The ocean carries 'Memories' of SARS-CoV-2

The memories that we humans encode and store in the neuronal networks of our brains are fundamental to our existence as individuals and as collective societies—for the recalling of those memories, especially during times of stress, can help us to anticipate and shape the future for our own well-being.

But we are not the only ones to benefit from the capacity to remember, nor are human memories the only ones from which we can benefit. Animals across a wide spectrum provide clear evidence of memory retention, and, perhaps surprisingly, so do plants, microorganisms and inanimate systems (think, artificial intelligence), all of which lack a neuronal brain yet can function within their own networks as entities with agency and memory. In these cases, as in neuronal life, memory expresses itself through priming and triggering events that cause the organism or the system to respond in a way that improves overall fitness.

Now consider the Earth’s ocean, our blue planet’s dominant feature over deep time and space from its formation about 4.3 billion years ago to its greatest current depth of nearly 11,000 meters in the Challenger Deep in the Pacific. Every aspect of this vast oceanic system can be viewed as holding memory, from short-term to long-term, individualized to collective. For example, the cold, salty surface waters in polar regions that sink to form the rest of the deep sea (cold, dense water sinks) carry the memory of their initial interactions with the polar atmosphere — in the form of a unique temperature/salinity signature — for a thousand years, in the process keeping the ocean circulating globally for the benefit of all life on the planet.

The chemistry of the ocean also carries memory of the atmosphere — of the carbon dioxide (and other gases) its waters have exchanged with the air, which can be stored at depth in the solid form of calcium carbonate for tens to hundreds of years, ready to be redissolved with the right priming or triggering event (anthropogenic inputs), in the process helping to regulate whether the ocean remains at a neutral pH or becomes acidic (which can harm many forms of life).

The geological formations at and below the seafloor today, particularly where volcanic processes are at work (think, hydrothermal vents), hold the longest-term memories of the hot water–rock reactions that may have spawned the first stirrings of life on the planet and continue to provide carbon and energy resources to life in the ocean.

And, of course, today’s ocean is filled with life — more life than land can support. And this life encodes memories of its ancestors and of earlier oceanic conditions in its genetic information, the DNA and the RNA that directs the production of protein and the other building blocks of life.

Inherent to all of this life is the entity we call a “virus.” We are not the only ones to experience viral infection and pandemics; infective viruses exist for every living organism, from the smallest of bacteria to the largest of marine mammals in the ocean. Some infections are lethal to the host, others neutral or even beneficial; humans have an ancient retrovirus to thank for the evolution of the mammalian placenta, for example (the placental wall is constructed of a retrovirus protein).

Lethal viruses can cause whole populations to crash (think, starfish along the US West Coast, or phytoplankton blooms in the ocean), but, importantly, they can recover due to genetic memories held by an individual organism or the collective ecosystem. To fully understand the origins of the coronavirus that has spread in human societies across the globe and transformed the nature of human health, society and connectivity, we look to a source few have discussed: the ocean and the memories it holds.

We find that exploring ocean memories, from the scientifically demonstrable to the richly metaphorical, yields insights about this pandemic and the challenges of the Anthropocene, and suggest that such exploring within a fluid medium that knows no boundaries like those we construct may also help us to discover a sense of well-being, intimacy and connection that could lead to healthier and more equitable human societies.

RNA VIRUSES

Unlike many viruses that encode their genetic information as DNA, the SARS-CoV-2 virus of today’s pandemic is an RNA virus, relying upon only RNA-encoded genes to take over the host cells it infects and direct its own reproduction. A growing body of gene-based evidence from the new discipline of paleoviromics points to an ancient common ancestor for all RNA viruses, one that originated and diverged genetically in the ocean before jumping to land during the early evolution of terrestrial animals and plants. This evidence implies that RNA viruses took root on the planet shortly after the ocean first formed, in settings that enabled what is called “the primordial RNA world.”

This relatively chaotic world is hypothesized to have preceded the DNA world and the first cellular organisms, such that RNA viruses have been termed “relics” of the primordial RNA world. The ocean, with its contemporary seafloor settings that themselves are relics of the early ocean, thus holds the memory of the earliest lineage of RNA viruses, one that eventually led to the coronaviruses that plague humans today.

When did the earliest coronavirus arise, and who were its hosts? The answer to the first part of the question is not well constrained, as estimates range from 10 thousand to 300 million years ago. But this span encompasses a time when the earliest mammals coexisted with dinosaurs (end of the Triassic Period, around 200 million years ago) and when large and diverse mammal species emerged following the demise of the dinosaurs (during the Cenozoic, 60 million years ago). Bats, recognized as the present-day source of most coronaviruses, have been observed in fossil records that date to 50–60 million years ago.

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The answer to the second part of the question begs analysis of genomic material. Comparative gene-sequencing of the virally essential enzyme RNA polymerase, which enables the RNA virus to reproduce within host cells, has revealed how these viruses have coevolved with their hosts and transformed over millennia, much as DNA sequencing has revealed the same about their hosts.

RNA viruses in today’s vertebrates are no different in reflecting the evolutionary history of their hosts. The picornavirus supergroup of RNA viruses, which encompasses the coronavirus, is remarkable for the wide range of hosts its viruses can infect, from single-celled protists (phytoplankton of the surface ocean) to invertebrates, vertebrates and plants. From this perspective, “host jumping” by RNA viruses is not unexpected.

VALUABLE VIRAL MISTAKES

The essential functions of storage, pruning and priming of memories that occur in all systems — the ocean, viruses and humanity alike — sustain some memories while erasing others, better preparing for the future. For viruses, the sustaining and erasing of memories occurs genetically through an enzymatic process (actions of the RNA polymerase) that is prone to mistakes — mutations — during replication. These mistakes lead to gene mismatches that help the virus avoid host defense mechanisms (that recognize infecting sequences and disable them) and thus enable evolutionary advantage, including access to new hosts.

In the ocean, the best-known host systems for RNA viruses are the single-celled algae, particularly diatoms, but other phytoplankton and protists serve similarly. As an RNA virus reproduces within the host, it mutates 0.01–0.1 percent of the time, a rate about a thousand times higher than that of a DNA virus. Each infected cell, therefore, produces a mutant cloud of 1,000–5,000 “quasispecies” of viruses, which means that an infected phytoplankton bloom in the ocean will be filled with billions of these mutant viral quasispecies. Molecular methods have confirmed the presence of such high numbers of quasispecies in viral populations, including in the ocean, and particularly for RNA viruses with smaller genomes (which include coronaviruses).

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The existence of these mutant clouds not only increases the genetic flexibility of viruses and thus their ability to overcome host resistance, but also enables viruses to jump to other hosts. At the same time, better-prepared hosts — those with genetic memories of how to defend against viruses — survive the population-level infection; in the ocean, for example, the seasonal cycle of spring phytoplankton blooms continues.

One can examine the sequenced genome of any living organism and recognize the presence of virally introduced genes, a measure of past relationships with viruses. But in many cases, the viral relationship to the host is simply unknown. Some 44 percent of human genes are transposable elements — “jumping genes” that can change position in a genome. A remarkable one-fifth of those genes, or 8 percent of the human genome, are derived from retroviruses. By far, most of these grafted-on pieces of us are of unknown function for us.

Life is not definable simply by singular units like genomes or cells, but rather by a dynamic network of relationships and communications among individuals, populations and their viruses, a network that ultimately connects the entirety of our planet.

Living in the midst of this pandemic caused by SARS-CoV-2 has prompted a global rethinking of many things, including human super connectivity, the enhanced vulnerabilities that brings, and what activities can be considered essential to our well-being. As we navigate this pandemic, long-standing, siloed social movements, such as the Movement for Black Lives, have burst into a larger global consciousness showing common themes even amid diverse circumstances. Interactive relationships between the spread of a virus and movements for social justice may be complex, but they are not trivial.

The oceanic origins of the early RNA virus thus offer us both a deeper scientific understanding of the behaviour of SARS-CoV-2, and an open space for creative inquiry: How might the current rapid social uprising and transformation mimic that early, messy, primordial RNA world, where information exchange was rampant and where big changes stemmed from unexpected sources?

OCEAN DISTANCING

The microorganisms that fill the ocean, from the smallest (less than one micrometre) marine bacteria to the larger diatoms (up to 200 micrometres) and other phytoplankton that generate blooms over extensive areas of the ocean (visible by satellite), are well-known for intensive relationships with their own viruses; microbes are easier to study than vertebrates. Not only do they suffer viral “pandemics” that crash a population when it gets too dense (at the end of a bloom, for example), but they have also acquired numerous helpful genes, known as auxiliary metabolic genes, from their viral relationships—genes that are retained by the host for improved fitness.

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Such gene-information exchange represents just one element of the highly evolved communication systems used by marine bacteria, in particular, to “network”—to exchange information and regulate their own activities, accomplishing much of the biogeochemical cycling (and pollution mediation) that has occurred throughout the entirety of the ocean’s history.

This microbial life in the ocean has limits on its super connectivity or runaway networking. Marine bacteria live and die in a balance dictated by available nutritional resources and potential predators, especially viral infectors, all dependent on diffusion through the fluid medium of seawater. This balance is sustained in part through cooperative chemical signalling among bacterial neighbours, a form of social communication called “quorum sensing” by microbiologists.

When the density of bacteria gets high enough for their chemical signals to reach each other’s diffusional spheres of influence (about 10 micrometres from the cell surface, or 10 times its diameter), then quorum sensing takes effect. With quorum reached and sensed, communities of networking bacteria pause their growth and shift gears to other life strategies, including attaching to a surface or becoming sessile, reminiscent of human “shelter in place” strategies of recent months.

The ocean can thus be seen as the original social medium and marine bacteria as having highly evolved social practices of community-alert messaging that leads to physical distancing. This ocean style of physical distancing enables communities to be “smart” about both resource use and viral safety, for viral infection requires contact, and contact rate is reduced as organism density drops.

Mobile hosts like us, and the bat hosts before us, are the metaphorical seas and oceans in which viruses like SARS-CoV-2 persist. In order to make contact with the next host they must hitch a ride in the tiny droplets of sea — aerosols — that people exhale or cough up. In doing so, these viruses become embodied within an individual’s own fluid networks, connected to their own cells, but extendable to other human spaces through relationships, chance encounters and other communications.

All organisms employ a suite of tools to communicate at a molecular level, with chemistry (as in quorum-sensing) serving to accomplish this metabolic “diplomacy” across habitat boundaries. Usually, an endless stream of communications provides a general sense of equilibrium, but imbalances or irregularities in the network can emerge, demanding “correction.”

Sometimes the correction yields chaotic behaviour, as in the jump by the coronavirus from bats to humans — evolutionary relationships have shown that such jumps are enabled by mistakes that enabled infection of a new host.

The chaos represents the making of a new memory, which will script itself into possibly both the viral and the human genome, towards a new equilibrium. As humans are tumbling towards a new social equilibrium — with laws and public opinion mutating rapidly — the virus continues to race through and change within human bodies.

OUR OCEANS, THIS VIRUS, THIS MOMENT

The human toll of this pandemic is devastating. This virus has exposed and amplified existing societal inequities, as well as the effects of human encroachment on the Earth’s biosphere. But no single act of negligence created this pandemic; collective human behaviour did.

SAR-CoV-2 is just a virus behaving like a virus, exposing and amplifying existing aspects of the distributed life of this moment: a high population density of humans that is hyperconnected and capable of propagating viral spread stealthily, with impacts that may not be recognizable for weeks.

Despite the omnipresent war rhetoric surrounding the pandemic, SAR-CoV-2 is not a warrior; it is a virus in search of a means to continue evolving. This particular coronavirus has simply taken advantage of anthropogenic bridges connecting previously stable, isolated habitats, in the process disrupting the existing equilibrium with consequences dreadful for humankind.

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At the same time, the initial quieting of human activity cleaned the air and caused a noted emergence of wildlife. For some, it also reactivated an individual capacity that the superconnected world otherwise shuns: listening to the rich tapestry of birdsong, the systemically silenced voices, the ecological potential of an individual action.

As the novel coronavirus becomes more familiar to the human body, it offers a memory of the deep connection that human evolution — all life — has to early ocean history. Might a shared focus on the surfacing of entrenched memories of human evolution, systemic racism and the trauma in individual lives lost galvanize humanity towards collective change that is mindful of our history and ecology?

Is there a way for us to search — individually and collectively — for ways to shift the paradigm from “ego to eco”? From separated humans, fearful of each other and of nature, to an ecologically entangled sense of self? And what will be encountered on such a search? Pruned memories, lost archives, oceanic embedded histories that have largely escaped awareness? Like ocean memory itself, metaphor and scientific precision need not be in contradiction. Invoking ocean memory as a guide towards thoughtful interconnectivity might make all the difference to how we interpret past events to anticipate the future, shape new memories to serve that future, and survive our own Anthropocene.