Virus World

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 19 (COVID-19) pandemic. Despite the urgent need, we still do not fully understand the molecular basis of SARS-CoV-2 pathogenesis and its ability to antagonize innate immune responses. Here, we use RNA-sequencing and ribosome profiling along SARS-CoV-2 infection and comprehensively define the mechanisms that are utilized by SARS-CoV-2 to shutoff cellular protein synthesis. We show SARS-CoV-2 infection leads to a global reduction in translation but that viral transcripts are not preferentially translated.

Instead, we reveal that infection leads to accelerated degradation of cytosolic cellular mRNAs which facilitates viral takeover of the mRNA pool in infected cells. Moreover, we show that the translation of transcripts whose expression is induced in response to infection, including innate immune genes, is impaired, implying infection prevents newly transcribed cellular mRNAs from accessing the ribosomes. Overall, our results uncover the multipronged strategy employed by SARS-CoV-2 to commandeer the translation machinery and to suppress host defenses.

Available as preprint in bioRxiv (November 25, 2020):

https://doi.org/10.1101/2020.11.25.398578 

The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor, and is a major determinant of host range and a dominant target of neutralizing antibodies.

Here we experimentally measure how all amino-acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD’s surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.

Preprint available at bioRxiv (June 17, 2020):

https://doi.org/10.1101/2020.06.17.157982

Scientists have created and described more than 3,800 variations of the protein that the new coronavirus uses to latch on to its targets — a feat that reveals which parts of the protein are crucial for binding to human cells. Scientists have created and described more than 3,800 variations of the protein that the new coronavirus uses to latch on to its targets — a feat that reveals which parts of the protein are crucial for binding to human cells.

Before SARS-CoV-2 invades a cell, a viral protein called spike fastens tightly to a receptor that sits on the surface of many human cells. Jesse Bloom at the Fred Hutchinson Cancer Research Center in Seattle, Washington, and his colleagues altered a single amino acid at a time in a key segment of spike to produce 3,804 variants of the protein (T. N. Starr et al. Preprint at bioRxiv http://doi.org/dz8r; 2020). Tests showed that many of these variants bind to the receptor at least as well as the protein in the coronavirus causing the current pandemic. 

The tests allowed the team to pinpoint the amino acids that, if altered, impair the spike protein’s binding ability. This knowledge could help researchers to develop molecules that neutralize the virus’s ability to infect cells. The findings have not yet been peer-reviewed.

Preprint available at BioRxiv (June 17, 2020):

https://doi.org/10.1101/2020.06.17.157982

Coronavirus has more than one gateway into cells. Two teams of European researchers, working independently, have identified a new entryway through which the coronavirus gets into cells and infects them, suggesting another approach to stopping it. One key route - via a protein on cell surfaces called ACE2 - is well known.

The newly identified gateway is a cell-surface protein called neuropilin-1, or NRP1. A "spike" on the surface of the coronavirus binds to NRP1, allowing the virus to break into the cell, similar to how a virus spike attaches itself to ACE2. Other viruses also employ NRP1 as an entry into cells, including the one that causes mononucleosis.

In laboratory experiments with human cells, one of the teams found that an antibody that binds to NRP1 can block the coronavirus spike from attaching and prevent infection. Neither of the studies has been through the peer-review process. One was posted on the preprint server bioRxiv on Wednesday and the other late last week. The research groups say their findings suggest that NRP1 could be another target for drugs and vaccines against the new virus....

Preprints of the studies available at bioRxiv:

https://www.biorxiv.org/content/10.1101/2020.06.07.137802v2

https://www.biorxiv.org/content/10.1101/2020.06.05.134114v1

The day after data appeared from the vaccine maker Sinovac showed complete protection of rhesus monkeys by their vaccine candidate (whole inactivated SARS-CoV-2 virus particles), scientists from the Jenner Institute in Oxford issued a press release announcing that their vaccine (an adenovirus vector based vaccine that carried the SARS-CoV-2 spike protein) worked to protect rhesus monkeys and that they were moving forward with large scale human safety trials. At the time, the substantiating data was not available. Now it is, in the form of a May 13 BioRxiv preprint. Does the data support the claim?

Not really. All of the vaccinated monkeys treated with the Oxford vaccine became infected when challenged, as judged by recovery of virus genomic RNA from nasal secretions. There was no difference in the amount of viral RNA detected from this site in the vaccinated monkeys as compared to the unvaccinated animals. Which is to say, all vaccinated animals were infected. This observation is in marked contrast to the results reported from Sinovac trial. At the highest dose studied, no virus was recovered from vaccinated monkeys from the throat, lung, or rectum of the vaccinated animals. 

There is a second troubling result of the Oxford paper. The titer of neutralizing antibody, as judged by inhibition of virus replication by successive serum dilutions as reported is extremely low. Typically, neutralizing antibodies in effective vaccines can be diluted by more than a thousand fold and retain activity. In these experiments the serum could be diluted only by 4 to 40 fold before neutralizing activity was lost. Again, by contrast the titer of neutralizing antibodies in the serum of those vaccinated with whole inactivated SARS-CoV-2 was high. What then is the argument for pressing forward with the adenovirus vector SARS-CoV-2 spike protein vaccine? The authors present evidence to the effect that, although the vaccine did not protect the animals from infection, it did moderate the disease....

Preprint of the Study Discussed Available at bioRxiv:

https://doi.org/10.1101/2020.05.13.093195

The blood from seriously ill Covid-19 patients on ventilators was found by researchers to be highly inflammatory and harmful to the body. Antibodies  generated by the immune system to neutralise 

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike protein that mediates SARS-CoV-2 entry into host cells, is one of the major targets for vaccines and therapeutics. Thus, insights into the sequence variations of S protein are key to understanding the infection and antigenicity of SARS-CoV-2.

Here, we observed a dominant mutational variant at the 614 position of S protein (aspartate to glycine, D614G mutation). Using pseudovirus-based assay, we found that S-D614 and S-G614 protein pseudotyped viruses share a common receptor, human angiotensin-converting enzyme 2 (ACE2), which could be blocked by recombinant ACE2 with the fused Fc region of human IgG1. However, S-D614 and S-G614 protein demonstrated functional differences. First, S-G614 protein could be cleaved by serine protease elastase-2 more efficiently. Second, S-G614 pseudovirus infected 293T-ACE2 cells significantly more efficiently than the S-D614 pseudovirus, Moreover, 93% (38/41) sera from convalescent COVID-19 patients could neutralize both S-D614 and S-G614 pseudotyped viruses with comparable efficiencies, but about 7% (3/41) convalescent sera showed decreased neutralizing activity against S-G614 pseudovirus.

These findings have important implications for SARS-CoV-2 transmission and immune interventions.

Preprint available in bioRxiv (June 20, 2020):

https://doi.org/10.1101/2020.06.20.161323

A trawl through a monkey genome using the CRISPR–Cas9 genome-editing system has identified a handful of genes that might help the new coronavirus to infect its hosts.

The discovery of host genes that aid viral activity could aid the development of new therapies, and reveal why some people are more susceptible to COVID-19 than others. John Doench at the Broad Institute of MIT and Harvard in Cambridge, Massachusetts, Craig Wilen at Yale School of Medicine in New Haven, Connecticut, and their colleagues used CRISPR–Cas9 to alter genes in cultured monkey cells. They then looked for those genes that influenced viral infection and host-cell death (J. Wei et al. Preprint at bioRxiv http://doi.org/dzz3; 2020).

The team’s survey found genes that code for several proteins not known to assist the coronavirus. Among them are proteins in the TGF-β signalling pathway, which is involved in cell growth and death. Chemicals that inhibit this pathway also prevented coronavirus-induced cell death. The findings have not yet been peer reviewed.

Preprint of the Original Study available at bioRxiv (June 17, 2020)"

https://doi.org/10.1101/2020.06.16.155101

The aim of this study is to evaluate if the sweat produced by COVID-19 persons (SARS-CoV-2 PCR positive) has a different odour for trained detection dogs than the sweat produced by non COVID-19 persons. The study was conducted on 3 sites, following the same protocol procedures, and involved a total of 18 dogs. A total of 198 armpits sweat samples were obtained from different hospitals. For each involved dog, the acquisition of the specific odour of COVID-19 sweat samples required from one to four hours, with an amount of positive samples sniffing ranging from four to ten. For this proof of concept, we kept 8 dogs of the initial group (explosive detection dogs and colon cancer detection dogs), who performed a total of 368 trials, and will include the other dogs in our future studies as their adaptation to samples scenting takes more time.

The percentages of success of the dogs to find the positive sample in a line containing several other negative samples or mocks (2 to 6) were 100p100 for 4 dogs, and respectively 83p100, 84p100, 90p100 and 94p100 for the others, all significantly different from the percentage of success that would be obtained by chance alone. We conclude that there is a very high evidence that the armpits sweat odour of COVID-19+ persons is different, and that dogs can detect a person infected by the SARS-CoV-2 virus.

Preprint Available in bioRxiv (June 5, 2020):

https://doi.org/10.1101/2020.06.03.132134

On 22 January, Dave O’Connor and Tom Friedrich invited several dozen colleagues around the United States to join a new workspace on the instant messaging platform Slack. The scientists, both at the Wisconsin National Primate Research Center, had seen news about a new disease emerging in China and realized researchers would need a primate model if they were going to answer some important questions about its biology. “We put out a call to a bunch of investigators and basically said: ‘Hey, let’s talk,’” O’Connor says. The idea is to coordinate research and make sure results are comparable, Friedrich adds. (They named the Slack workspace the Wu-han Clan, a play on the hip-hop group Wu-Tang Clan.)

The Wu-han Clan is just one example of how the COVID-19 outbreak is transforming how scientists communicate about fast-moving health crises. A torrent of data is being released daily by preprint servers that didn’t even exist a decade ago, then dissected on platforms such as Slack and Twitter, and in the media, before formal peer review begins. Journal staffers are working overtime to get manuscripts reviewed, edited, and published at record speeds. The venerable New England Journal of Medicine (NEJM) posted one COVID-19 paper within 48 hours of submission. Viral genomes posted on a platform named GISAID, more than 200 so far, are analyzed instantaneously by a phalanx of evolutionary biologists who share their phylogenetic trees in preprints and on social media.

“This is a very different experience from any outbreak that I’ve been a part of,” says epidemiologist Marc Lipsitch of the Harvard T.H. Chan School of Public Health. The intense communication has catalyzed an unusual level of collaboration among scientists that, combined with scientific advances, has enabled research to move faster than during any previous outbreak. “An unprecedented amount of knowledge has been generated in 6 weeks,” says Jeremy Farrar, head of the Wellcome Trust....