Lecture 11 - Emerging Pathogens

What are emerging diseases?

• Have not occurred in humans before

• Have occurred previously but affected only small numbers of people in isolated places

• Have occurred throughout human history but have only recently been recognized as distinct diseases resulting from an infectious agent

What are re-emerging diseases?

Historically, major health problems globally or in a particular country, declined dramatically, and are again becoming health problems

What are the characteristics of emerging pathogens?

• More likely to be zoonotic than not

• More likely to have a broad host range

• Each pathogen group is represented

• Many fall within CDC Category C

What are factors that influence (re)emergence?

• Changes in land use or agricultural practices

• Changes in human demographics and society

• Poor population’s health

• Hospitals and medical procedures

• Pathogen evolution

• Contamination of food sources or water supplies

• International travel

• Failure of public health programs

• International trade

• Climate change

What is the CDC’s prioritization of pathogens?

• A meeting in 2015 to prioritize emerging pathogens

• Development of a tool to evaluate diseases for accelerated R&D

1. Crimean-Congo haemorrhagic fever

2. Filovirus diseases (EVD & Marburg)

3. Highly pathogenic emerging Coronaviruses relevant to humans (MERS Co-V and SARS)

4. Lassa Fever

5. Nipah

6. Rift Valley Fever

7. Chikungunya, severe fever with thrombocytopenia syndrome, Zika virus

What are the prioritization elements?

• Human transmissibility

• Severity or case fatality rate

• Spillover potential

• Evolutionary potential

• Countermeasures

• Difficulty of detection or control

• Public health context of the affected area(s)

• Potential outbreak scope

• Potential societal impacts

What is severe acute respiratory syndrome?

• SARS-CoV-2 is the 7th coronavirus known to infect humans

• SARS-CoV, MERS-CoV, and SARS-CoV-2 can cause severe disease

• Whereas HKu1, NL63, OC43, and 229E are associated with mild symptoms

What do we know about SARS-CoV-2?

• It is an enveloped β-coronavirus, with similarity to SARS-CoV-1 (80%) and bat coronavirus RaTG13 (96.2%)

• The viral envelope is coated by spike (S) glycoprotein, envelope (E), and membrane (M) proteins

• Host cell binding and entry are mediated by the S protein

• The first step in infection is the virus binding to a host cell through its target receptor

• The S1 subunit of the S protein contains the receptor-binding domain that binds to the peptidase domain of angiotensin-converting enzyme 2 (ACE2)

What is the mechanism of action of SARS-CoV-2?

• The virus binds to ACE2 receptor and viral entry

• Release of viral genome

• Translation

• Proteolysis

• RNA replication

• Transcription and replication of the viral genome

• Viral protein translocation

• Viral assembly

• Virus maturation

• Virus release

How does SARS-CoV-2 have pandemic potential?

• Increased transmission relative to SARS-CoV-1

• Tropism is potentially enhanced for nasal epithelial cells

• Receptor recognition likely recognizes ACE2 from a diversity of animal species, including humans, and it has intermediate affinity for human ACE2

• The highest infectious potential of SARS-CoV-2 is just before or within first 5 days of symptom onset

What are the arguments in support that SARS-CoV-2 was a lab construct?

• The SARS-like virus that caused the pandemic emerged in Wuhan, a city where the world’s foremost SARS-like virus research lab is located

• The year before the outbreak, the Wuhan Institute, working with US partners, had proposed creating viruses with SARS-CoV-2’s defining feature

• The Wuhan lab pursued this type of work under low biosafety conditions that could not have contained an airborne virus as infectious as SARS-CoV-2

• The hypothesis that COVID-19 came from an animal at the Huanan Seafood Market in Wuhan is not supported by strong evidence

• Key evidence that would be expected if the virus had emerged from the wildlife trade is still missing

What are the arguments against the idea that SARS-CoV-2 was a lab construct?

• Bat coronavirus spillover events into humans are common

• The Wuhan lab studied a coronavirus strain called WIV1: a bat coronavirus like SARS-1 that could grow in monkey cells in the lab but didn’t cause disease in people; a US intelligence assessment in 2023 confirmed that there was no evidence of researchers sick with COVID before the outbreak

• Researchers weren’t working with SARS-CoV-2

  • If they were, BSL-2 containment is considered adequate

  • If the virus leaked from the Wuhan Institute of Virology, then most, if not all, the early cases should have been around the Institute, not 9 miles away

• Two lineages of the SARS-CoV-2 virus were detected early in the outbreak

  • When the outbreak began, Chinese authorities shut down the Huanan Wholesale Seafood Market, disinfected the area, and killed the animals likely to have served as intermediates between bats and humans (no available animals to test)

• Researches have found genetic evidence of SARS-CoV-2 in carts, drains, metal cages, machines, and other things that processed or made contact with the animals after they had been slaughtered in the wet market stalls

  • In the same specimens, they found mammalian DNA consistent with raccoon dogs, bamboo rats, and palm civets - all likely intermediate hosts as bat coronaviruses spilled into the human population

Genetic tracing of market wildlife and viruses at the epicentre of the COVID-19 pandemic: Background

• Early SARS-CoV-2 sequences belong to two lineages, denoted A and B, separated by two nucleotide substitutions (C8782T & T28144C)

• The SARS-CoV-2 rooting between lineages is uncertain:

  • A detected in environmental samples from the market

  • B detected from patients with direct market contact

• This is consistent with two successful zoonotic spillover events of SARS-CoV-2 into humans

• Animals infected with a highly transmissible virus at market-multiple zoonotic events are primed to occur

Genetic tracing of market wildlife and viruses at the epicentre of the COVID-19 pandemic: Method

• Start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market

• Analyzed environmental qPCR and sequencing data collected from the market in early 2020

Genetic tracing of market wildlife and viruses at the epicentre of the COVID-19 pandemic: Results

• Common ancestor of SARS-CoV-2 linked to Huanan market matches the global common ancestor

• Wildlife mtDNA found in samples from stalls positive for SARS-CoV-2

• Found additional animal viruses, so live mammals shedding viruses

• Data consistent with a spillover event from a bat reservoir south of Wuhan and viral transmission chain via animal trade

What are the dangers of misinformation?

• Casts unsupported blame on scientists

  • Those who studied coronaviruses or led the response - they must have engineered it or allowed it to escape

  • Scientists are part of an international cover-up and are accused of taking bribes from the NIH

  • Scientists collecting data or communicating evidence to support a zoonosis origin to the media, are under attack - harassment, intimidation, threats, and violence

• Long-term consequences:

  • Withdraw from social media platforms

  • Reject opportunities to speak in public

  • Divert work to less controversial/timely topics

  • Fewer experts available to help in future pandemics

  • Fewer experts are willing to communicate findings that are important to global health

  • Research that could prepare for future pandemics has been deferred, diverted, or abandoned

Where are the potential threats for SARS-CoV-2?

• CDC: SARS-CoV-2 was isolated in the lab and is available for research by the scientific and medical community

• Sheahan et al. 2008: used synthetic biology to create a chimeric SARS virus

• From Wan et al 2020: based on decade-long structural studies on SARS-CoV, data predicts that a single N501T mutation may significantly enhance the binding affinity between 2019-nCoV RBD and human ACE2

What are research areas of SARS-CoV-2?

• Antiviral research: aimed at testing the ability of existing or experimental antiviral medication to treat/prevent infection

• Vaccine development

• Pathogenesis research: determine various ways the virus can be transmitted to a host, the severity of illness it causes in a host, and how much virus is produced in the body, and what organs the virus can spread to within the body

• Virus stability research: how long the virus can survive under certain conditions

What is Zika virus?

• Part of the Flaviviridae virus family

• Icosahedral symmetry, enveloped, spherical in shape

• +-sense ssRNA genome

  • Small

  • 1 ORF sequence translated into a single polyprotein

  • ORF is flanked by two non-coding regions

• First full genome sequence in 2007

• 3 main clusters originating from a common ancestor

What are the vectors and transmission of Zika?

• Abovirus - transmitted by arthropods

• Mosquitoes are the dominant vector of ZIKV

• Non-human primates could be a reservoir

• Mosquito bites, sexual, perinatal, blood transfusion

• Spreads in the lymph and blood, but can also be present in semen/vaginal fluids and saliva

What are the clinical manifestations of Zika?

• <20% show symptoms

• Mild symptoms lasting up to a week (rarely death)

• Can result in misdiagnosis due to flu-like symptoms

• Guillain-Barré Syndrome affects the nervous system (a link with ZIKV?)

What is the detection and diagnosis of Zika?

• Take a urine, blood, or saliva sample and complete serological/PCR tests

  • Detect viral RNA using RT-PCR

  • Can also use ELISA, neutralization assay

    • Detecting or neutralizing IgG and/or IgM ZIKV antibodies

    • Should be completed within the first 2 weeks of symptom onset

• Current challenges

  • Lack of standardized and sensitive tests

  • No commercial kits available for the detection of ZIKV

  • Some Ab cross-reactivity with dengue virus and yellow-fever virus

What is the prevention and treatment of Zika?

• Prevention by avoiding mosquito bites

• Prevention of sexual transmission by using condoms

• Pregnant individuals should not travel to Zika-infected areas

• No vaccine and no anti-viral → treat the symptoms

How would Zika be a bioterrorism threat?

Genetic weaponization

• May change the genome to allow for weaponization

Can purchase online

• Ethical argument for the availability for vaccine research vs. facilitating bioterrorism

What is Nipah (NiV)?

• Paramyxoviridae virus family; genus = Henipavirus

• Enveloped, filamentous capsid, pleomorphic (variable shape)

• -sense, non-segmented, ssRNA genome

  • 18.2 kb total

  • 6 genes corresponding to 6 structural proteins: nucleocapsid (N), phosphoprotein (P), matrix protein (M), fusion protein (F), glycoprotein (G), and large RNA polymearse (L)

What are the vectors and transmission of Nipah?

• Transmitted by fruit bats, pigs, or humans

  • Less often cattle, horses, or goats

• Direct exposure, or exposure to contaminated products/fruits, could result in infection

• Largely in East and Central Asia

What are the clinical manifestations of Nipah?

• In humans, the incubation period is 5-14 days, illness presents with 3-14 days, symptoms resemble the flu

  • Fever

  • Severe headaches

  • Muscle pain

  • Dizziness

  • Vomiting

• More serious symptoms affecting the CNS include come, seizure, and the inability to breathe

• Altered mental status

• Disease may progress to encephalitis or meningitis

• 40-70% mortality rate

What is the detection and diagnosis of Nipah?

• Identification of symptoms

• Viral isolation, followed by RT-PCR

• Detecting anti-Nipah antibodies using ELISA

What is the prevention and treatment of Nipah?

• There is no vaccine and no anti-viral → supportive care only

• Ribavirin is effective against the virus in vitro, but human investigations are inconclusive

• Antibody targeting Nipah G glycoprotein could be beneficial for post-exposure therapy

How would Nipah be a bioterrorism threat?

• Has attributes in which it could be made to have very damaging symptoms, easily spread from human to human, transmissible to many common mammals

• Result in high mortality rate

• Previous natural outbreaks caused fear, disease, disabilities, death, social disruption, and severe economic loss

• No good vaccines, no antiviral

• Genetic manipulation is possible since the viral genome is published

• Possible dispersal via deliberate infection of pigs

What is the Ebola virus?

• Part of the Filoviridae virus family (genus = Ebolavirus)

• Enveloped, cylindrical/tubular in shape

• 5 species: Ebola virus (EBOV; Zaire), Sudan virus (SUDV), Reston virus (RESTV), Tai Forest virus (TAFV) Bundibugyo virus (BDBV)

• -sense ssRNA genome

  • 19 kb total

  • 7 genes encoding 11 proteins

What are the vectors and transmission of Ebola?

• Natural reservoir is unknown

  • Fruit bats are suspected

• Can infect humans, bats, monkeys, apes (primates)

• Virus spreads through direct contact of the mucous membranes, wounds, or abrasions on the skin with infected body fluids

  • It is not spread though food, water, or the air, and is not transmissible through arthropods

• Also infected by Ebola virus-contaminated objects

• Primarily in Africa

What are the clinical manifestations of Ebola?

• Symptoms include: Fever/chills, severe headache, muscle pain, weakness, fatigue, diarrhea, vomiting, abdominal pain

• Peak is unexplained hemorrhage

• Death from shock and multi-organ failure

• Incubation period is 2-21 days → death can occur within 3 weeks of infection

What is the detection and diagnosis of Ebola?

Within a few days after symptoms begin:

• Antigen-capture ELISA

• IgM ELISA

• PCR
  Virus isolation

Later in the disease course or after recovery

• IgM and IgG antibodies

Retrospectively deceased patients

• PCR

• Virus isolation

What is the prevention and treatment of Ebola?

• Ebola vaccine rVSV-ZEBOV, protective against the Ebola virus

• A live, attenuated recombinant vesicular stomatitis virus (rVSV) vaccine manufactured by Merck (contains the EBOV glycoprotein)

• Pre-exposure vaccination for: EVD responders, lab techs, and healthcare personnel

• Treatment: provide fluids, maintaining O2 levels, treating secondary infections

How would ebola be a bioterrorism threat?

• Societal disruption

• Symptoms and mortality

• Vaccine is readily available so would have to modify the virus genetically