Virus discoveries other than the new crown are rewriting the long article in Biology "Nature"

Original author: Amber Dance The new coronavirus (SARS-CoV-2) is just a drop in the ocean among the endless viruses on earth
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Scientists are quickly identifying a large number of new virus species
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In African termite mounds, Antarctic seals, and the body of the Red Sea, Mya Breitbart has discovered a variety of new viruses
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But to make a big discovery, just step into the backyard of her home in Florida
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Strolling in her swimming pool is the Gasteracantha cancriformis-a fantastic spider with a spherical white body, black spots, and six scarlet spikes that looks like a medieval weapon
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As a virus ecologist at the University of South Florida, Breitbart is even more surprised by the inner nature of this spider
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After collecting and grinding some spider samples, she and her colleagues discovered two viruses previously unknown to the scientific community [1]
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Although we humans have paid special attention to a particularly annoying virus since the beginning of 2020, there are still many other viruses to be discovered
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Scientists predict that there are about 1031 virus particles living in the ocean alone at any time-ten billion times the estimated number of stars in the known universe
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We gradually understand that ecosystems and organisms depend on viruses
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Viruses are as light as a feather, but they are more important than Mount Tai.
They jump between hosts and change host genes, thus driving millions of years of evolution.

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In the ocean, the virus cuts through the microorganisms and dumps the contents into the ocean, making the food web rich in nutrients
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Curtis Suttle, a virologist at the University of British Columbia, said: "If there were no viruses, humans would not exist
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" Viruses of different shapes and sizes, such as giant pseudobacterial viruses (upper right) and lunar-shaped phages (center) are shown
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Source: False color electron micrograph (inconsistent scale)
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The first row from left to right: variola virus, acid bacteria bottle-shaped virus, and pseudobacterial virus
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Middle row from left to right: rabies virus, T4 bacteriophage, rotavirus
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Bottom row from left to right: Ebola virus, tobacco rattle virus, HIV-2 virus
.

SPL; M.
Häring et al.
/J.
Virol.
; E.
Ghigo et al.
/PLOS Pathog.
; Frederick A.
Murphy/CDC Global International Committee on Classification of Viruses (ICTV) only lists 9110 named viruses.
Obviously just the tip of the iceberg
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Part of the reason is that the formal classification of a virus in the past required the ability to cultivate the virus in the host or in the host cell
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Even if this can be done, it is quite time consuming
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On the other hand, previous studies have tended to focus on viruses that cause disease to humans or other organisms of concern to humans, such as livestock or crops
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However, the new crown epidemic has sounded the alarm for us, and we need to understand more about viruses that can transform their hosts and threaten livestock, crops, and humans themselves
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In the past 10 years, the number of known and named viruses has skyrocketed, thanks to advances in virus discovery technology, coupled with recent changes in the rules for determining new virus species, and viruses can be named without cultivating viruses and hosts
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Metagenomics technology is one of the most far-reaching technologies.
Researchers can use this technology to extract environmental genome samples without cultivating individual viruses
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Newer technologies (such as single-virus sequencing technology) have further supplemented the list of viruses, including some very common viruses that have only received attention until now
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Doing this kind of research is catching up with an exciting era
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Breitbart said: "I think, in every sense, now is the era of viromics
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" In 2020 alone, ICTV added 1044 viruses to its official list, and there are thousands more waiting to be described and Naming
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The surge in genomes has not only prompted virologists to rethink the way viruses are classified, but also helped clarify the evolution of viruses
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There is strong evidence that the virus has appeared multiple times, rather than a single origin
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Even so, Jens Kuhn said, the true scope of the virus world is mostly unknown
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He is a virologist at the National Institute of Allergy and Infectious Diseases.
He said: "We really don't know what's there
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" Ubiquitous viruses have two common characteristics: the genome of each virus is wrapped in In the protein capsid, each virus relies on the host (which may be a human, spider or plant) to complete self-replication
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But beyond that, the virus is very different
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The tiny circovirus has only two or three genes, and the huge pseudovirus "size" can surpass some bacteria, carrying hundreds of genes
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In terms of shape, there are bacteriophage viruses that infect bacteria like a moon landing gear, and there are also coronaviruses that are hated in the world today, like a killer thorn ball
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Some viral genes to DNA storage, some of an RNA; kind even phages, using another set of genetic alphabet in the standard system A base ACGT replaced named Z molecules
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Research on Papilloma spinosa discovered two viruses previously unknown in the academic world
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Source: Scott Leslie/Minden Pictures/Alamy viruses are everywhere, even if scientists don’t find them
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When Frederik Schulz read the genome sequence in the wastewater, he did not intend to study the virus
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In 2015, he was a graduate student at the University of Vienna, using metagenomics technology to find bacteria
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This technology separates DNA from mixed organisms, divides them into fragments and then sequence them all, and then assembles the fragments into individual genomes through computer software, similar to putting together hundreds of shuffled tiles
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Schulz could not help but notice that there is a large piece of viral genome in the bacterial genome (obviously because of the viral capsid gene), with up to 1.
57 million base pairs [2]
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Later it was discovered that this was a giant virus, belonging to a type of virus with a very large genome and absolute size (usually more than 200 nanometers in diameter)
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This type of virus infects amoeba, seaweed and other protists, so it is in a position that can affect land and water ecosystems.
Schulz is now a microbiologist at the Joint Genome Institute of the United States Department of Energy.
He decided to list the metagenomic database.
To find related viruses
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An article published by Schulz and colleagues in 2020 [3] described more than 2,000 genomes in a group containing giant viruses; before that, there were only 205 such genomes in public databases
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Virologists are also looking for new virus species in the human body
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Viral bioinformatics scientist Luis Camarillo-Guerrero and colleagues from the Wellcome Sanger Institute worked together to analyze the metagenomics of the human intestinal tract and built a database containing more than 140,000 phages, more than half of which were newly discovered
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Their study [4] was published in February and found that the most common phage that infects our intestinal bacteria is a type of virus called crAssphage (named after the cross-assembly software that discovered it in 2014).
This finding is in line with the results of others Match
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Camarillo-Guerrero said that in addition to their abundance, little is known about the effects of these viruses on the human microbiome
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He currently works for Illumina, a DNA sequencing company
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Although a variety of viruses have been detected in the metagenomics, many have been overlooked
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The general metagenomics does not detect RNA viruses, so Colin Hill, a microbiologist at the University of Cork in Ireland, and his colleagues searched for RNA viruses in an RNA database called the metatranscriptome
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These data are usually used to understand genes in a population that are actively transcribed into messenger RNA to make proteins, but RNA virus genomes will also emerge from them
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Colin Hill's team used computational techniques to extract virus sequences from the data, and found 1,015 viral genomes in the metatranscriptome of silt and water samples [5]
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Once again, researchers have greatly increased the number of known viruses in a single study
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The picture shows the giant virus Tupanvirus (tupanvirus), found in the amoeba, more than 1,000 nanometers long, and its coding gene is the largest among known viruses
.

Source: J.
Abrahão et al.
/Nature Commun.
Although these technologies occasionally integrate unreal virus genomes, researchers will use quality control techniques to prevent this
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In addition, there are other blind spots
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For example, if the genome of a single virus changes greatly, it is difficult for people to find this virus because it is difficult for computer software to piece together sequences that are far apart
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Another method is to test the genome of only one virus at a time, as the microbiologist Manuel Martinez-Garcia of the University of Alicante did
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He decided to try to isolate a single virus by slowly dripping seawater through a sorter, amplify its DNA and then sequence it
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For the first time, he found 44 genomes, and later found that one of them corresponds to the most abundant virus in the ocean [6]
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This virus is very diverse—its genetic puzzles are vastly different from each other—so its genome has never been detected in metagenomic studies
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The research team named it 37-F6, which is derived from the number of its original laboratory petri dish, but Martinez-Garcia joked that since this virus can hide so well, it is hidden in front of our eyes, it should follow the fictional super Spy James Bond, named 007
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The virus evolution tree marine virus Bond lacks an official Latin species name.
In fact, most of the thousands of viral genomes discovered in the metagenomics in the past ten years have no official species name
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The discovery of these sequences poses a dilemma for ICTV: Is a genome alone enough to name a virus? By 2016, scientists still need to cultivate viruses and their hosts before they can submit a new virus species and taxonomy to ICTV, with few exceptions
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In that year, virologists finally reached a consensus after verbal battles: the genome is enough [7]
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So applications for new viruses and new populations flocked (see "Virus Family Growth")
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But the evolutionary relationship between each other is often unclear
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Virologists mainly classify viruses based on their shape (for example, long and thin, or with one end and one tail), and genome (DNA or RNA, single-stranded or double-stranded), but this cannot reveal much information about the common ancestor
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For example, a double-stranded DNA virus may have at least 4 independent origins
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Source: ICTV's initial classification of ICTV viruses is completely different from the cell biology lineage diagram, and only involves the lower levels of the evolutionary hierarchy, from species, genus to order-similar to the classification of primates or conifers in the classification of multicellular organisms
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There was no higher level before
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Moreover, many virus families exist independently and are not related to other viruses
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Therefore, ICTV added a higher level in 2018: class, door, boundary [8]
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The top level is "realms", which corresponds to the "domains" of cell organisms-bacterial domains, archaea domains and eukaryotic domains-(in English) different words are used to distinguish the two Evolution tree
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(A few years ago, some scientists suggested that certain viruses can melt into the evolutionary tree of cell biology, but this idea has not been widely accepted
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) ICTV outlines the branches of the virus evolution tree and classifies RNA viruses as Riboviria (Riboviria)
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SARS-CoV-2 and other coronaviruses are single-stranded RNA genomes, so they belong to this domain
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But the latter phylogenetic classification depends on virologists
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Coincidentally, Eugene Koonin, an evolutionary biologist at the National Center for Biotechnology Information in the United States, has assembled a research team to analyze the genomes of all viruses, combined with the latest research on viral proteins, and established the first version of the virus classification system [9]
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They re-divided the ribovirus domain and proposed adding three other domains (see "Virus Domain")
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Koonin said that although the details are somewhat controversial, this classification will come into effect in 2020, and ICTV members have no objection
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Two more domains were approved in 2021, but he said that the original four domains should still be the largest
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Koonin speculated that the final number of virus domains may reach as many as 25
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Source: ICTV (talk.
ictvonline.
org/taxonomy); ICTV Coronavirus Research Group.
Nature Microbiol.
5, 536–544 (2020) This number is consistent with the speculation of many scientists that viruses do not have a single common ancestor
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Koonin said: "Viruses do not have a single root cause
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" That is to say, viruses may have originated many times on the earth-and this origin is likely to appear again
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Mart Krupovic said: "The re-originating of the new virus is still ongoing
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"He is a virologist at the Pasteur Institute in Paris.
He was involved in the ICTV new classification decision and is also a member of the Koonin classification research team
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Virologists are at odds on the origin of the domain
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One theory is that they were in the early cells of the earth.
Before forming, each is derived from independent genetic fragments
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Another is that they are separated or "transferred" from intact cells, discarding most of the organelles, and achieving minimal existence
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Koonin and Krupovic support two Hypothetical combination: The original genetic fragments steal the genes of some cell organisms to assemble their own virus particles
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Because viruses may have multiple origins, they may originate in many ways, Kuhn said
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He was also on the ICTV committee.
Members and participated in the proposal of the new classification
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Therefore, although the virus and the cell evolution tree are completely different, the branches of the two are intertwined and genes are passed on to each other
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Whether a virus is a "living body" depends on the individual's definition of a living thing
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Many people think that viruses are not living organisms, but others think they are
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Information biologist Hiroyuki Ogata said: "I tend to think of them as living organisms
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"He works at Kyoto University in Japan and is dedicated to virus research
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"Viruses are constantly evolving, and their genetic material contains DNA and RNA.
They are also of great significance to the evolution of all living things
.
"
"Most people think that the current classification system is only the first attempt
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Some virologists find this division to be a little messy
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And there are many subjects that are not included in the six domains
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"The good thing is that we are trying to sort out this mess," Martinez-Garcia said
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The virus has changed the world.
The total weight of the virus on the earth is equivalent to 75 million blue whales.
Scientists are sure that the virus has changed the food web, ecosystem and even the atmosphere of the earth
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The process of accelerating the discovery of new viruses "has become a watershed, revealing new ways for viruses to directly affect ecosystems
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" said Matthew Sullivan, an environmental virologist at Ohio State University
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However, it is still difficult for scientists to quantify the impact of the virus
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Ogata said: "We can't put it in a nutshell right now
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" In the ocean, viruses disassemble their microbial hosts and release carbon.
Other organisms or viruses recycle the host's substances and produce carbon dioxide
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Recently, however, scientists have also discovered that exploded cells often gather together and then sink to the bottom of the sea, thereby sequestering carbon away from the atmosphere
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The picture shows the thawing frozen soil of the Stodarlin swamp in Sweden
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The genes contained in the viral genome collected from it may participate in the decomposition and release of carbon
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Source: Bob Gibbons/AlamySullivan said that melting frozen soil is one of the main sources of carbon on land, and viruses seem to play a major role in the carbon emissions of microorganisms in this environment
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In 2018, he and his colleagues described 1907 viral genomes and fragments from Sweden’s thawing permafrost.
Some of these genes encode proteins that may affect the decomposition of carbon complexes and the potential conversion to greenhouse gases [10]
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Viruses can also change other organisms by affecting the genome
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For example, after a virus transfers a drug-resistant gene from one bacteria to another, the latter becomes a drug-resistant strain
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Over time, this transformation becomes an important evolutionary change in the population, Camarillo-Guerrero said
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This effect is not limited to bacteria-about 8% of human DNA originates from viruses
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For example, our mammalian ancestors obtained a gene necessary for placental development from the virus
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To answer many questions about the virus, in addition to its genome, more information is needed
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They need to find the host of the virus
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The virus itself may have some clues: For example, the virus may carry a small amount of host genetic material in its genome
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Martinez-Garcia and colleagues used single-cell genomes to identify microorganisms containing the newly discovered 37-F6 virus
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Its host is also one of the most abundant and diverse life forms in the ocean, and is a bacterium belonging to the genus Pelagibacter [11]
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In some water bodies, these bacteria can account for half of the existing cells
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Martinez-Garcia said that even if only this virus disappears suddenly, the marine biological system will be completely out of balance
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Alexandra Worden said that to understand all the effects of the virus, scientists need to understand how the virus affects the host
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She is an evolutionary ecologist and works at the Marine Research Center in Kilhelmholtz, Germany
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She is studying a giant virus that carries a gene that codes for rhodopsin, a light-harvesting protein
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In theory, these genes can be used by the host—for energy conversion, signal transmission, etc.
—but the sequence alone cannot confirm this
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In order to explore the follow-up process of rhodopsin gene, Worden plans to cultivate the host and virus together, and study how the two work together in a "virocell" state
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She said: "Only cell biology can confirm its true role and how it will affect the carbon cycle
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" Back to Florida
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Although Breitbart has not yet cultivated spider viruses, its understanding of them is deepening
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The tiny circular genomes of these two viruses surprised Breitbart.
They only encode two proteins, one is the protein coat and the other is the replication protein
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One of the viruses was only found in the spider’s torso, and was never detected in the spider’s feet.
Therefore, she believes that this virus may actually infect certain organisms eaten by the spider
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The other is found in the torso, feet, and larvae of spiders, so she believes that this virus can be passed on from parents to offspring[12]
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As far as Breitbart knows, this virus does not seem to cause any harm to the spiders
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Speaking of viruses, "discovering them is actually the easy part," she said
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It is much harder to analyze how viruses affect the life history and ecology of their hosts
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Virol.
100, 1253–1265 (2019).
The original article was titled Beyond coronavirus: the virus discoveries transforming biology and was published in the news feature section of Nature on June 30, 2021 © naturedoi: 10.
1038/d41586-021-01749 -7 Click to read the original text to view the original text in English.
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