coronaviruses are phylogenetically related to RATG13.
• Newer data is emerging that suggest precursors are in other regions outside of just Wuhan.
• Pangolins are unlikely intermediate hosts due to genetic distinctions, but they show useful information regarding mammalian adaptations.

Spike Protein Adaptations

• Mutations in the receptor-binding site of the spike protein enable person-to-person transmission.
• Amino acid changes in the receptor-binding domain are absent in RATG13 but present in pangolin viruses.
• These adaptations enable the spike protein to bind to the ACE2 receptor.
• Human virus picked up insertion of basic amino acids in the polybasic cleavage site.
• Insertion of basic amino acids in the polybasic cleavage site means that the spike protein is more readily cleaved, enabling conformational change, that can facilitate, fusion of the spike protein, in the viral, and host membranes.
• The more readily cleaved spike protein facilitates fusion of viral and host membranes.
• This basic cleavage site is not present in pangolins.

SARS CoV-2 Transmission

• The spike protein attaches to the ACE2 receptor on human cells, particularly in vascular endothelial cells and lung epithelial cells.
• Adaptations in the receptor-binding site increase the affinity for human ACE2.
• TMPRSS2 is a co-receptor that cleaves the spike protein after it binds to ACE2, triggering infection.

SARS CoV-2 Transmission

• The virus is easily transmitted with a reproductive number (R0) of 2.5 at the start of the pandemic (2-3 people infected per case), increasing exponentially for every 100 cases.
• The current Omicron variant has an R0 of about 8 due to the virus' mutation rate.