https://apologeticspress.org/going-viral-exploring-virus-mutations-and-evolution-extended/
Going Viral: Exploring Virus Mutations and Evolution Using SARS-CoV-2 [Extended Version]
Part 1: Understanding SARS-CoV-2
Introduction
For the past two years, the world has been given a front-row seat to the process of science as the pandemic of SARS-CoV-2 has made its way around the world and back again. This article examines the virus and its components with a goal to understand how the virus works and how it is changing over time. Further, we will seek to consider the implications of viral evolution and step back to think about how viruses fit into a biblical worldview.
Before January of 2020, relatively few individuals used the term “coronavirus” in everyday language, much less understood the implications of it. While there are a few different coronaviruses that cause things like the common cold, prior to SARS-CoV-2, only two had caused major problems in humans: severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). An outbreak of SARS-CoV occurred in 2002-2004, which infected over 8,000 people and killed nearly 10% of those infected.1 MERS-CoV was associated with the Arabian Peninsula and occurred from 2012-2015 with about a 30% death rate, but a very low transmission rate.2 As of October, 2021, there have been a total of 2,578 cases with 888 reported deaths (34.4%) since 2012.3 By contrast, SARS-CoV-2 has spread globally in just over two years with over 419 million cases worldwide and over 5.8 million deaths (~1.4% of those infected) so far according to the Johns Hopkins Coronavirus Resource Center.4 Unfortunately, these numbers do not clarify for us the difference between people who died from the effects of COVID versus those who died of other causes but had COVID.
In general, SARS-CoV and MERS-CoV are naturally found in rodents and/or bats but have undergone “zoonotic transmission” to infect humans. Zoonosis is a term used to describe a disease that has undergone “spillover” from vertebrate animals to humans.5 As you might guess, there are barriers and challenges that prevent many diseases from infecting different organisms. However, some barriers are not insurmountable. Many questions still surround how and what changes took place to give us SARS-CoV-2—were they natural mutations in animal populations or were they part of experimental efforts perhaps aiming to thwart an epidemic? There are those on various sides of these issues.6, 7, 8, 9
This article is not intended to settle the question of the origin of the virus or to take a particular side. Instead, we want to ask more fundamental questions: what is different between SARS-CoV-2 and previous deadly coronaviruses? Why does it spread so quickly? What will happen moving forward? And what are the apologetic implications of the coronavirus?
What is SARS-CoV-2?
Before discussing the specifics of SARS-CoV-2 and how it has changed, some fundamental details and concepts need to be covered. First, the basic route and mechanism of infection needs to be mentioned. Each virus or family of viruses have specific routes by which they infect cells and organisms. For instance, does the virus infect via the gastrointestinal tract, the airways, or some other route? With SARS-CoV-2, the airways are the route of infection, and this has brought on many discussions around masks, face shields, distancing, etc.
Once inside the body, how does the virus infect cells? This requires a specific protein(s) on the host cell that the virus can bind to. For SARS-CoV-2, the S or Spike protein of the virus, discussed later, binds to specific proteins like ACE2 on the cells of the host. For this interaction to occur, the S protein and ACE2 must be able to bind to one another. The Receptor Binding Domain (RBD) region of S protein can bind specifically to ACE2. After binding, there is a process that then allows the virus to enter the cell and hijack the cellular machinery to produce additional viral particles before exiting the host cell. There are a couple possible routes (e.g., membrane fusion, endocytosis) that could be used here, and there is evidence of these routes for SARS-CoV-2.10 Additional details of this process for SARS-CoV-2 including the role of S protein and the RBD will also be discussed in more detail later.
Before diving into those details, we need to understand a little more about what the virus is made of and how it works. Viruses are categorized into groups based upon various features in addition to their specific genetic (DNA or RNA) sequences. For example, SARS-CoV-2 is an enveloped virus meaning that it has a lipid bilayer around the viral particle or virion that originates from the host cell as the virion (complete virus particle) is released. Other viruses, in contrast, lack this envelope and simply have a protein “shell” (known as a capsid) surrounding the viral contents (called a non-enveloped virus). Polio and rhinovirus (a major cause of the common cold) are examples of non-enveloped viruses.
As seen in Figure 1, SARS-CoV-2 has a characteristic structure that involves several key proteins. Note that many “accessory” proteins needed by the virus are not depicted. The name “coronavirus” is a reference to the crown-like image caused by the S protein. Corona is Latin for crown.
Another critical point related to understanding the virus is how information is stored in the virus. Living cells such as human or bacterial cells use double-stranded DNA (deoxyribonucleic acid) to store their genetic information. We call the sum of all the DNA information in a cell the genome of the organism because it encodes all the genes needed by the organism. These genes include DNA information that is used to build the machines needed by the cell to control the various cellular functions. In this context, DNA is the long-term information storage molecule.
Cells also have another molecule known as RNA (ribonucleic acid). RNA strands are made using the DNA sequence as a template (in the process called transcription), and RNA typically only lasts for a relatively short period of time. Some of the RNA made in cells, called “mRNA” for messenger RNA, provides the information used to build proteins (in the process called translation). RNA is generally single-stranded compared to the double-stranded form of DNA. However, RNA can fold on itself in complex structures and shapes.
In contrast to cells, viruses can have DNA or RNA genomes. SARS-CoV-2 has a positive sense, single-stranded RNA (+ssRNA) genome. Single-stranded means that, unlike DNA, the RNA does not come with a complementary strand. Being positive sense is analogous to being already in the mRNA form. This means that the RNA can be translated by the “host cell” (infected cell) ribosome directly into proteins without needing to be transcribed before translation. As will be discussed later, having a +ssRNA genome means that this cell has to encode some of its own machinery for copying itself.
One approach to studying genomes is to map out the genes and features of different portions of the DNA sequence. Think of this like mapping out the chapters and sections of a book. A genome map of SARS-CoV-2 is shown in Figure 2. Some sections appear as large “open reading frames” (ORFs) meaning that they get translated into long protein sequences and then cut into smaller functional proteins. Other protein-encoding segments are also denoted such as the now-famous (or infamous) S protein introduced earlier. The accessory factors and ORF1a and ORF1b include several proteins critical to the ability of the virus to hijack host cell machinery and for the repackaging of virus particles.
DNA, the genetic material of humans, and RNA, the genetic material of SARS-CoV-2, are made of long polymers of nucleotide bases. Five different nucleotide bases exist: adenine (A), guanine (G), cytosine (C), uracil (U), and thymine (T). DNA and RNA each use four of the five bases. A, G, C and T are used by DNA, while A, G, C, and U are used by RNA. The full SARS-CoV-2 +ssRNA sequence (its genome) is made up of nearly 30,000 nucleotide bases in a very specific sequence. While the map in Figure 2 does not show the nucleotide sequence, an example of a portion of the sequence is shown in Figure 3 comparing a region of SARS-CoV-2 with other viruses as explained below. Note that this sequence is from a database that records the information in DNA form, which uses thymine (T) instead of uracil (U).
Genetic Comparisons Between Viruses
One way to study viruses is to see how the sequences vary from other known viruses. Interestingly, SARS-CoV-2 is only 79% similar to SARS-CoV.11 The closest sequences to SARS-CoV-2 are viruses isolated from bats found in Yunnan province 1000+ km from Wuhan denoted RaTG13 and RmYN02.12, 13 RaTG13 is the closest sharing 96.2% identify while the RmYN02 shares 93.3% identity with SARS-CoV-2 reference sequence (note the reference sequence is the first sequence that was released by Chinese researchers before the variants). In this context, nucleotide “identity” means that two sequences are identical at that percentage of sites. Thus, 100% identity would mean that they have the same nucleotides at all possible sites. In a 30,000 nucleotide sequence, a 90% identity means that 27,000 sites match between two sequences. In Figure 3, sequences from a small portion of these genomes are aligned demonstrating both regions where they match as well as regions where differences are found. Where spaces (dashes) exist in the alignment represent sequences that are not found in all four sequences.
The differences between SARS-CoV-2 and RaTG13 may seem subtle, but they are significant. One of the most significant differences is that SARS-CoV-2 has a sequence called a Furin cleavage site in the Spike protein, while RaTG13 lacks this sequence. Parts of the protein sequence of the Spike protein are mapped in Figure 4 for comparison. The Furin cleavage site is named such because a protease (an enzyme that can cut proteins at a specific site) named Furin is able to make a cut at this site splitting the protein into two segments. Interestingly, the cleavage of this site by Furin makes the virus able to infect human cells more readily.14 It is worth noting that RmYN02 has some amino acids near this region that are similar to the Furin sequence, though it does not match up exactly with SARS-CoV-2, and it does not appear to be a functional Furin site. However, this is not the only difference in the Spike protein that is important. For instance, the RBD is another region where SARS-CoV-2 Spike protein differs from other viruses, and it is a region that has changed during the pandemic.15, 16 These changes are among some of the key changes that may explain how the virus was able to jump from infecting other animals to now infecting humans.
In the next part, we will examine how SARS-CoV-2 has mutated throughout the pandemic. This is a live example of “evolution” in real time, and it offers opportunities to ask questions about what is possible in terms of evolutionary change in a virus.
Part 2: What Is and Is Not Changing In SARS-CoV-2
In the first part of this article, we spent time trying to understand SARS-CoV-2 and the general process of infection. We explored the features of SARS-CoV-2 including the genome sequence and some of the key proteins that participate in infection. We noted that some key regions were different from other viral sequences found in nature—notably specific regions in Spike protein: the furin site and the receptor binding domain (RBD). Now we look at a larger question: how is this virus changing over time? Yet again, we have another opportunity to expand our vocabulary as we hear about “variants.” Let’s unpack this a bit and then investigate what types of changes we are seeing.
As a virus infects an individual, the virus attaches to a cell and then enters the cell (called penetration). Once inside the host cell, the virus is “uncoated”, which means that it is “opened up” so the viral genome can be copied using protein machinery from the host cell. Viral proteins are also built during this time. Then, viral particles are assembled before they are released by the host cell. To understand changes occurring in the virus, we will look for a moment at the portion of the viral life cycle that includes copying of the genetic information.
Proteins Involved in Replication and Repair in SARS-CoV-2
SARS-CoV-2 copies the viral genome using a protein not found in human cells (or most organisms for that matter!): an RNA-dependent (or directed) RNA polymerase (RdRp).17 The RdRp in SARS-CoV-2 is called Nsp12 (nonstructural protein 12). Since humans have a DNA genome, we do not use an enzyme like this—we use DNA polymerases to copy our DNA. In SARS-CoV-2, Nsp12 copies the RNA genome (with the help of some other proteins like Nsp7 and Nsp8).
To say that Nsp12 “copies” the genome is to say that it “reads” the RNA strand and assembles complementary bases into a new strand (Figure 5). Where there is adenine (A) in the genomic RNA, it will place uracil (U); where there is guanine (G), it will place cytosine (C), and vice versa. The strand built by this process is called the complement to the genomic RNA and is negative sense or (-)RNA (meaning it is not used directly to make a protein). Then, the polymerase can use this (-)RNA strand as a template to build copies of the positive (+) sense genomic RNA.18
Why is this important? Well, copying DNA or RNA is an opportunity for errors to creep into the sequence. Perhaps like me, you took keyboarding or typing in high school. One of the goals of that class is to learn how to type as fast as possible with as few errors as possible (while not looking at the keyboard). As the polymerases do their job, it is possible for a wrong nucleotide to be inserted (like hitting the wrong key on the keyboard). This accumulation of mutations over time is referred to as genetic drift and is the basis of why some viruses change year after year (like influenza).
In our genome, our polymerases use proof-reading (that’s really what it is called) to check for errors and correct them. This leads to a fidelity of one error for every billion bases inserted!19 Most RNA polymerases do not use proofreading since RNA generally doesn’t last very long. Similarly, many viruses do not have proofreading in their genome—but SARS-CoV-2 does!20 Nonstructural protein 14 (nsp14) in SARS-Co-V-2 is a bifunctional protein including one portion that serves as an exoribonuclease (called ExoN).20 ExoN is a 3’ to 5’ exoribonuclease and can remove ribonucleotides that are incorrectly inserted by the polymerase. Think of this like the backspace key, enabling you to undo errors in typing so they can be replaced with the correct “letters.” What this means in a practical sense is that this virus doesn’t change (evolve) very quickly. Yet, in the past two years, we have heard repeatedly about new “variants” of the virus. While this seems like a contradiction, we must consider several important factors: how large is the genome? How many virions are made per infection? How many infections have occurred? With a genome of 29,000 ribonucleotides and an estimated mutation rate of 1.25×10-6 per nucleotide per infection multiplied out by millions of infections, it isn’t surprising that we have seen changes in the virus.21 But, just how much has the virus changed?
Exploring the Changes in SARS-CoV-2
As the virus began to spread, researchers quickly began sequencing the genomes of the viruses and cataloging the sequenced viruses in databases—some publicly available and some only available to other researchers. There are now over 4.3 million SARS-CoV-2 viral sequences for us to be able to compare in the public NCBI Virus Variation database.22 This is a bit of a unique situation because we’ve never had such a large pandemic occur while we have had the ability to sequence the genetic information of the virus in real-time worldwide. This massive effort has provided a way to track genomic changes (i.e., mutations in the virus) over time to see: what types of changes are occurring? And, what types of changes are not occurring?
In Figures 6 and 7, portions of the nucleotide sequence (shown as DNA nucleotides) are compared for the reference sequence versus several variants including the infamous delta and the rapid-spreading omicron. It is clear even from this snapshot that some positions rarely (if ever) change while others seem to have changed more than once. In Figure 6, we see examples of deletion (loss of nucleotides) and insertion (addition of nucleotides). Note that these instances occur with nucleotides in multiples of 3 (3 deleted and 9 inserted). Because the genetic code works by using three nucleotides (called a codon) to encode one amino acid, it means that the protein product will retain most of its original sequence. Thus, it is likely to fold and function generally—though the specific mutations (insertions and deletions) may have functional consequences on the protein. This also explains why mutations involving the insertion or deletion of 1 or 2 nucleotides (or any number not divisible by 3) are far less likely to occur: changes like these are more likely to have larger, usually negative, effects on the protein products.
In Figure 7, a portion of the Spike protein Receptor Binding Domain (RBD) sequence is shown. In this region, several of the variants have single nucleotide changes. These show up in the figure as uncolored spaces with letters that differ from those above (or below) in the alignment. The RBD is important for interacting with the human ACE2 receptor, which serves as both a “landing site” for the virus and helps the virus make entry into the cell through a critical enzymatic step.10, 23 Changes in the RBD sequence are likely to impact how tightly the Spike protein interacts with ACE2. Thus, these are of particular interest to researchers trying to predict the threat posed by the variant.
Note, these figures show only small sections of the >29,000 ribonucleotide sequence. In these examples, we see deletion, insertion, and single nucleotide changes. These represent the types of changes seen throughout the viral genome with the single nucleotide changes being by far the most common. At this point, perhaps you are wondering: how many changes are in the variants when compared to the reference sequence? By using a multiple sequence alignment approach like what is seen in Figures 6 and 7, we can get quantifiable numbers of differences among the variants and the reference sequence. In even the most extreme cases—like the Omicron variant—the total number of nucleotide changes (including insertions and deletions) is around 100 (less than 1%). Thus, for over 99% of the sequence there are no changes! Admittedly, this is a bit surprising, but considering the proofreading function of ExoN, perhaps it is to be expected.
It is worth noting that the “new” variant of Omicron, termed BA.2, does have some additional mutations. However, early reports indicate that this variant may act similarly to BA.1 and though there does appear to be some evasion of antibodies, it is not necessarily evading all approaches.24, 25 The ability to evade antibodies is most likely due to changes in Spike protein. This simply means that Spike protein has changes in areas that antibodies typically bind causing the antibodies to bind more weakly to this variant than to other versions. Due to its similarities with BA.1, BA.2 has probably been circulating for some time but has not been noticed because the changes are relatively subtle.
As of this writing, ten variants are considered “Variants Being Monitored” (VBM) by the Centers for Disease Control, two are listed as “Variants of Concern” (VOC): delta and omicron.26 In reviewing mutation data on these variants, most of the mutations tend to occur in the Spike protein-coding region with additional mutations in the ORF1ab region and some variants showing mutations in the nucleocapsid (N) protein-coding region.27 Mutations in the Spike protein tend to be focused within the N-terminal domain or the RBD, as noted above. These are the regions that antibodies typically bind, especially those formed through vaccination with the mRNA vaccines.
As seen in Figure 8, Spike protein point mutation sites for the RBD are mapped onto a three-dimensional model of the protein for the Omicron variant. The mutation sites are highlighted as red spheres. The region in red is the RBD. The concentration of red spheres in this area underscores the importance understanding how this region is changing and what impact that has on viral transmission and treatability. Changes in this region can result in evasion of antibodies that target Spike protein.28 In other words, some of these mutations in the Spike protein make this region less able to be bound by antibodies from vaccination and/or prior infection. It is also worth noting that in addition to antibodies, T-cells also respond to SARS-CoV-2 and T-cell response includes binding to Spike (or other viral proteins). Notably, T-cell response in vaccinated and/or prior infected individuals still mostly retain the ability to recognize Omicron.29
Implications of the Mutations Observed in SARS-CoV-2
What can we learn from this? There are a few key takeaways for us to consider. First, mutations in SARS-CoV-2 are still rare in the sense that we do not see widespread mutation throughout the viral genome. This is due to the error correction mechanism and apparently a low tolerance of genetic change. The mutations that are occurring are enabling the virus to survive and spread more readily while causing more mild symptoms in general. Thus, you could argue that natural selection is filtering out mutations that do not enable the virus to spread. As noted by Dutch botanist and geneticist Hugo de Vries, “Natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest.”30 Natural selection does not provide the mechanism for the origin of new information, which is necessary for the evolution of new viruses and organisms.31
Second, the types of changes we are seeing fall into the basic categories of insertions, deletions, and single-nucleotide changes. The largest insertion in the sequences examined was 9 nucleotides. Interestingly, this sequence is not found anywhere in the virus or in any of the variants examined except Omicron. There is a similar sequence in the genome (about 4,000 nucleotides away) that is off by one nucleotide, but I have not seen a lot of speculation around this sequence.
There are some limitations to this brief study. For instance, there are 10’s to 100’s of thousands of sequences for some of these variants. So, there will undoubtedly be variability among the various samples. Yet, even with such variability, the general themes noted above remain: no novel sets of information have been generated by the DNA changes observed. More specifically, no new proteins or enzymatic functions have been observed. Instead, mutation and selection appear to be at work on the existing protein-coding genes, which is why we see most mutations focused on regions like the Spike protein-coding sequence. In order for new features to develop as in the Neo-Darwinian model of evolution, new genetic information is needed, but we do not observe this occurring.31, 32
In conclusion, SARS-CoV-2 is mutating (or evolving), but it also clear that it is still SARS-CoV-2. We are seeing first-hand what types of mutations are possible. Note that this does not necessarily mean that we know what is possible in a living organism—viral growth and mutation has unique constraints. Other studies have argued that mutations tend to modify or break existing features rather than build new ones.32, 33 This appears to hold true in SARS-CoV-2.
As we reflect on this, we will next turn toward thinking about what can be expected as we look ahead in terms of the pandemic. Then, we will spend a moment reflecting on larger questions: did God create viruses? Where do they fit in the larger picture of the creation?
Part 3: What Are Viruses Good For?
In the first part of this article, we examined the structure of SARS-CoV-2 and mechanism of infection. While the type of virus is similar to some viruses known to infect humans, this is the first time this particular version has been found, and it appears to be adapted to infect humans compared with other similar viruses in bats. We followed this with a second part discussing the types and numbers of mutations observed in SARS-CoV-2 during the pandemic. While this virus has accumulated on average around 100 mutations throughout the pandemic, most of these changes are concentrated in the spike protein and a few other regions. In addition, the mutations fall into the typical categories of point mutations, insertions, and deletions. Interestingly, SARS-CoV-2 has an enzyme that proofreads the genome, which minimizes mutations and helps explain why the virus seems to be changing relatively slowly.
In considering this, it is worth asking, why do we have viruses anyway? From a human perspective, it can often seem like all viruses are bad. After all, the only time the media (or society more generally) tends to focus on viruses is in the context of the seasonal flu or in the case of an outbreak of some deadly virus—like MERS or SARS. In fact, the word “virus” originated from the Latin term for poison.34 Our language has clear implications for how we view viruses. Do viruses provide evidence against God’s design in nature by implying He created something “bad”?
Do Viruses Have Roles In Nature?
As a little exercise in considering the roles and purposes of viruses, let’s first ask: how many types of viruses are there? Current taxonomy of viral species by the International Committee on the Taxonomy of Viruses lists 10,434 species.35 It seems generally agreed that this is an under-representation of the total number of viruses in nature, as additional viruses continue to be discovered year by year. In support of this idea, it has been stated that there are ~1031 bacterial viruses (called bacteriophages) in the biosphere, which exceeds the estimate of the number of stars in the universe!.36, 37 Interestingly, only approximately 219 viruses have been found to infect humans.38 Of these viruses, relatively few cause disease or death in humans.38 Far fewer have been found to cause epidemics or pandemics.38, 39 Yet, as humans, we generally focus on these few cases that cause disease rather than on the thousands of viruses (perhaps hundreds of thousands or millions?) that exist throughout nature.37
To be clear, the 1918 Spanish flu, HIV, SARS, MERS, and SARS-CoV-2 have all had a major impact on our world. Many lives were lost or dramatically changed because of these viruses and their associated epidemics or pandemics. Yet, the integral role of viruses in nature has not been all negative as will be pointed out below.
Second, if there are so many different viruses, what do they do? Are there natural and ecological functions and roles for viruses. The answer to that is YES. In fact, there are many functions and roles for viruses in nature. For example, bacteriophages, mentioned above, help control bacterial populations.40 In addition, bacteriophages can aid in transfer of genes between bacteria, serve as a nutrient repository, and defend bacteria against other bacteria.40 Further, viruses may also play similar roles in eukaryotes and higher organisms including symbiotic relationships.41, 42 In humans, infection with GB-virus C has been associated with slowed progression of HIV infection, suggesting that this virus helps block HIV from infecting host cells.43 Some have argued that the roles of viruses worldwide are so important that life as we know it would not exist without viruses.37
So, does coronavirus have a natural role in bats or pangolins? This is a harder question to answer as few people are looking at this question—the general starting assumption is that viruses are “poison” or “pathogens”.42 Interestingly, this assumption, based upon evolutionary presuppositions, may be impeding our understanding of the roles of viruses in nature. Additional research will be needed to identify and explore such roles.
Why Do We Have Viruses?
Consider for a moment: why would God allow viruses? Again, recall that most viruses do not cause problems and disease in humans, and it is reasonable to consider that many viruses have useful roles in nature. Could viruses be originally created entities that perhaps have also decayed since the fall like our own genomes37? If viruses were originally created by God to serve specific roles in nature, then it is possible that the nature and roles of viruses have been corrupted over time by genetic mutation.31 The biochemical components in viruses are highly sophisticated—for example, reverse transcriptase (making DNA from RNA), error-correction, self-assembly, etc. These complex systems are best explained in a design model.
This perspective on viruses being designed entities will prove to be a very fruitful research endeavor.37 In fact, understanding the original design of viruses may help us identify the roles of viruses and how those roles have become corrupted over time. This may help us understand virulence and the ability of a virus to spread and mutate, which may help us predict future pandemic threats.
What can we expect moving forward? As we move forward, we can expect that SARS-CoV-2 will remain around continuing to change. The rate of change may slow since the virus is infecting fewer individuals than when it was spreading at its peak. Changes in the virus may enable it to continue to spread and possibly even cause new outbreaks, but the changes also seem to reduce the ability of the virus to cause serious illness in most people. Note that serious illness is still happening especially in individuals with multiple risk factors, and we need to be serious about looking after those who are most at risk. The good news is that new treatments and approaches are becoming available to help minimize the health impact where possible.
Conclusion
SARS-CoV-2 has spread around the world over the last two and a half years and caused major loss of life. Though the virus has mutated over the past two years, no new genetic information has been generated nor have novel features developed as needed by a Neo-Darwinian model. Further, while the origin of this strain of the virus may remain contentious and debated, it is clear that viruses as a whole are designed entities fulfilling important roles in nature. It may be hard for us to identify those roles in the present time due to the genetic changes that have taken place in those viruses since the Fall in Genesis 3. Nevertheless, viewing viruses as designed entities that have experience genetic change and decay since the Fall will serve as a valuable framework for research in this area. In addition, this view helps remind us of God’s power in creation and of the consequences of sin that have been building since the Fall.
Endnotes
1 “Revised U.S. Surveillance Case Definition for Severe Acute Respiratory Syndrome (Sars) and Update on Sars Cases–United States and Worldwide, December 2003” (2003), MMWR: Morbidity and Mortality Weekly Report, 52[49]:1202-1206.
2 B. Rha, J. Rudd, D. Feikin, J. Watson, A. T. Curns, D. L. Swerdlow, M. A. Pallansch, and S. I. Gerber (2015), “Update on the Epidemiology of Middle East Respiratory Syndrome Coronavirus (Mers-Cov) Infection, and Guidance for the Public, Clinicians, and Public Health Authorities – January 2015” MMWR: Morbidity and Mortality Weekly Report, 64[3]:61-62.
3 WHO (2021), “Mers Situation Update”.
4 Coronavirus Resource Center Global Map. (2022), Johns Hopkins University & Medicine, https://coronavirus.jhu.edu/map.html.
5 World Health Organization (2020), “Health Topics: Zoonosesd” https://www.who.int/news-room/fact-sheets/detail/zoonoses.
6 K. G. Andersen, A. Rambaut, W. I. Lipkin, E. C. Holmes, and R. F. Garry (2020), “The Proximal Origin of Sars-Cov-2” Nature Medicine, 26[4]:450-452.
7 Y. Deigin, and R. Segreto (2021), “Sars-Cov-2’s Claimed Natural Origin Is Undermined by Issues with Genome Sequences of Its Relative Strains: Coronavirus Sequences Ratg13, Mp789 and Rmyn02 Raise Multiple Questions to Be Critically Addressed by the Scientific Community” Bioessays, 43[7]:e2100015.
8 M. Seyran, D. Pizzol, P. Adadi, T. M. A. El-Aziz, S. S. Hassan, A. Soares, R. Kandimalla, K. Lundstrom, M. Tambuwala, A. A. A. Aljabali, A. Lal, G. K. Azad, P. P. Choudhury, V. N. Uversky, S. P. Sherchan, B. D. Uhal, N. Rezaei, and A. M. Brufsky (2021), “Questions Concerning the Proximal Origin of Sars-Cov-2” Journal of Medical Virology, 93[3]:1204-1206.
9 J. van Helden, C. D. Butler, G. Achaz, B. Canard, D. Casane, J. M. Claverie, F. Colombo, V. Courtier, R. H. Ebright, F. Graner, M. Leitenberg, S. Morand, N. Petrovsky, R. Segreto, E. Decroly, and J. Halloy (2021), “An Appeal for an Objective, Open, and Transparent Scientific Debate About the Origin of Sars-Cov-2” Lancet, 398[10309]:1402-1404.
10 Cody B. Jackson, Michael Farzan, Bing Chen, and Hyeryun Choe (2022), “Mechanisms of Sars-Cov-2 Entry into Cells” Nature Reviews Molecular Cell Biology, 23[1]:3-20.
11 G. A. Rossi, O. Sacco, E. Mancino, L. Cristiani, and F. Midulla (2020), “Differences and Similarities between Sars-Cov and Sars-Cov-2: Spike Receptor-Binding Domain Recognition and Host Cell Infection with Support of Cellular Serine Proteases” Infection, 48[5]:665-669.
12 Hong Zhou, Xing Chen, Tao Hu, Juan Li, Hao Song, Yanran Liu, Peihan Wang, Di Liu, Jing Yang, Edward C. Holmes, Alice C. Hughes, Yuhai Bi, and Weifeng Shi (2020), “A Novel Bat Coronavirus Closely Related to Sars-Cov-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein” Current Biology, 30[11]:2196-2203.e2193.
13 Peng Zhou, Xing-Lou Yang, Xian-Guang Wang, Ben Hu, Lei Zhang, Wei Zhang, Hao-Rui Si, Yan Zhu, Bei Li, Chao-Lin Huang, Hui-Dong Chen, Jing Chen, Yun Luo, Hua Guo, Ren-Di Jiang, Mei-Qin Liu, Ying Chen, Xu-Rui Shen, Xi Wang, Xiao-Shuang Zheng, Kai Zhao, Quan-Jiao Chen, Fei Deng, Lin-Lin Liu, Bing Yan, Fa-Xian Zhan, Yan-Yi Wang, Geng-Fu Xiao, and Zheng-Li Shi (2020), “A Pneumonia Outbreak Associated with a New Coronavirus of Probable Bat Origin” Nature, 579[7798]:270-273.
14 M. G. Hossain, Y. D. Tang, S. Akter, and C. Zheng (2021), “Roles of the Polybasic Furin Cleavage Site of Spike Protein in Sars-Cov-2 Replication, Pathogenesis, and Host Immune Responses and Vaccination” Journal of Medical Virology.
15 Michael I. Barton, Stuart A. MacGowan, Mikhail A. Kutuzov, Omer Dushek, Geoffrey John Barton, and P. Anton van der Merwe (2021), “Effects of Common Mutations in the Sars-Cov-2 Spike Rbd and Its Ligand, the Human Ace2 Receptor on Binding Affinity and Kinetics” eLife, 10:e70658.
16 Jun Lan, Jiwan Ge, Jinfang Yu, Sisi Shan, Huan Zhou, Shilong Fan, Qi Zhang, Xuanling Shi, Qisheng Wang, Linqi Zhang, and Xinquan Wang (2020), “Structure of the Sars-Cov-2 Spike Receptor-Binding Domain Bound to the Ace2 Receptor” Nature, 581[7807]:215-220.
17 M. Romano, A. Ruggiero, F. Squeglia, G. Maga, and R. Berisio (2020), “A Structural View of Sars-Cov-2 Rna Replication Machinery: Rna Synthesis, Proofreading and Final Capping” Cells, 9[5].
18 Isabel Sola, Fernando Almazán, Sonia Zúñiga, and Luis Enjuanes (2015), “Continuous and Discontinuous Rna Synthesis in Coronaviruses” Annual review of virology, 2[1]:265-288.
19 David L. Nelson, Michael M. Cox, and Albert L. Lehninger (2017), Lehninger Principles of Biochemistry (New York, NY Houndmills, Basingstoke: W.H. Freeman and Company ;
Macmillan Higher Education).
20 Mohammed Tahir (2021), “Coronavirus Genomic Nsp14-Exon, Structure, Role, Mechanism, and Potential Application as a Drug Target” Journal of Medical Virology, 93[7]:4258-4264.
21 Massimo Amicone, VÃtor Borges, Maria João Alves, Joana Isidro, LÃbia Zé-Zé, SÃlvia Duarte, LuÃs Vieira, Raquel Guiomar, João Paulo Gomes, and Isabel Gordo (2021), “Mutation Rate of Sars-Cov-2 and Emergence of Mutators During Experimental Evolution” bioRxiv:2021.2005.2019.444774.
22 E. L. Hatcher, S. A. Zhdanov, Y. Bao, O. Blinkova, E. P. Nawrocki, Y. Ostapchuck, A. A. Schäffer, and J. R. Brister (2017), “Virus Variation Resource – Improved Response to Emergent Viral Outbreaks” Nucleic Acids Research, 45[D1]:D482-d490.
23 Shuai Xia, Qiaoshuai Lan, Shan Su, Xinling Wang, Wei Xu, Zezhong Liu, Yun Zhu, Qian Wang, Lu Lu, and Shibo Jiang (2020), “The Role of Furin Cleavage Site in Sars-Cov-2 Spike Protein-Mediated Membrane Fusion in the Presence or Absence of Trypsin” Signal Transduction and Targeted Therapy, 5[1]:92.
24 Emi Takashita, Noriko Kinoshita, Seiya Yamayoshi, Yuko Sakai-Tagawa, Seiichiro Fujisaki, Mutsumi Ito, Kiyoko Iwatsuki-Horimoto, Peter Halfmann, Shinji Watanabe, Kenji Maeda, Masaki Imai, Hiroaki Mitsuya, Norio Ohmagari, Makoto Takeda, Hideki Hasegawa, and Yoshihiro Kawaoka (2022), “Efficacy of Antiviral Agents against the Sars-Cov-2 Omicron Subvariant Ba.2” New England Journal of Medicine.
25 Jingyou Yu, Ai-ris Y. Collier, Marjorie Rowe, Fatima Mardas, John D. Ventura, Huahua Wan, Jessica Miller, Olivia Powers, Benjamin Chung, Mazuba Siamatu, Nicole P. Hachmann, Nehalee Surve, Felix Nampanya, Abishek Chandrashekar, and Dan H. Barouch (2022), “Neutralization of the Sars-Cov-2 Omicron Ba.1 and Ba.2 Variants” New England Journal of Medicine.
26 SARS-CoV-2 Variant Classification and Definitions. (2022), CDC, https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-classifications.html.
27 A. O’Toole, V. Hill, O.G. Pybus, and et al. (2022), “Tracking the International Spread of Sars-Cov-2 Lineages B.1.1.7 and B.1.351/501y-V2 [Version 1; Peer Review: 3 Approved].” Wellcome Open Res, 6[121].
28 C. Chakraborty, A. R. Sharma, M. Bhattacharya, and S. S. Lee (2022), “A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of Sars-Cov-2 and Their Emerging Variants with Escape Mutations” Frontiers in Immunology, 13:801522.
29 V. Naranbhai, A. Nathan, C. Kaseke, C. Berrios, A. Khatri, S. Choi, M. A. Getz, R. Tano-Menka, O. Ofoman, A. Gayton, F. Senjobe, Z. Zhao, K. J. St Denis, E. C. Lam, M. Carrington, W. F. Garcia-Beltran, A. B. Balazs, B. D. Walker, A. J. Iafrate, and G. D. Gaiha (2022), “T Cell Reactivity to the Sars-Cov-2 Omicron Variant Is Preserved in Most but Not All Individuals” Cell, 185[6]:1041-1051.e1046.
30 Hugo de Vries, and Daniel Trembly MacDougal (1905), Species and Varieties, Their Origin by Mutation; Lectures Delivered at the University of California (Chicago,: The Open court publishing company;).
31 J.C. Sanford (2008), Genetic Entropy & the Mystery of the Genome (Waterloo, NY: FMS Publications).
32 Michael J. Behe (2019), Darwin Devolves : The New Science About DNA That Challenges Evolution (New York, NY: HarperOne, an imprint of HarperCollins Publishers).
33 M. J. Behe (2010), “Experimental Evolution, Loss-of-Function Mutations, and “the First Rule of Adaptive Evolution”” Quarterly Review of Biology, 85[4]:419-445.
34 Harald Brüssow (2021), “On the Role of Viruses in Nature and What This Means for the Covid-19 Pandemic” Microbial Biotechnology, 14[1]:79-81.
35 Peter J. Walker, Stuart G. Siddell, Elliot J. Lefkowitz, Arcady R. Mushegian, Evelien M. Adriaenssens, Donald M. Dempsey, Bas E. Dutilh, Balázs Harrach, Robert L. Harrison, R. Curtis Hendrickson, Sandra Junglen, Nick J. Knowles, Andrew M. Kropinski, Mart Krupovic, Jens H. Kuhn, Max Nibert, Richard J. Orton, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Donald B. Smith, Arvind Varsani, Francisco Murilo Zerbini, and Andrew J. Davison (2020), “Changes to Virus Taxonomy and the Statutes Ratified by the International Committee on Taxonomy of Viruses (2020)” Archives of Virology, 165[11]:2737-2748.
36 F. Rohwer, and R. Edwards (2002), “The Phage Proteomic Tree: A Genome-Based Taxonomy for Phage” Journal of Bacteriology, 184[16]:4529-4535.
37 Georgia Purdom, and Joe Francis (2009), “More Abundant Than Stars” Answers Research Journal, 2:85-95.
38 Mark Woolhouse, Fiona Scott, Zoe Hudson, Richard Howey, and Margo Chase-Topping (2012), “Human Viruses: Discovery and Emergence” Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 367[1604]:2864-2871.
39 M. E. Woolhouse, R. Howey, E. Gaunt, L. Reilly, M. Chase-Topping, and N. Savill (2008), “Temporal Trends in the Discovery of Human Viruses” Proceedings: Biological Sciences, 275[1647]:2111-2115.
40 Z. Naureen, A. Dautaj, K. Anpilogov, G. Camilleri, K. Dhuli, B. Tanzi, P. E. Maltese, F. Cristofoli, L. De Antoni, T. Beccari, M. Dundar, and M. Bertelli (2020), “Bacteriophages Presence in Nature and Their Role in the Natural Selection of Bacterial Populations” Acta Bio-Medica: Atenei Parmensis, 91[13-S]:e2020024.
41 M. J. Roossinck (2015), “Move over, Bacteria! Viruses Make Their Mark as Mutualistic Microbial Symbionts” Journal of Virology, 89[13]:6532-6535.
42 Marilyn J. Roossinck (2011), “The Good Viruses: Viral Mutualistic Symbioses” Nature Reviews Microbiology, 9[2]:99-108.
43 Nirjal Bhattarai, and Jack T. Stapleton (2012), “Gb Virus C: The Good Boy Virus?” Trends in Microbiology, 20[3]:124-130.