LII:COVID-19 Testing, Reporting, and Information Management in the Laboratory/Overview of COVID-19 and its challenges

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1. Overview of COVID-19 and its challenges

Please note: Information during a pandemic changes, sometime rapidly, in regards to test methods, reported figures, and social situations. Efforts will be made to keep this guide up-to-date as best as possible given time constraints and resources.

1.1 COVID-19: The terminology

Novel Coronavirus SARS-CoV-2 (49640655213).jpg

A pneumonia-like outbreak was fully in process in Wuhan—located in the Hubei province of China—by December 2019. The World Health Organization (WHO) was notified by the end of the month that the cause could be a novel threat to the larger populace.[1] By the end of January 2020, the WHO had declared the growing viral threat a Public Health Emergency of International Concern (PHEIC), an act which includes with it a need "to implement a comprehensive risk communication strategy."[2] As the disease progressed beyond its Chinese origins, public confusion slowly grew regarding the terminology surrounding the disease. Leaders at the WHO and the Coronavirus Study Group (CSG) of the International Committee on Taxonomy of Viruses came to different naming conclusions, differing in their naming conventions while adding to the confusion.[3][4] In the end, "COVID-19" has ended up as the common disease name, caused by the SARS-CoV-2 virus, which is a member of the coronavirus family. Today, however, some still refer to the disease simply as "coronavirus," which is in error.

This isn't the first time a disease has had a different name from its associated virus. One should look back to 1982, when the U.S. Centers for Disease Control and Prevention (CDC) gave the name "acquired immune deficiency syndrome" or "AIDS" to the disease associated with the human immunodeficiency virus (HIV) (a member of the retrovirus family).[5] It took time for the layman to get used to the terminology, and even then some still ended up mistakenly referring to the disease as "HIV."

Consistent terminology is vital to communicating technical material to a global audience.[6][7] With that in mind, it's beneficial to ensure everyone is clear on the terms used. For purposes of this guide:

  • Coronavirus disease 2019 (otherwise known as COVID-19) is the respiratory disease being discussed in this guide.
  • SARS-CoV-2 is the virus responsible for COVID-19.
  • Coronavirus (or Coronaviridae) is a family of related viruses, of which SARS-CoV-2 is a member.
  • Severe acute respiratory syndrome (otherwise known as SARS) is a different respiratory disease, which surfaced in the early 2000s, caused by a related but different type of coronavirus (SARS-CoV or SARS-CoV-1).
  • Middle East respiratory syndrome (otherwise known as MERS) is a different respiratory disease, which surfaced in 2012, caused by a related but different type of coronavirus (MERS-CoV).


1.2 COVID-19: History and impact (so far)

COVID-19 is an infectious disease caused by the SARS-CoV-2 virus, typically yielding varying levels of short- and long-term symptoms, including fever, cough, shortness of breath, loss of taste or smell, headaches, fatigue, joint pain, chest pain, heart palpitations, brain fog, and mood changes.[8][9] A majority of cases yield relatively mild symptoms, but some progress to life-threatening short- and long-term situations involving pneumonia, organ failure, cardiovascular complications, renal complications, neurological complications, and psychiatric issues.[9][10][11][12][13]

The first known case of COVID-19 dates back to November 2019, "according to government data seen by the South China Morning Post"[14], though additional research has suggested an even earlier timeline. A non-peer-reviewed report released by Harvard Medical School in June 2020 suggested that circumstantial evidence of higher traffic around hospitals even a month earlier may push the Wuhan timeline back further.[15] Stories of routinely analyzed wastewater samples from locations in Brazil[16] and Italy[17] may likewise indicate that the SARS-CoV-2 virus was circulating earlier than initially gauged. And June 2021 peer-reviewed research by Roberts et al. suggests the possibility of COVID-19 beginning to spread as early as early October.[18]

By the middle of December, infections were at 27, and by the end of the year the number was 266.[14] By that time, Chinese health authorities had been updated that the pneumonia-like symptoms of patients in China's Hubei province may have been the symptoms of a disease caused by a novel (new) coronavirus[14], and the WHO was notified.[1] At the start of 2020, that number grew to 381 known cases[14], jumping to more than 7,700 confirmed and 12,000 suspected cases by the end of January.[2] By that time, the WHO had convened a second meeting of its Emergency Committee to discuss the declaration of a PHEIC, saying the then-called "2019-nCoV" constituted a health emergency of international concern.[2] This spurred the publishing of WHO technical advice to other countries, with a focus on "reducing human infection, prevention of secondary transmission and international spread, and contributing to the international response."[2] However, at the same time, the virus was already beginning to spread in locations such as Australia[19], France[20], Germany[21] Italy[22], Japan[23], South Korea[24], Spain[25], the United Kingdom[26], and the United States.[27]

As the disease continued to spread in February 2020, naming conventions came together, with the WHO declaring the disease's name "COVID-19," short for "coronavirus disease 2019."[3][4] By the end of the month, the WHO warned a "very high" likelihood the virus's spread could turn into a full pandemic.[28] Less than two weeks later, on March 11, 2020, the WHO declared the outbreak of SARS-CoV-2 a pandemic, noting more than 118,000 confirmed cases and 4,000 deaths on all continents except Antarctica.[29] By November 2020, the pandemic had become more serious, in the U.S. in particular; hospitals became overwhelmed—the most recorded COVID-19 hospitalizations since the pandemic started[30]—and the pandemic became "a humanitarian crisis."[31] The U.S. FDA issued its first and second Emergency Use Authorization (EUA) for a COVID-19 vaccine, the Pfizer-BioNTech COVID-19 Vaccine[32] and Moderna COVID-19 Vaccine[33], in December 2020, giving hope that a much wider vaccine roll-out would happen by late winter and early spring of 2021 in the U.S.[34] However, concerns that wealthier residents and countries would largely lead the charge while leaving poorer residents and countries behind were heavily vocalized.[34][35]

Governmental reaction to the pandemic around the globe has varied significantly since the pandemic's declaration in March 2020. Some of that variance can be seen when reviewing the various policies implemented by the world's governments. The International Monetary Fund's policy tracker for COVID-19 response, for example, paints a picture of the laboratory testing, social, transportation, trade, and financial situations of each country. Reviewing the policy tracker reveals a diverse set of approaches from country to country, some significant and enduring, others limited and weak. [36] Another source for examining government reaction is through the collation of data on how governments have implemented technological tracking measures in the name of slowing the epidemic. Groups like Privacy International collate such information through their collective tracking project, which links to hundreds of news stories concerning the use of mobile phone data, drones, and other surveillance mechanisms for tracking and enforcing quarantines; geolocation tracking though phones; and the implementation of facial recognition technology as part of a COVID-19 mitigation strategy.[37] Other projects such as the University of Oxford's COVID-19 Government Response Tracker also paint a broad picture of governments' responses to the pandemic using a wide variety of indicators, including school closures, travel restrictions, and vaccination policies. The University of Oxford maintains a core working paper and monthly regional reports, painting a picture of more governments decreasing policy changes as vaccination roll-out continues.[38]

Citizen reaction to the pandemic has also varied. Local governments in China have been criticized[39][40], while the central government has, at least at times, been seen in positive light for its handling of the pandemic.[41][42][43] Some Indians have criticized their government for its police brutality during lockdowns[44], while some Italians have criticized their government for trivializing the situation for too long.[45] In the U.S.—and in other parts of the world—criticism has at times been significant concerning the United States government's response[46][47][48][49], though some governors have received praise for standing up for their state's citizens.[50][51][52] American's views of presidential handling of the COVID-19 crisis have varied. During President Trump's tenure, Americans increasingly expressed disapproval with the U.S. president's handling of the COVID-19 crisis, from 47.8% dissapproval on April 8 to 57.1% disasapproval by the end of his term.[53], which seemingly aligned with his attempts to downplay the existence of the COVID-19 virus.[54][55] Americans' perceptions of President Biden's handling of COVID-19 began strong, at above 60% approval, but has weakened over time to 52.9% as of September 2021, largely falling along partisan lines.[53]

It's difficult to truly quantitatively (or qualitatively) measure the impact of COVID-19 on the world, let alone the United States. From the start of the pandemic there have been significant job losses[56] and bankruptcies[57], to poor mental health impacts[58] and postponed cancer surgeries.[59] With time, some firmer numbers have become known, however. As of August 31, 2021, the number of global confirmed cases of COVID-19 was more than 216 million, with more than 4.5 million people dead.[60] As of July 2021, out of more than 320 vaccine candidates, 99 were still in clinical testing, 25 had reached Phase III efficacy studies, and 18 had received some form of formal approval.[61] Some 3.2 billion doses of vaccine had been administered globally as of July 2021 (with the caveat that only ~1% of people in low-income countries have received at least one dose), and nearly 11 billion doses were still needed to fully vaccinate 70% of the world's population.[62] Other statistics include:

  • "The global economy contracted by 3.5 percent in 2020 according to the April 2021 World Economic Outlook Report published by the IMF, a 7 percent loss relative to the 3.4 percent growth forecast back in October 2019."[63]
  • "At a global scale, the fiscal support [applied to COVID-19] reached nearly $16 trillion (around 15 percent of global GDP) in 2020."[63]
  • As of July 2021, some 10 percent of American adults have reported sometimes or often not having enough to eat in a given week, compared to 3.4 percent for the entirety of 2019.[64]
  • "An estimated 11.4 million [U.S.] adults living in rental housing—16 percent of adult renters—were not caught up on rent" as of the beginning of July 2021, with an additional 7.4 million estimated to not be caught up on mortgage payments.[64]
  • "Some 63 million [U.S.] adults—27 percent of all adults in the country—reported it was somewhat or very difficult for their household to cover usual expenses in the past seven days," as of the beginning of July 2021.[64]

Despite the remaining unknowns and difficulties facing societies everywhere, what has long been known and remains true, however, is that preventative measures such as wearing masks[65], getting vaccinated[61], and getting tested for exposure[66] remain vital in order to further limit the negative consequences of the pandemic.


1.3 Challenges of managing the disease in the human population

The graphical abstract from Li et al. 2020, showing general features of SARS-CoV-2, current knowledge of molecular immune pathogenesis, and diagnosis methods of COVID-19 based on present understanding of SARS-CoV and MERS-CoV viral infections

COVID-19 has presented numerous societal challenges, from supply line interruptions and economic sagging to overwhelmed healthcare systems and civil disorder. However, these are largely the social, economic, and political ripple effects of a disease that has brought with it a set of inherent attributes that make it more difficult to manage in human populations than say the flu.

However, COVID-19 is not the flu, and it is indeed worse in its effects than the flu, contrary to many people's perceptions. Yes, COVID-19 and the flu have some symptom overlap. Yes, COVID-19 and the flu have some transmission type overlap. But from there it diverges. COVID-19 and SARS-CoV-2 is different in that it is more prone to be transmitted to others during the presymptomatic phase. And the body of evidence has grown since early on in the pandemic[67] that SARS-CoV-2 is transmittable predominately via an airborne route[68][69][70][71], though transmission from contaminated surfaced or physical intimacy are also believed possible.[72][73] Hospitalization rates are higher, perhaps up to 10 times higher than the flu, and hospital stays are longer with COVID-19. People are dying more often from COVID-19 too, up to 10 times more often than people stricken with the flu.[74][75][76] And while flu vaccines are largely the norm around the world, and COVID-19 vaccines are gradually becoming more available, those who willing choose to not get the vaccine have a massively higher chance of dying from COVID-19 (as of August 2021, more than 99 percent of all deaths from COVID-19 are found with the unvaccinated[77], compared to some 80% of children who die from the flu while unvaccinated[78]).

Other aspects of the disease that make it difficult to manage include:

  • Median incubation period: According to research published in Annals of Internal Medicine, the median (i.e., the central tendency, which is less skewed than average[79]) incubation period is 5.1 days (Note that as new variants arrive, incubation times my change; the delta variant is thought to have an incubation period of four days, for example.[80]), with 97.5% of symptomatic carriers showing symptoms within 11.5 days. The authors found this to be compatible with U.S. government recommendations of monitored 14-day self-quarantines if individuals were at risk of exposure.[81] However, many people continue to not take mask-wearing—and vaccination—seriously, and thus unmasked presymptomatic (and asymptomatic) carriers are thus largely more prone to spreading the virus.[82][83] This has become even more precarious with the highly contagious delta variant, which can be spread even by the vaccinated, highlighting that "measures such as masks and hand hygiene which can reduce transmission are important for everyone, regardless of vaccination status."[84]
  • Presymptomatic and asymptomatic virus shedding: As mentioned in the previous point, carriers can be contagious during the presymptomatic phase of the disease, even while remaining symptom-free.[82][83][85][86] (The latest comprehensive research, from August 2021, appears to indicate that 35.1 percent of infected people may go without any recognizable symptoms after infection occurs.[87]) This contagion is a result of what's called viral shedding, when the virus moves from cell to cell following successful reproduction. When the virus is in this state, it can be actively found in a carrier's body fluids, excrement, and other sources. Depending on the virus, the virus can then be introduced to another person via those sources. In the case of COVID-19, the core route of transmission appears to be through the air via aerosolized and other forms of water droplets, though saliva and other bodily constituents pose a transmission hazard due to shedding (see previous bulletpoint). Early in the pandemic, uncertainty about transmission routes of viral shedding, along with mixed messages early on about masks and their effectiveness for COVID-19[88][89][90], caused problems. Today we know that masks and social distancing—when appropriate—are an even stronger necessity to limit community transmission of the disease from presymptomatic and asymptomatic individuals, even for those who are vaccinated.[84]
  • Understanding of high viral loads and infectious doses: Respiratory diseases such as influenza, SARS, and MERS see a correlation between the infectious dose amount and the severity of disease symptoms, meaning the higher the infectious dose, the worse the symptoms.[91] Similarly, viral load—a quantification of viral genomic fragments—also tends to correlate with clinical symptoms.[92] However, even with the breakthroughs in COVID research since the start of the pandemic, we are still in the investigative stages of definitively determining if that similarly holds true to COVID-19.[91][93][94] Research early on indicated, for example, there is little difference between the viral load of those with mild or no COVID-19 symptoms and those with more severe symptoms.[91] However, Pujadas et al. suggested a link between high viral load and overall mortality rate.[95] Research later in 2020 has suggested more of a positive correlation between severity of symptoms and viral load[96][97], as has a July 2021 study published in Science.[98] However, more research must be performed to better understand how the viral load infectious dose plays a role in transmission. Given the continued unknowns in this realm, wearing masks and getting vaccinate help minimize exposure and remain the best defense against the worst outcomes of the disease.[91]
  • Cardiovascular issues: Coronaviruses and their accompanying respiratory infections are known to complicate issues of the cardiovascular system, which in turn may "increase the incidence and severity" of infectious diseases such as SARS and COVID-19.[99][100][101] While the exact cardiac effect COVID-19 has on patients is still unknown, suspicion is those with "hypertension, diabetes, and diagnosed cardiovascular disease" may be more prone to having cardiovascular complications from the disease.[102][103] Current thinking is SARS-CoV-2 either attacks heart tissues, causing myocardial dysfunction, or inevitably causes heart failure through a "cytokine storm,"[99][100][102][103][104][105][106], an overproduction of signaling molecules that promote inflammation by white blood cells (leukocytes).[107][108] What's scary is that like the 1918 Spanish flu, SARS, and other epidemics, some otherwise healthy patients' immune responses are entirely overreactive, leading to acute respiratory distress syndrome (ARDS) or heart failure.[106][105][109] Additionally, as the disease has progressed, medical professionals have noted two additional cardiovascular issues. First, an atypical amount of blood clotting has shown up in some infected patients, which may be related to overreactive immune systems, autoantibodies, and underlying health conditions.[110][111] Second, what is being called pediatric multisystem inflammatory syndrome (PMIS) or multisystem inflammatory syndrome in children (MIS-C) has shown up in children after the infection has passed, characterized by inflamed blood vessels and toxic shock syndrome.[112][113][114] While research is ongoing to determine whether these seemingly hyperactive cardiovascular responses are directly linked to the virus[115] or if virus-independent immunopathology is responsible[116], these uncertainties only emphasize the level of difficulty of properly treating COVID-19.
  • Other systemic and bodily issues: As the pandemic has progressed, researchers have discovered SARS-CoV-2 appears to negatively impact other organs and systems in the human body, including the renal system, digestive system, endocrine system, neurological system, and even the reproductive system.[106][8][117][118][119] Another bodily issue that appears to remain for a subset of post-recovery COVID-19 patients is fatigue. The University of Minnesota's Center for Infectious Disease Research and Policy reports on an observational study published in PLOS One' that showed more than half of people who recovered from their COVID-19 infection still dealt with the lingering effects of fatigue at a median of 10 weeks after recovery. The study reports no link between the persistent fatigue and severity of symptoms, need for hospitalization, concentration of laboratory biomarkers, and age.[120] These systemic and body issues have added further complication to an already complicated disease, making extended treatment planning difficult. The long-term affects of these and other organ system injuries remains to be fully understood.
  • Mental health concerns: The mental health toll of the pandemic is becoming increasingly apparent as it wears on. A June 2020 CDC survey of 5,412 U.S. adults (regardless of infection status) "found that 40.9% of respondents reported 'at least one adverse mental or behavioral health condition,' including depression, anxiety, posttraumatic stress, and substance abuse, with rates that were three to four times the rates one year earlier." More than 10 percent of respondents also indicated they had seriously considered suicide in a time period thirty days prior to responding.[121] From an inability to grieve communally with loved ones, to income loss, increased anxiety, and long periods of social isolation, these increasing numbers are not surprising, particularly in light of research on previous pandemics.[121][122] Without proper treatment, these conditions may worsen into prolonged grief disorder, only exasperating a growing mental health crisis.[121] Further, at least one study suggests that those who contract COVID-19 may be at a greater risk of developing some sort of mental illness within 90 days, including anxiety, depression, and insomnia. This effect may be worse for those who already have a history of mental health illness.[123] Mitigating the effects of these mental health concerns will require further study, greater funding, expanded screening, and improved focus on community methods of dealing with tragedy and loss.[121]

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Citation information for this chapter

Chapter: 1. Overview of COVID-19 and its challenges

Edition: Fall 2021

Title: COVID-19 Testing, Reporting, and Information Management in the Laboratory

Author for citation: Shawn E. Douglas

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Publication date: September 2021