Virus World

In a U.S. government lab in Bethesda, Maryland, virologists plan to equip the strain of the monkeypox virus that spread globally this year, causing mostly rash and flulike symptoms, with genes from a second monkeypox strain that causes more serious illness. Then they’ll see whether any of the changes make the virus more lethal to mice. The researchers hope that unraveling how specific genes make monkeypox more deadly will lead to better drugs and vaccines. Some scientists are alarmed by the planned experiments, which were first reported by Science. If a more potent version of the outbreak strain accidentally escaped the high-containment, high-security lab at the National Institute of Allergy and Infectious Diseases (NIAID), it could spark an “epidemic with substantially more lethality,” fears epidemiologist Thomas Inglesby, director of the Center for Health Security at the Johns Hopkins University Bloomberg School of Public Health. That’s why he and others argue the experiments should undergo a special review required for especially risky U.S.-funded studies that might create a pathogen that could launch a catastrophic pandemic.

But it’s not clear that the rules apply to the proposed study. In a 2018, a safety panel determined it was exempt from review. Monkeypox did not meet the definition of a “potential pandemic pathogen” (PPP), the panel decided, because it didn’t spread easily. Now, with monkeypox widespread, the National Institutes of Health (NIH) is planning to reexamine the work, but it still might not qualify as “enhancing” a PPP, the agency says. That’s because the study will swap natural mutations, not create new ones, so it is not expected to create a monkeypox strain more virulent than the two already known. The monkeypox controversy marks just the latest flare-up in a decade-old debate over exactly when a study that alters a pathogen is too risky for the U.S. government to fund—and who should have the power to decide. That wrangling became especially ferocious over the past 2 years, as the COVID-19 pandemic spawned allegations, so far unproven, that SARS-CoV-2 escaped from a laboratory in China. Now, in the pandemic’s wake, the U.S. government appears poised to make sizable changes to how it manages so-called gain-of-function (GOF) studies that tweak pathogens in ways that could make them spread faster or more dangerous to people.

Last month, an expert panel convened by NIH and its parent agency, the Department of Health and Human Services (HHS), released a draft report that recommends the GOF rules be broadened to include pathogens and experiments that are exempt from the current scheme. If the recommendation is adopted—which could come next year—the monkeypox study could come under tighter scrutiny. And other researchers working with viruses such as Ebola, seasonal flu strains, measles, and even common cold viruses could face new oversight and restrictions.

Some scientists are watching nervously, worried that an expanded definition could worsen what they already see as a murky, problematic oversight system. The existing rules, they say, have caused confusion and delays that have deterred scientists from pursuing studies critical to understanding emerging pathogens and finding ways to fight them. If not implemented carefully, the proposed changes could “greatly impede research into evolving or emerging viruses,” worries virologist Linda Saif of Ohio State University, Wooster. She and others say expanding the regulations could add costly red tape, potentially driving research overseas or into the private sector, where U.S. regulations don’t apply or are looser......

The MIT Press Journal Rapid Reviews: COVID-19 (RRC:19) has openly published the first official scholarly peer reviews of pre-print research from Li-Meng Yan, Shu Kang, Jie Guan, and Shanchang Hu that claims to show that unusual features of the SARS-CoV-2 genome suggest sophisticated laboratory modification rather than natural evolution. Reviewers Robert Gallo, Takahiko Koyama, and Adam Lauring rate the study as misleading and write that the "manuscript does not demonstrate sufficient scientific evidence to support its claims." Find peer reviews and information about this study at Rapid Reviews website.

While this research has been widely debunked in popular media, scholarly peer review represents a different type of rebuke from the scientific community. The original study was posted on a public pre-print server without the benefit of peer review--a necessary part of the scientific publishing process in which scientists review one another's work, vetting research for accuracy and evaluating methods and evidence. Pre-prints enable researchers to share information quicker, but they have created a need for rapid and transparent peer review to correct misinformation about COVID-19 and to minimize the influence of unverified research. "While pre-print servers offer a mechanism to disseminate world-changing scientific research at unprecedented speed, they are also a forum through which misleading information can instantaneously undermine the international scientific community's credibility, destabilize diplomatic relationships, and compromise global safety," explains the RR:C19 Editorial Office.

RR:C19 was launched in June 2020 to provide rapid and transparent peer review of COVID-19 pre-prints. When the 'Yan Report' was published in September, RR:C19 quickly sought out peer reviews from world-renowned experts in virology, molecular biology, structural biology, computational biology, vaccine development, and medicine. These reviews are now openly published, along with a response from the RR:C19 Editorial Office, that states, "Collectively, reviewers have debunked the authors' claims that: (1) bat coronaviruses ZC45 or ZXC21 were used as a background strain to engineer SARS-CoV-2, (2) the presence of restriction sites flanking the RBD suggest prior screening for a virus targeting the human ACE2 receptor, and (3) the furin-like cleavage site is unnatural and provides evidence of engineering. In all three cases, the reviewers provide counter-arguments based on peer-reviewed literature and long-established foundational knowledge that directly refute the claims put forth by Yan et al. There was a general consensus that the study's claims were better explained by potential political motivations rather than scientific integrity."

Reviewer Dr. Robert Gallo, biomedical researcher and co-founder of The Institute of Human Virology Evidence Scale Rating: Misleading "Widely questionable, spurious, and fraudulent claims are made throughout the paper about the thought-to-be precursor of SARS-2, RaTG13, found in bat caves. The author's attacks include quotes which have not been referenced, including how this 'has been disputed and its truthfulness widely questioned. Soon a paper proving that will be submitted.' She then goes on to attack several genome sequences as fraudulent, ranging from pangolin coronaviruses to bat coronaviruses, again without evidence. The reference she cites for that, in fact, does not make that claim." 

Reviewer Dr. Takahiko Koyama, IBM Research, Computational Biology Center Evidence Scale Rating: Misleading "[The] authors' speculation of furin cleavage insert PRRA in spike protein seemed quite interesting at first. Nevertheless, recently reported RmYN02 (EPI_ISL_412977), from a bat sample in Yunnan Province in 2019, has PAA insert at the same site[2]. While the authors state that RmYN02 is likely fraudulent, there are no concrete evidences to support the claim in the manuscript. In addition, argument of codon usage of arginine in PRRA is not convincing since these are likely derived from some kind of mobile elements in hosts or other pathogens. Further investigations are necessary to unravel the mystery of the PRRA insert. For these reasons, we conclude that the manuscript does not demonstrate sufficient scientific evidences to support genetic manipulation origin of SARS-CoV-2."

Reviewer Dr. Adam Lauring, University of Michigan, Internal Medicine Evidence Scale Rating: Misleading "A key aspect of research ethics and the responsible conduct of research is to include information on who supported the work - financially or otherwise. The authors' affiliation is the "Rule of Law Society & Rule of Law Foundation." It is not clear who supports this Foundation or what its purpose is. It is important for there to be transparency regarding research support, especially for a manuscript that is based on conjecture as opposed to data or empiricism. It is also unethical to promote what are essentially conspiracy theories that are not founded in fact."

Rapid Peer Review (October 2, 2020):

https://rapidreviewscovid19.mitpress.mit.edu/pub/r94z275c/release/2

The achievement promises to unlock the potential for making new classes of chemicals — for medicine, food production, and manufacturing. Two years ago, scientists in Britain swapped out the DNA of the bacteria Escerichia coli for a genetic coding program that was entirely human-made. At the time, it was the largest and most complex synthetic genome ever created. On Thursday, that same group of researchers at the Medical Research Council Laboratory of Molecular Biology reported in Science that with continued tinkering, they’ve made their artificial life form virtually invincible to viral infection. Other adjustments to the bacteria’s designer genome endowed the bug with the ability to string together non-natural amino acids to produce proteins never before seen inside a living cell. In an accompanying editorial, scientists not involved in the work said the achievement promises to unlock the potential for making all sorts of new classes of chemicals — for medicine, food production, and industrial manufacturing.  “It’s brilliant work,” Tom Ellis, director of the Center for Synthetic Biology at Imperial College London, who was not involved in the new study, told STAT via email. “It shows two really exciting applications that can be achieved by having cells with synthetic genomes that have been genetically recoded.” 

DNA, fundamentally, is an information storage system; your DNA stores all the information required to build the molecules and cells and tissues that make you, you. But to actually build those things, you also need a storage-retrieval and decoding system. And on Earth, all of life — from pond scum to peregrine falcons — evolved to use a single system. Every organism decodes DNA using the same 64 codons (three-letter combinations of the DNA bases known as A’s, T’s, C’s, and G’s)  to specify which of the 20 amino acids are going into the proteins it makes. Which means there are redundancies.  So, TCA, for example, tells the cell to grab an amino acid called serine and stick it next in the chain of whatever protein it’s building. But so does TCT. And AGT. In fact, there are six codons that all specify serine.  For years, Jason Chin, a molecular biologist at the MRC lab who led the new study, worked to whittle down some of those redundant codons and assign them new functions. Previously he and his team had systematically eliminated three codons across their E. coli’s genome, creating a bacteria, dubbed Syn61, that lived and squirmed and formed colonies despite using 61 codons rather than nature’s 64. But Syn61 still possessed the genetic program for creating all the molecules that actually read the codons and shuttle the correct amino acid to the site of protein production. These critical decoding molecules are called transfer ribonucleic acids, or tRNAs. In their latest work, Chin and his colleagues went through and deleted the tRNAs that recognize the codons they had already removed. The exercise wasn’t just about further streamlining their synthetic genome. Viruses don’t have any of their own decoding or protein production machinery. They rely on a host cell to do that. And in theory, if a virus invaded a bacteria that didn’t have the ability to read all of the codons in the viral genome, it would stymie the would-be hijacker’s plans for self-replication.  “The hypothesis was that the cells should be completely resistant to viruses,” said Chin. And indeed, that’s exactly what his team found. When mixed together with a cocktail of five different bacteriophages — viruses that prey on bacteria — their genetically reformulated E. coli rebuffed the viral onslaught. Eliminating the tRNAs was crucial. Colonies of their original synthetic strain, Syn61, were blasted apart by the phage invaders.

A team of researchers from the Broad Institute, Harvard and Boston's Children's Hospital has developed a new way to improve the editing efficiency of base editors using a system called "phage assisted continuous evolution of base editors," or BE-PACE. 

The development of the CRISPR gene editing system has led to the possibility of editing genes to prevent inherited diseases. But problems with the system have persisted—most notably, instances of the wrong genes being edited. Because of this, scientists are seeking ways to improve the  accuracy of such systems to make them safe enough for use in human patients. 

the team in Massachusetts has developed a system they call BE-PACE, which can be used to improve cytosine base editors (CBEs). The researchers used their system to evolve a CBE called evoAPOBEC1-BE4max. They report that testing showed it to be 26 times as efficient at editing cytosines (in the GC context) than prior systems, even as it maintained its efficiency in editing all other tested sequences. They further report that that testing of an evolved deaminase called evoFERNY showed it to be 29 percent smaller than APOBEC1.

The findings were published on the July 22 issue of Nature Biotechnology:

https://doi.org/10.1038/s41587-019-0193-0