“Music is the space between the notes.” (Attrib. Claude Debussy 1862-1918, FR Composer)
Nearly four months into what has become the most serious pandemic since the Spanish influenza erupted in 1918, my colleagues and I are led once again to re-consider the foundational role that viruses play in the great net of being. The Spanish influenza pandemic resulted from the adaption of an avian virus (H1N1) to the human genome, and in two years (1918-19), is estimated to have infected 500 million people (one-third of earth’s population), with a mortality of some 50 million. Susceptibility and mortality were particularly high among children younger than age 5, people 65 years and older, and oddly among adults age 20-40.
The current pandemic, although indeed tragic for many – and many yet to come – does not at least appear to be on a similar morbidity course, yet.
SARS-CoV-19, (the virus that causes COVID-19 disease) is a member of the coronavirus zoonotic subgroup of viruses that can cause disease in birds and mammals. Coronavirus prefer respiratory tract cells, and are composed of a lipid-protein envelope that surrounds a single strand of RNA.
Viruses are not living organisms. They are not cells. They do not metabolize, cannot move, and must commandeer the genomes of living cells, or hosts, where they issue instructions for their own replication and assembly. Their origins are puzzling, but like living organisms, they utilize DNA and/or RNA as a reproductive means – many in fact, are naked DNA or RNA in some cases. We thus refer to them as biological, or life-like, entities.
Viruses generally utilize two strategies for replication, or what could be called viral reproduction. The first, lytic, involves taking over the host genome and forcing the cell to encode multiple virus copies. Here (and in the case of SARS-CoV-2), the cell bursts and new virus are released to invade other cells. Ultimately, new virus particles are transmitted to other host individuals wherein the cycle is repeated. In a second strategy (lysogenic), viruses insert themselves into host cell genomes and remain dormant. As living cells make copies of themselves, the viral DNAs are also copied and inherited by host daughter cells. As in the case of HIV, lysogenic viral DNAs can remain dormant for many years, but in the end become lytic, and kill host cells once they activate (AIDS). During the dormancy period, viral DNAs can be transmitted to new individuals.
All living organisms examined contain native viruses, and the diversity of viruses on our planet is quite simply staggering. Work published in April of 2019, reports at least 200,000 different kinds of viruses in the oceans alone. Amazingly, this number is over ten times higher than a consensus published only three years earlier, in 2016.
Very much indeed remains to be discovered about viruses. Scientists were astonished in 2003, when the first giant viruses were reported to have been discovered as symbionts of single celled Amoeba. These were on the order of 600nm (nanometers) in size, which is about one-fifth of the size of a red blood cell. Considering the relationship between surface area and volume (as surface area increases 4x, volume increases 8x), these are enormous entities. Polio virus are on the order of approximately 30nm and SARS-CoV-19 is 50-200nm, and neither are visible by light microscope.
Biologists hunt viruses by looking in living tissues and environmental samples for what are called open reading frames, or ORFs. ORFs are sequences of DNA or RNA that are known to encode proteins, or would likely signal regulatory regions of a genome. SARS-CoV-2 has a typical virus genome of about 30 thousand RNA bases (29,903 NT) and 4 ORF. Fortunately for humans, SARS-CoV-2 exhibits a relatively low mutation rate (inserting an RNA base in the wrong position during replication) of about 2 bases per month. Said conservation may allow biologists to develop vaccines and treatments by not having to constantly face a quickly changing entity.
Giant viruses, on the other hand, can have upward of 900 ORF and can be infected by smaller virus particles known as virophages. This month (April 2020), one research group reports that some larger viruses have “stolen” whole genes from their hosts that encode proteins involved in energy metabolism. Does that mean that viruses can metabolize chemical compounds into energy for themselves or a host? Not necessarily. Until laboratory work demonstrating that likelihood is completed, their function, from the viral point of view, remains a mystery. Does it mean that viruses with so-called “stolen” genes represent an evolutionary link between living cells and non-living replicator collections of complex chemistries? Perhaps, but any number of scenarios are equally likely, and life itself may well have originated more than once.
Viruses and viral DNAs/RNAs are also incredibly mobile, as well as heritable. Approximately 8% of the human genome is made up of ancient viral DNA sequences acquired, and passed down, from our pre-modern civilization ancestors (ERVs, endogenous retroviruses), and close to 50% of the human genome is composed of mobile genetic elements (transposons) that can, and do, physically move in and out of genomes.
Indeed, complex life itself may be partly a result of viral movement and association. Over the last two decades a number of molecular and experimental biologists have brought us to the conclusion that the very existence of placental mammals is in major part due to capture of a viral gene (env – encodes the viral envelope protein) by proto-mammals, sometime after the extinction of the dinosaurs. Expressed in mammals, the sequence encodes a protein, syncytin, that directs formation of a cellular boundary between the placenta and maternal tissue. Laboratory studies with strains of mice wherein the gene is knocked out (deleted) in the parents, produce embryos that cannot implant in the maternal uterine wall. Horizontal gene transfer (HGT), between unrelated organisms (not parent to offspring), is widespread in nature and symbiosis itself is common.
Why the preceding recitative of viral natural history? Why think about host-virus, or virus-virus interaction during a major human pandemic? What has become very clear to many of us, is that although we study nature as entity, it’s true significance is found in relationality and consequently in wholeness. For example, the hosts of metabolism-gene-thieving viruses are marine phytoplankton. Phytoplankton form the base of the entire marine photosynthetic food web, which is a major determinate of gas exchange on the planet – part of the lungs of the planet if you will. Humanity almost completely prefers to view viruses as disease causing agents – those agents that wreak havoc on human health, crops, and livestock – or as complex assemblages of biochemicals that can be utilized to transform other entities into products with economic value.
The so-called Laws of Nature are not really rules to be followed – they are our current, and so far, best, descriptions of relationships at many levels. At some point our thinking about the substance of the universe must be radically softened by the admission, and acceptance, of a relational ontology. A dualistic approach to nature, or a blissfully blind concentration on entity, is simply false.
The Spanish influenza pandemic of 1918 has not faded from nature, but our collective memory has become amnesiac. H1N1 is alive and well, is monitored annually for new genomic combinations, and causes global misery and death every few months. H1N1 has passed through a little over 100 years of natural selection, but the original variant and its progeny have successfully adapted to a human host. Ultimately, biologists predict that a similar scenario will unfold with SARS-CoV-19, but not necessarily with its host.
[Viruses, and other pathogens or parasites, that kill their hosts before being transmitted to subsequent hosts are unsuccessful and become extinct. Many new diseases that cause high host mortality, at the beginning of epidemics, become milder over time.]
What of the interim, and future? Viruses transmit from host to host most efficiently when host density is high. That is why those groups that best enculturate some kind of host containment at the beginning of potentially widespread infection tend to fare reasonably well. A stellar example can be found in the Indian state of Kerala. Other peoples do not live in such organization and are already at an edge with respect to daily existence. Many in India live in conditions of high density, are unable to quarantine effectively, and must travel far from family in order to labor or make subsistence wages. Many are already hungry and most have comparatively inadequate access to health care. Africa is a dauntingly disorganized patchwork of its own. Many countries are little more than loosely organized tribal tensions. The eastern part of the continent is currently plagued by the cyclic emergence and invasion of locusts that have destroyed crops and both Africa, as well as parts of India, have been seriously drought stricken for some time. Hunger is widespread and numerous experts predict widespread famine within the year.
Latin America as well, is a patchwork of social conditions ranging from strict containment in Chile, to out outright coronavirus denial in Brazil. The very late acceptance of the seriousness of the pandemic in Mexico, denial in Brazil, refusal to contain in Nicaragua, and the two decades long collapse of the Venezuelan government and economy, can only mean to population biologists that those geographic regions will continue to act as coronavirus reservoirs for an unpredictable, and potentially lengthy, period of time. North America, western Europe, and parts of Asia, may be better off initially, but it is difficult to imagine that life will ‘return’ to what here-to-fore has been considered normal.
The relational shift that is currently underway in the part of nature immediately affecting humans stems from predicating a way of life centered on unlimited consumption and growth. The model, often called a free market model, has been very successfully exploited by the United States, Canada, western Europe, and the viciously repressive one-party of China. Indeed, India is committed to, and desires, an equivalent wide scale success with the same model. However, one hundred+ years of experiments, by biologists in particular, tell us that all populations crash once resources are exhausted. As we continue to consume life, from the Amazon to Wuhan to the Congo, we will continue to encounter and interact with the totality of the web of nature – providing grist for relationships that may ultimately become detrimental to all. The remaining few Indigenous Peoples, and their collective wisdom, are especially endangered.
In closing, some 3.6 billion years of planetary history has taught science that extinction followed by diversification is regular, and the ‘Law’. Symbiosis, diversity and complexity, are the fundamental nature of life itself. In a very real sense, ideas of living entities at the level of simple reduced isolates are an intellectual convenience, initial matters for detection and discovery, yet evidence of an immediate necessity of transforming our intellectual framework. The relevant issues go well beyond expansion of our points of view to the very act of transformation itself. Transformation is the intricate, delicate, and beautiful, symphony that continues as the Cosmic Christ; as Creation.
Donald Frohlich
Evolutionary Biologist, Houston, USA