virology blog

About viruses and viral disease

ecology

Pandemics and anthropogenic environmental change

by

All human viruses have their origin in a virus that crossed from a different animal species. The encounters that lead to these spillovers are driven by explosive human population growth and incredible change occurring in all ecosystems brought about by human occupation of almost every corner of the planet. The extent to which land-use change contributes to zoonotic diseases has always been suspected and was recently established by a global study of the effect of such changes on local zoonotic host communities.

One of my favorite stories about how land use changes drive zoonotic emergence is about Argentine hemorrhagic fever. Between the two world wars, the Argentine pampa was converted to fields for the massive growth of maize by eliminating weeds by the use of herbicides. The maize grew, but in its shadow a new shade-tolerant weed flourished. This weed led to the emergence of a new dominant mouse, Calomys musculinus (pictured; image credit). A novel human hemorrhagic fever was first described in this area in 1953, and the causative agent, Junin virus, was isolated from the new mouse.

To examine the global importance of such land use changes in the exposure of humans to new zoonotic diseases, a global database of 6,801 ecological assemblages was examined. The database compiles >3.2 million species records from 666 published studies in which biodiversity across land use was sampled. Records of 376 host species in 6,801 survey sites were identified across 6 continents.

The analysis revealed that known wildlife hosts of pathogens shared with humans make up a greater proportion of local species richness (18–72% higher) and total abundance (21–144% higher) in sites under extensive human use (secondary, agricultural and urban ecosystems) compared with nearby undisturbed habitats. The magnitude of this effect varies according to the species, but it is the strongest for rodent, bat and passerine bird zoonotic host species. These taxa are important as zoonotic reservoirs. In addition, mammals that harbor more pathogens are more likely to be present in human-managed ecosystems.

These findings indicate that that anthropogenic global land use changes are establishing interfaces between people, livestock and wildlife reservoirs of zoonotic disease that will increase the chances of future outbreaks and pandemics.

Some readers might be asking, how did land use change lead to emergence of SARS-CoV-2? We know that the virus emerged from a bat reservoir in rural China, where farming has intensified in recent decades. Such activities place farmers in contact with wildlife, allowing regular spillover of viruses. Eventually these events will hit the jackpot – a randomly emerged virus that just so happens to be able to efficiently infect humans.

A potential solution to this problem? There are many reasons for anthropogenic land use modification by humans, but a major one is for farming. Move this activity indoors, to Vertical Farms.

TWiEVO 49: A giant podcast on giant viruses

by

Rich joins Nels and Vincent for a debriefing on the 4th Ringberg Symposium on Giant Virus Biology in Tegernsee, Germany.

Click arrow to play
Download TWiEVO 49 (68 MB .mp3, 113 min)
Subscribe (free): iTunes, Google Podcasts, RSS, email

Become a patron of TWiEVO

Show notes at microbe.tv/twievo

TWiV 536: A flock of seagulls, a herd of seals

by

Vincent and Alan travel to Tufts Veterinary School where they meet up with members of the Runstadler lab to talk about their work on influenza virus circulation in water birds and seals.

Click arrow to play
Download TWiV 536 (54 MB .mp3, 96 min)
Subscribe (free): iTunes, Google Podcasts, RSS, email

Become a patron of TWiV!

Show notes at microbe.tv/twiv

The Arctic fresh water virome

by

SpitsbergenAlthough we now understand that viruses are the most abundant organisms on Earth, there are gaps in our knowledge about their distribution in different environments. Results of a new study reveal the diversity and distribution of viruses in Arctic fresh waters.

Fresh waters in high latitudes such as the Arctic and Antarctic have low levels of nutrients (e.g. are oligotrophic) and support the growth mainly of microorganisms. They are good model systems for understanding how viruses affect microbial communities and the entire ecosystem. It is known that diverse viral communities, comprising novel families of single-stranded (ss) DNA viruses, dominate the fresh waters of the Antarctic Lake Limnopolar. However no large scale studies of the Arctic fresh water virome have been done.

Fresh water was collected in three different years from six lakes in Spitsbergen, Norway (red symbol on map). Viral particles were purified from the water samples and their genome sequences were determined. Only about 10% of the viral sequences could be assigned to a previously known virus family. Most (86%) of the recognizable sequences were from ssDNA viruses, and similar viruses were found in all six lakes.

Comparisons with viromes from other freshwater locations revealed similar taxonomic distributions in Antarctic freshwater but not elsewhere. As these locations are at opposite ends of the global poles, the results suggest that some viruses may be dispersed over long distances. The Arctic and Antarctic fresh water viromes do contain different viral species, despite being quite similar environments. On the other hand, the Arctic fresh water virome is very different from the Arctic Ocean virome. The finding of diverse viral communities in Arctic and Antarctic fresh waters indicates that, unlike larger organisms, viral richness might not decrease with distance from the equator.

The authors of this study did not characterize the RNA virome of Arctic fresh water lakes, but they did find sequences of single-stranded RNA viruses in their data sets. Because the authors sequenced DNA only (their protocol did not include a step to convert RNA to DNA before amplification), these RNA viral sequences likely represent DNA-RNA hybrid viruses. These viruses probably were produced by recombination of a DNA virus with DNA produced by reverse transcription of an RNA virus.

When Lake Limnopolar thaws in the spring, its viral community changes from ssDNA viruses to dsDNA viruses, perhaps as the hosts also change. Whether similar changes take place in Spitsbergen should be determined to help illuminate how viruses control high latitude microbial communities.

TWiV 289: Vinny and the capsids

by

On episode #289 of the science show This Week in Virology, Vinny and the capsids answer listener questions about the definition of life, state vaccination laws, the basic science funding problem, viral ecology, inactivation of viruses by pressure, and much more.

You can find TWiV #289 at www.microbe.tv/twiv.

The Vertical Farm

by

I’ve been hearing about the vertical farm concept from Dickson Despommier for years – as a faculty colleague of his here at Columbia University Medical Center, and more recently as co-host of TWiV and TWiP. I could not help but be enthusiastic as the idea grew from a seed, to seeing Dickson jetting around the globe trying to build the first prototype. Now that the eponymous book is out, does it stand up to the hype?

The Vertical Farm begins with a brief history of agriculture: how humans learned how to grow their food, slowly developing the technology to eke more and more from the earth. We learn about how machinery, petroleum, and fertilizer have impacted farming. But more importantly, Dr. Despommier reveals how farming, while growing more efficient, has slowly destroyed earth’s ecology. The burning of forests to provide farm lands and the resulting increase in global carbon dioxide, and the agricultural runoff that has lead to destruction of coral reefs, to name just two. Along the way we learn just how destructive big cities can be – New York City alone discards 1 billion gallons a day of grey water. These were the most compelling parts of the book, where I learned how good and bad growing food has been.

Next, Dr. Despommier turns to his solution to these problems and more – the vertical farm. He is clearly excited about how growing crops in skyscrapers, with aeroponic technology and extensive recycling, will solve many of the world’s environmental problems as they relate to agriculture. No longer will we have to discard so much precious water; land can be allowed to return to hardwood forests, decreasing carbon dioxide levels in the atmosphere; and perhaps the coral reefs can rebound as we stop dumping fertilizers into the oceans.  These all seem reasonable scenarios. But will they work?

No one knows – not even Dr. Despommier, the consummate optimist, because a vertical farm has not yet been built. The last parts of the book, which deal with the specifics of the vertical farm, are singularly unsatisfying, because there are no details. As Dr. Despommier admits, this is because he is not an architect or engineer. We would like to know exactly how these farms of the future will be built, and their yields and energy costs, but that information cannot yet be provided. I understand all the reasons why – but perhaps Dr. Despommier should have engaged some experts to provide more details. As a result the latter half of the book is unsatisfying because you just can’t wrap your mind around exactly what these farms will be like.

In the end, The Vertical Farm is a dream by a particularly good dreamer. Whether or not those dreams will come true – Dr. Despommier certainly believes they will – is anyone’s guess. I’m rooting for Dickson and the solution to earth’s future food needs, but we’ll know the answer only when a vertical farm – or two – have been built.

Please accept my apologies for this brief foray away from virology – vrr