A Chemist’s Guide to the COVID-19 Outbreak

June 22, 2020

This informational article is an attempt to organize all of the pertinent information about COVID-19 and pandemics from a chemistry point of view.

The COVID-19 pandemic has created a plethora of misinformation regarding viruses, transmission, eradication, and prevention. This information brief is an attempt to organize all of the pertinent information from a chemistry point of view.

The COVID-19 pandemic has created a plethora of misinformation regarding viruses, transmission, eradication, and prevention. Outbreaks of disease which have led to pandemics have been frequent throughout history, including the smallpox outbreaks which decimated the Incan empire in the 1500s to the more recent SARS pandemic and the Ebola epidemics in the past decades. It wasn’t until the first electron microscopes that the actual virus structures were observed in the 1930s. Since those early discoveries, there have been more than 5000 additional viruses detailed with millions more still uncharacterized in the environment.

What Are Viruses?

A virus (Latin for poison) is a very small infectious agent that can only replicate inside living cells of another organism (microorganisms, plants, and animals). Most viruses can range in size from 20–300 nm (Figure 1). In essence, viruses are parasites that cannot live and replicate outside host cells. Viruses lack the cellular organelles and processes to survive and replicate on their own. The host cell’s replication system is hijacked by the virus and produce viral genetic material. (See upper right for Figure 1, click to enlarge.)

Virus Structure

Outside of a host cell, viruses are independent particles called virions. There are three basic parts to viruses: the genome (genetic material-either deoxyribonucleic acid [DNA] or ribonucleic acid [RNA]); the capsid (a protein capsule surrounding the genetic material); and in some cases, a lipid or protein outer envelope. Viruses can be found in a variety of shapes, from simple to complex. There are four morphological forms of viruses: icosahedral, spherical, helical, and complex (Figure 2). The viruses can also vary in size from under 50 nm to over 900 nm in length (helical or filamentous viruses). (See upper right for Figure 2, click to enlarge.)

The COVID-19 virus is a new virus that is part of the Coronavirus family (Coronaviridea). The coronavirus was named for the Latin for crown because the projections (spike proteins) on the surface of the spherical virus looked like points on a crown (Figure 3). The coronaviruses have a membrane enveloping the capsid and are in the middle to large range of the virus size scale at around 100 nm. (See upper right for Figure 3, click to enlarge.)

The coronavirus contains RNA genetic material rather than DNA. RNA viruses have higher mutation rates than DNA viruses because the enzymes, which catalyze RNA replication (RNA polymerases), lack the ability to proofread or error correct the genetic material being coded unlike DNA and DNA polymerases. This reason is why these types of viruses mutate so quickly and are difficult to create vaccines to combat.

Viruses, Disease, and Health

Most viruses are species-specific, meaning an equine virus does not spread to a human. However, there are zoonotic viruses that can spread between animals and humans. In some cases, a virus can mutate and jump to other species, which seems to be the case with the COVID-19 virus.

In most cases, viruses are infamous for being instigators of disease, but viruses can also be used to combat illness and diseases, such as cancer by hijacking the cellular reproduction of cancer cells. Viruses are also instrumental in human health. It is well known that humans have beneficial bacteria in their body.

Another resident of the human microbiome are viruses (called the virome). The virome inhabits humans within the first months of life. Each person has a unique virome. Retroviruses are RNA viruses that change the genome of the host cell. The host cell then incorporates the new genetic material into its own code when it reproduces. Endogenous retroviruses, viruses that originate within an organism, tissue, or cell, are prevalent in humans (up to 8% of our genetic material) (1). These viruses were once considered junk material, but have been discovered to have a role in human health. In a recent study, it was hypothesized that since humans diverged from chimpanzees, up to 30% of protein adaptations have been due to viruses (2).

Viral Infections

Each type of virus can enter a host cell in a different process. SARS and COVID-19 attach to receptors on host cell surfaces that can result in membrane fusion, which allows the virus to penetrate the host cell. Once inside the host cell, the capsid is degraded by enzymes or dissociation and releases the viral genome into the host cell. Once inside the cell, the genome hijacks the genetic replication machinery of the host cell and produces more copies of the virus.

Individuals who are shedding the virus are contagious. Some viruses have symptomatic shedding where the person is infectious upon showing symptoms or shortly before showing symptoms. Viruses with asymptomatic shedding or a silent infectious period are contagious for a longer period of time before or if symptoms occur. COVID-19 can have asymptomatic shedding, resulting in infections being transmitted without the carrier knowing they are infected. The time line of an infections starts with the exposure of an uninfected individual to the virus. As the virus infects the host cells and replicates there is a period of incubation where the virus is latent. At some point during incubation, the first infected host cells begin to shed virus particles and begin the infectious period. This period may or may not include symptoms as was stated previously (Figure 4). (See upper right for Figure 4, click to enlarge.)

The rate at which viral infections increase is dependent upon several risk factors including: population density, geography, sanitation, age, sex, immunity, viral stability, virulence, ease of replication, and mode of transmission. Geography determines if a virus can reach the stage of an outbreak, epidemic, or pandemic. An outbreak is a localized number of infections beyond normal for the area. An epidemic is an increased number of infections in a larger geographical area than in an outbreak. Finally, a pandemic is the spread of an infection over several countries or continents. Geographically isolated areas have a better ability to contain outbreaks. The relatively easy access and world connectivity of the outbreak center for the COVID-19 outbreak in Wuhan, China made it difficult to contain, thus it spread into an epidemic and then a pandemic.

Viruses increase rapidly in areas of high density, which is why it is recommended to limit the size of groups and practice social distancing during outbreaks, epidemics, and pandemics. This strategy reduces contact rates, which are the rates at which an infected individual is in contact with other people. Individuals in high density living arrangements, cities, or professions have a higher contact rate and have a higher incidence of exposure to infected individuals or infecting others. Two other factors in rates of infection are the mode of transmission of a virus and the basic reproduction number (R0). The mode of transmission of a disease is the way in which a disease causing agent is transferred from an infected individual to another uninfected individual. A virus can be transmitted via direct physical contact or indirect physical contact.

Direct physical contact includes sexual contact, kissing, or exposure to secretions and usually occurs within friends, households, or families. Indirect physical contact can be contamination from physical surfaces. The COVID-19 virus has been shown to spread through direct contact with infected oral and nasal fluids and through indirect contact on surfaces where droplets of the virus can be deposited. The COVID-19 virus can live from several hours to several days on various surfaces. The half-life of a virus is how long up to half of the virus initially deposited will remain viable and the viability is the amount of time in total viable virus particles can be detected (Table I). (See upper right for Table I, click to enlarge.)

Additional modes of transmission include airborne or droplet transmission from coughing, sneezing, and breathing. Viruses can be transmitted by poor hand washing or sanitary conditions in which fecal matter infects food or water sources. Finally, viruses can be transmitted from other organisms or vectors such as flies, mosquitoes, or an intermediate host.

The number of individuals on average that an infectious individual will expose to a contagion is called the basic reproductive number or R0 (pronounced R naught). The higher the value, the more infections will result from exposure. COVID-19 currently has an R0 value of 2–5 (this value is constantly changing as the pandemic progresses). Some common diseases such as Measles and Whooping Cough are highly infectious with R0 values over 10 (Table II). (See upper right for Table II, click to enlarge.)

Basic reproduction numbers are calculated on a population without any immunity. If a population has some immunity, then less people will become infected and if a population is vaccinated, increasing the population immunity, then the virus is not able to spread efficiently. COVID-19 is a new virus and the population at large appears to have little natural immunity from it. There were also no vaccines available to treat the population to increase immunity at the time of the start of the pandemic.

A vaccine is a biological preparation of potentially infectious disease that can impart immunity to the disease. The process of creating a new vaccine can take anywhere from months to years. There is the possibility that the vaccine is developed for a strain that has dramatically mutated into another resistant form before the vaccine is ready for distribution.

Vaccine Production

The development of a vaccine is a complex multistep process (4) (See upper right for Figure 5, click to enlarge.):

  • Exploratory: research to identify and study antigens for prevention or treatment. This stage includes genetic material extraction from the virus and replication using polymerase chain reaction (PCR).

  • Preclinical: tissue or cell cultures and animal tests are used to determine if a potential vaccine will produce immunity. It is during this phase that most vaccines fail to produce either immunity or are harmful to the test subjects.

  • Clinical development: approval by the US Food and Drug Administration (FDA) for three or more rounds of human trials. Each round of analysis includes the safety of the proposed vaccine, immunogenicity, immunization schedule, dose, size, and overall effectiveness. 

  • Regulatory review and approval: upon passing of vaccine, it is subject to regulatory review and approval by the FDA. 

  • Manufacturing: mass production of vaccine

  • Quality control: quality control that monitors performance and safety by the Vaccine Adverse Event Reporting System and the Vaccine Safety Datalink

Stopping Transmission of Viruses

As a disease progresses from an initial outbreak to an epidemic it becomes important to use policies to contain and slow the spread of the disease before it hits pandemic proportions. In other historical outbreaks, it was easier to contain viral outbreaks due to limitations of travel and geography. In our modern world, however, our international community and ability to travel easily and frequently has only aided in the spread of COVID-19.

The essential methods of dealing with an outbreak or pandemic is a multipronged attack to limit exposure by isolating those infected, keep risk of exposure to a minimum for the uninfected, practice good health and hygiene practices, develop and employ effective viricides to stop transmission and alleviate symptoms, and develop prophylactic measures such as vaccines to stop future emergence. The Centers for Disease Control and Prevention (CDC) has issued guidelines for limiting exposure for the general population (Figure 6) (6). (See upper right for Figure 6, click to enlarge.)

The concept of social distancing and reduced groups is part of the strategy involved in reducing the contact rate of infectious patients and not letting COVID-19 infected individuals pass on the disease to other people and end the reproductive rate for that avenue of the disease. This practice has come to be known as “flattening the curve,” which originated with a study of the 1918 Spanish influenza epidemic where the spread of the disease was examined in two cities that took different approaches to controlling the disease. In Philadelphia, there was no early isolation or social distancing practices mandated and the number of cases grew sharply over a small period of time overwhelming resources. In St. Louis, social distancing and quarantine practices were instituted quickly upon outbreak and their growth was slowed and the rate of cases reduced allowing for better handling of resources (6,7).

The second line of defense is for all individuals to practice behaviors to limit exposure, which includes cleaning of common areas, hand washing, and isolating oneself when sick. The laboratory approach to the COVID-19 crisis should follow the same advice but expand to encompass the laboratory space, equipment, and personnel.

In the laboratory, social distancing and not gathering in groups translates into several policies such as:

  • Staggering work schedules and changing to shifts

  • Work from home (WFH)

  • Stop travel and in-person meetings

  • Limited contact from outside vendors, sales people, visitors, and food delivery

Cleaning and Disinfecting in the Laboratory

The first step in disinfecting a laboratory is general cleaning. Dust and dirt attract and collect particles of mold and viruses. After general cleaning, the process of disinfection can then occur. There are many commercial products for all types of settings from home to healthcare and laboratory. Most of these products have familiar active chemical agents such as alcohols, acids, chlorides, and so on.

The mode of action for these products is usually one of the three processes:

  • Dehydration: the virus or biological agent is dehydrated by a chemical and rendered inactive

  • Cell disruption: denaturing proteins or dissolving lipid capsules allow spilling of viron contents out and inactivation

  • Process inhibition: disrupts genetic, protein, or amino acid processes and inhibits replication

The Environmental Protection Agency (EPA) has published an extensive list of all of the commercial products for use in cleaning against viruses and COVID-19 on their website (8). The European Union (EU) has also provided guidance on agents that have been tested on viruses in the Coronavirus family with their concentrations for use (Table III) (9–10). Instructions on use and dilution of common laboratory chemicals such as ethanol, sodium hypochlorite, and more can be found on the disinfection pages of the CDC for healthcare settings (11). (See upper right for Table III, click to enlarge.)

The common theme for all of these disinfectants is that the product must be applied and allowed to disinfect for a period of time before being wiped away (dwell or contact time). There are very few instantaneously effective products and in most cases the solution needs to be applied for up to 10 min before wiping or washing the surface clean to ensure proper disinfection.

An additional method of sanitization is the use of heat and steam. Temperatures from 75 ºC to 100 °C are best for disinfecting viruses. These methods reduce the risk of chemical contamination from commercial or laboratory-based cleaners, but do have risks for moisture sensitive laboratory areas or chemicals.

It is important to remember in the use of cleaners and cleaning agents that they are still chemicals capable of contaminating daily processes and operations. Additional actions may be needed to ensure normal laboratory processes are not contaminated by the updated cleaning procedures. Before cleaning and disinfecting an area, all porous materials such as paper, paper towels, and so on, should be removed from the areas to be cleaned so as not to absorb chemicals. Select cleaning agents appropriate for the area to be cleaned with thought in mind as to the type of work that occurs in these areas and how that work will be affected by these agents. If possible, airflow and hood flow should be increased to drive fumes away from work areas. Chemical odor traps can be used to absorb volatile chemical fumes. Hoods and sensitive areas should be decommissioned during cleaning and allowing several hours for fumes to dissipate.

Personal cleaning and hygiene plans and expectations should be discussed or notices posted to remind everyone to keep a cleaning plan. One of the most important acts a person can do to reduce their exposure is to wash their hands for a minimum of 20 s with soap and water. Most soap compounds are composed of materials whose molecules have a dual nature: hydrophilic end and binds to polar solvents such as water and lipophilic end binds to long hydrocarbon chains, proteins, and lipids. The action of the soap and water together allows for viral particles to become bound to the soap’s lipophilic structure and allows water to wash the particles away after the appropriate dwell time of at least 20 s (Figure 7). (See upper right for Figure 7, click to enlarge.)

Personal Protective Equipment

Most laboratory personnel are familiar with common laboratory personal protective equipment (PPE), but there are some differences in equipment and use that one often takes for granted as correct. There are different uses for each type of PPE and different ratings for equipment such as masks, respirators, gloves, and so forth, which are dependent on the function they are intended for in the laboratory. There are some specialized PPEs that are only used in specific settings that tend to benefit the laboratory’s clean setting rather than the laboratory technician.

Items such as sticky mats, shoe covers, and clean rooms stop the transfer of particles (dirt and otherwise) to and from locations. In chemistry laboratories, these items are used mostly to protect the laboratory from added contamination. In a hospital or healthcare setting these items can also protect the environment from the transfer of contaminated particles outside a quarantined or contaminated area. Clean rooms or controlled quarantine rooms have sealed air flow and ventilation with high efficiency particulate air (HEPA) filters to reduce particle transmission. Most clean rooms are rated by the amount and size of particles that are filtered by the system.

Respirators, face masks, and face shields cover different parts of the face but generally cover the mouth and nose. Face shields offer the least amount of respiratory protection since they are only physical barriers to splashes and respiratory expulsions directed at the face. Respirators filter particles, chemicals, and fumes depending on their specification using filtration chemicals or materials. Respirators are meant to protect the wearer from these agents and must be properly fitted and tested by a professional to ensure good seal and appropriateness for use. Face masks can also potentially be a tool for the filtration of particles depending on their rating. Fitted face masks are very different from the surgical masks being seen in pictures during this outbreak. All of the world organizations warn that a generic face mask is not a substitute for a fitted and regulated face mask or respirator (13,14).

During the COVID-19 pandemic, the use of N95 respirators is often called for and requested. These particle respirators trap up to 95% of particles. For more information, refer to CDC, Occupational Safety and Health Administration (OSHA), National Institute for Occupational Safety and Health (NIOSH), and International Organization for Standardization (ISO) guidelines and instructions on selection and use of respirators and masks.

It is more common that chemists and other laboratory scientists use basic PPE such as goggles, glasses, gloves, and lab coats. All of these PPE items are needed for chemical protection, but can also be used for protection against biological agents. As with the respirators, there are different classes of goggles, glasses, and gloves that are dependent upon use.

Goggles and glasses protect the eyes from splashes and can be made from a multitude of materials resistant to a range of agents. Gloves as well can be made from a variety of materials, which is important to understand since each type of glove has its own strengths and weaknesses. Many gloves are subject to issues of chemical or biological resistance meaning not all materials are resistant to all agents and therefore offer limited protection. Resources such as online databases for glove compatibility are available (15).

The choice of the proper PPE is not the only factor in protection for the wearer. The matter in which PPE is put on and removed after use is important. Many laboratories or healthcare settings have isolation PPE procedures for strict quarantine and contamination control. Smaller commercial laboratories with lower risk for infection often have simple, if any, procedures for proper PPE use. There are some tips to help use PPE efficiently.

Gloves must:

  • Be compatible material for the purpose

  • Fit snugly but not so tight that they stretch and become compromised more quickly during use.

  • Not gap at the fingers.

  • Be removed to limit exposure and contain contamination such as by pulling one glove off with the still gloved hand and then using the inside portion of the glove to remove the second glove folding them into each other so the glove disposal packet has the contaminated or exposed areas contained inside the packet.

Lab coats must:

  • Fit properly and button.

  • Have cuffs that do not hang down into the work area nor are too short to not cover the tops of the gloves when worn.

  • Pockets should not contain items that cannot be exposed to contamination or infection such as personal phones.

  • Be changed frequently.

  • Removed similar to the gloves where the sleeves are removed inside out and the outside is folded inside to contain the contaminated area.

In the event of a known viral exposure, all PPE items and trash should be isolated from the common waste stream and disposed of in a separate location.

Conclusions

During this time of heightened anxiety, it is good to know most common laboratory procedures used to keep scientists safe from chemical exposures also work well for limiting biological exposures. More diligence must be paid in common areas and with common touch points in our offices, laboratories, and lives. Check on all of the protective equipment used in the laboratory and make sure it is up to the task that is being set. Isolate all potential contaminants and dispose of them quickly. Most importantly, use your knowledge, training, and understanding of science to promote calm and educate your coworkers, employees, families, and others of the real facts of infectious diseases and prevention. For more information and details see the full technical note “A Chemist’s Guide to the COVID-19 Outbreak” (17) or the on demand webcast (18).

References:

  1. J. Tetro, Popular Science. Accessed March 27, 2020. https://www.popsci.com/our-viral-friends/ (2015).
  2. D. Enard, C.W. Le Cai, and D.A, Petrov, “Viruses Are a Dominant Driver of Protein Adaptation in Mammals,” Gilean McVean, Ed. ELife 5 (May): e12469. https://doi.org/10.7554/eLife.12469 (2016).
  3. N. Lanese, Live Science, Accessed March 30, 2020 https://www.livescience.com/ coronavirus-can-spread-as-an-aerosol.html (2020).
  4. https://www.cdc.gov/vaccines/basics/test-approve.html.
  5. Cole-Parmer: coleparmer.com
  6. Centers for Disease Control and Prevention, “Coronavirus Disease 2019 (COVID-19) – Prevention & Treatment,” https://www. cdc.gov/coronavirus/2019-ncov/prevent-getting-sick/prevention.html.
  7. R.J. Hatchett, C.E. Mecher, and M.Lipsitch, Proceedings of the National Academy of Sciences of the United States of America104(18), 7582–87. https://doi.org/10.1073/pnas.0610941104 (2007).
  8. US EPA, OCSPP,  “List N: Disinfectants for Use Against SARS-CoV-2,” Overviews and Factsheets. US EPA. March 13, 2020. https://www.epa.gov/ pesticide-registration/list-n-disinfectants-use-against-sars-cov-2 (2020).
  9. European Centre for Disease Prevention and Control, “Interim Guidance for Environmental Cleaning in Non-Healthcare Facilities Exposed to SARS-CoV-2” https://www.ecdc.europa.eu/en/publications-data/interim-guidance-environmental-cleaning-non-healthcarefacilities-exposed-2019 (2020).
  10. “Coronavirus-SARS-CoV-2-Guidance-Environmental-Cleaning-Non-Healthcare-Facilities.Pdf.”
  1. “Chemical Disinfectants | Disinfection & Sterilization Guidelines | Guidelines Library | Infection Control | CDC.” https://www.cdc. gov/infectioncontrol/guidelines/disinfection/disinfection-methods/chemical.html.
  2. “Using Disinfectants to Control the COVID-19 Virus.” http://npic.orst.edu/ingred/ptype/amicrob/covid19.html.
  3. U.S. Department of Health and Human Services, Public Health Service, Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health. “NIOSH Fact Sheet: NIOSH Approval Labels-Key Information to Protect Yourself.” https://doi.org/10.26616/NIOSHPUB2011179.
  4. U.S. Department of Health and Human Services, Public Health Service, Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health. “Preparedness through Daily Practice: The Myths of Respiratory Protection in Healthcare.” https://doi.org/10.26616/ NIOSHPUB2016109.
  5. https://www.coleparmer.com/safety-glove-chemical-compatibility.
  6. C.V. Muñoz, C. Varela Santos, L. van Kranendonk, C. Bartels, J. de Boer, and European Centre for Disease Prevention and Control, “Safe Use of Personal Protective Equipment in the Treatment of Infectious Diseases of High Consequence a Tutorial for Healthcare Settings: Version 2: 2 December 2014.” Stockholm: ECDC. http://bookshop.europa.eu/uri?target=EUB:NOTICE:TQ0714051:EN:HTML.
  7. P.L. Atkins and R.A. Biermann, “A Chemist’s Guide to the COVID-19 Outbreak,” Technical Note www.spex.com.
  8. https://www.cannabissciencetech.com/e-learning-tools/editors-series-limiting-laboratory-exposure-chemists-guide-covid-19-outbreak.

About the Author

Patricia Atkins is a Senior Application Scientist with SPEX CertiPrep in Metuchen, New Jersey. Rebekah Biermann is a Territory Sales Manager with SPEX CertiPrep. Direct correspondence to: patkins@spex.com

How to cite this article:

P. Atkins and R. Biermann, Cannabis Science and Technology, 3(5), 39-45 (2020).