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Archived news – Decoding SARS-CoV-2

Johns Hopkins Scientists Discover Possible Key to Controlling COVID-19 Immune Response (October 19) – Newly identified protein, known as factor D, appears essential to the inflammatory process of SARS-CoV-2. Based on this study it is believed that by inhibiting factor D the inflammatory reactions would be reduced that make COVID-19 so deadly.

Cytokine elevation in severe and critical COVID-19: a rapid
systematic review, meta-analysis, and comparison with
other inflammatory syndromes
(October 16) – The systemic inflammatory profile of COVID-19 is distinct from that of non-COVID-19 ARDS, sepsis, and CAR T cell-induced cytokine release syndrome; applying the descriptor cytokine storm to COVID-19 might be particularly problematic.

SARS-CoV-2 viral load peaks prior to symptom onset: a systematic review and individual-pooled analysis of coronavirus viral load from 66 studies (September 30)

Interferon and the Coronavirus (September 28) – About the discovery of differing immune profiles among Covid-19 patients. Both inherited and acquired “customizations” of our immune systems produce dramatic differences in severity of the disease.

The lasting misery of coronavirus long-haulers (September 14) – Months after infection with SARS-CoV-2, some people are still battling crushing fatigue, lung damage and other symptoms of ‘long COVID’.

Citizen Scientists Take on the Challenge of Long-Haul COVID-19 (September 3) – Interesting survey summary by a group of citizen scientists, the online Body Politic COVID-19 Support Group , who decided to take matter in their own hands to better understand COVID-19 symptoms, recovery and testing details, etc.

The coronavirus may shut down the immune system’s vital classrooms (August 25) – Autopsied people who died from COVID-19 lack so-called germinal centers, classrooms in the spleen and lymph nodes in which immune cells learn to mount a long-lasting antibody response to a pathogen.

Coronavirus re-infections raise concerns about immunity (August 24) – Two European patients are confirmed to have been re-infected with COVID-19, raising concerns about people’s immunity to the coronavirus as the world struggles to tame the pandemic.

Scientists reveal structural details of spike protein used in leading COVID-19 vaccine (August 7) – Electron microscopy techniques showed that the coronavirus spikes maintained the desired shape in the vaccine, which should help stimulate an appropriate immune response.

Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity (August 19) – Annotation analysis looks at variants in SARS-CoV-2 genomes from first phase of pandemic.

AI: Cracking Covid-19’s Code – STAT News discussion scheduled for August 18. AI experts talk about how AI is accelerating a worldwide effort to crack Covid-19’s molecular code. With individuals from Microsoft and Adaptive Biotechnologies

The Coronavirus May Mess With Thyroid Levels, Too (August 10) – To the many organs affected by COVID-19, the thyroid is now added to the list as well.

We’ve Seen the COVID-19 Future and It Is Concerning (July 27) – A wide variety of symptoms seem to persist post-recovery.

SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19 (July 29) – The presence of S-cross-reactive T cells in a sizable fraction of the general population may affect the dynamics of the current pandemic, and has important implications for the design and analysis of upcoming COVID-19 vaccine trials.

Is there a relationship between blood type and covid-19 infection? (July 14)

Extrapulmonary manifestations of COVID-19 (July 10) – A review of the extrapulmonary organ-specific pathophysiology, presentations and management considerations for patients with COVID-19 to aid clinicians and scientists in recognizing and monitoring the spectrum of manifestations, and in developing research priorities and therapeutic strategies for all organ systems involved.

Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein (July 19) – This study defines sites of vulnerability on SARS-CoV-2 S and demonstrates the speed and robustness of advanced antibody discovery platforms and why neutralizing antibodies are our best near term shot against COVID-19.

Interferon Plays Pivotal, Inflammatory Role in Severe COVID-19 Cases (July 13) – New study suggest that patients with severe COVID-19 experience increased regulation of the type I interferon (IFN-I) inflammation-triggering pathway—a signature that the researchers also observed in patients hospitalized with severe cases of influenza. Based on their results, the scientists propose that the IFN-I response exacerbates inflammation in patients with severe COVID-19. Their results, along with past mouse studies that highlight how the timing of IFN-I expression is critical to determining the outcome of SARS-CoV-2 infection, support targeting IFN-I as a potential treatment strategy for severe COVID-19.

Seeing Coronavirus Replicate in Kidney Cells (July 7) as depicted in the high-resolution micrograph using rich pseudo-colors.

Six months of coronavirus: the mysteries scientists are still racing to solve (July 3) – From immunity to the role of genetics, Nature looks at five pressing questions about COVID-19 that researchers are tackling.

Potential causes and consequences of gastrointestinal disorders
during a SARS-CoV-2 infection
(July 3) – Discusses the role of the gut microbiota during respiratory viral infections and suggest that targeting gut dysbiosis may help to control the pathogenesis of COVID-19.

Neurological associations of COVID-19 (July 2) – An excellent review of all the clinical cases of diverse neurological manifestations.

Primary exposure to SARS-CoV-2 protects against reinfection in rhesus macaques (July 2).

How many COVID-19 infections are undetected? Studying its mutations may hold the answer (July 1) – As of the end of June, there were more than 10.4 million confirmed cases of COVID-19 worldwide. The real number, of course, is much higher, though unknown, because of limited tests and because of how many people who are infected never have symptoms and so never think to get a test. At the nonprofit Chan Zuckerberg Biohub, researchers are using changes in the virus genome to estimate the number of undetected infections—and found that in some areas, more than 90% of cases weren’t discovered.

Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies (June 15) – Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent Ab features.

This coronavirus mutation has taken over the world. Scientists are trying to understand why (June 29) – Of the approximately 50,000 genomes of the new virus that researchers worldwide have uploaded to a shared database, about 70 percent carry the mutation, officially designated D614G but known more familiarly to scientists as “G.” At least four laboratory experiments suggest that the mutation makes the virus more infectious. Another unpublished study asserts that patients with the G variant actually have more virus in their bodies, making them more likely to spread it to others.

Watch: It’s not just the lungs: The Covid-19 virus attacks like no other ‘respiratory’ infection (June 26) – We are starting to understand that the coronavirus has such a diversity of effects on so many different organs.

Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections (June) – The data suggest that asymptomatic individuals had a weaker immune response to SARS-CoV-2 infection. The reduction in IgG and neutralizing antibody levels in the early convalescent phase might have implications for immunity strategy and serological surveys. It is suggested that timely RT–PCR and serological testing should be used in conjunction, which would benefit accurate estimation of the asymptomatic proportion. However, serological testing has limitations, and tests vary in their specificity and sensitivity. Results might also be confounded by previously existing antibodies to SARS-CoV, MERS-CoV or common cold coronaviruses.

Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease (June 19) – A promising drug target is the viral main protease Mpro, which plays a key role in viral replication and transcription. Dai et al. designed two inhibitors, 11a and 11b, based on analyzing the structure of the Mpro active site. Both strongly inhibited the activity of Mpro and showed good antiviral activity in cell culture. Compound 11a had better pharmacokinetic properties and low toxicity when tested in mice and dogs, suggesting that this compound is a promising drug candidate.

Genomewide Association Study of Severe Covid-19 with Respiratory Failure (June 17) – Results of association study imply role of ABO blood type in COVID-19 disease outcome.

India to have own genome data bank to decode COVID-19 virus (June 12) – The IGIB has proposed a collaborative resource IndiCoV, an open data source, to ensure that the genome data is appropriately organised and annotated to researchers so they can make best use of it.

Mapping SARS-CoV-2 Infections in the Respiratory Tract (June 3) – Study characterizes some of the ways the coronavirus infects the nasal cavity and infects and replicates progressively less well in cells lower down the respiratory tract—including the lungs. The findings suggest the virus tends to become firmly established first in the nasal cavity, but in some cases the virus is aspirated into the lungs, where it may cause more serious disease, including potentially fatal pneumonia.

QF scientists study Covid-19’s varying effect on different populations (June 1) – The focus is on how genomic variations in hosts do affect the way the virus behaves.

Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses (May 18) – This study combined advanced machine
learning methods with well-established genome comparison
techniques, to identify the potential genomic determinants of
pathogenicity of the high-CFR coronavirus strains.

Coronavirus May Be a Blood Vessel Disease, Which Explains Everything (May 28) – Many of the infection’s bizarre symptoms have one thing in common:  An impairment in blood circulation. Add in the fact that 40% of deaths from Covid-19 are related to cardiovascular complications, and the disease starts to look like a vascular infection instead of a purely respiratory one.

Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions (May 27) – Enhanced receptor binding by SARS-CoV-2 is believed to contribute to the highly contagious transmission rate of coronavirus disease 2019. An understanding of the structural and energetic details responsible for protein–protein interactions between the host receptor ACE2 and SARS-CoV-2 can be useful to epidemic surveillance, diagnosis, and optimization of neutralizing agents. This study unravels a delicate balance of specific and nonspecific hydrogen-bonding and hydrophobic networks to help elucidate the similarities and differences in receptor binding by SARS-CoV-2 and SARS-CoV.

Viral and host factors related to the clinical outcome of COVID-19 (May 20) – The determinants of disease severity seemed to stem mostly from host factors such as age, lymphocytopenia, and its associated cytokine storm, whereas viral genetic variation did not significantly affect the outcomes.

An outbreak of severe Kawasaki-like disease at the Italian epicentre of the SARS-CoV-2 epidemic: an observational cohort study (May 13) – In the past month we found a 30-fold increased incidence of Kawasaki-like disease. Children diagnosed after the SARS-CoV-2 epidemic began showed evidence of immune response to the virus, were older, had a higher rate of cardiac involvement, and features of MAS. The SARS-CoV-2 epidemic was associated with high incidence of a severe form of Kawasaki disease. A similar outbreak of Kawasaki-like disease is expected in countries involved in the SARS-CoV-2 epidemic.

New partnership to sequence human genomes in the fight against coronavirus (May 13) – A major new human whole genome sequencing study will take place across the NHS, involving up to 20,000 people currently or previously in an intensive care unit with coronavirus, as well as 15,000 individuals who have mild or moderate symptoms. Genomics England, is partnering with the GenOMICC consortium, Illumina and the NHS to launch the research drive, which will reach patients in 170 intensive care units throughout the UK.

A Global Effort to Define the Human Genetics of Protective Immunity to SARS-CoV-2 Infection (May 12) – SARS-CoV-2 infection displays immense inter-individual clinical variability, ranging from silent infection to lethal disease. The role of human genetics in determining clinical response to the virus remains unclear. Studies of outliers—individuals remaining uninfected despite viral exposure and healthy young patients with life-threatening disease—present a unique opportunity to reveal human genetic determinants of infection and disease.

Immunology of COVID-19: current state of the science (May 6)

Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop (May 1) – Compared to SARS-CoV and all other coronaviruses in Betacoronavirus lineage B, an extended structural loop containing basic amino acids at the interface of the receptor binding (S1) and fusion (S2) domains is identified. It is suggested that this loop confers fusion activation and entry properties more in line with betacoronaviruses in lineages A and C, and be a key component in the evolution of SARS-CoV-2 with this structural loop affecting virus stability and transmission.

How Coronavirus Mutates and Spreads (April 30) – How the coronavirus mutates, how those mutations record its history and how they will shape its future.

Geographic and Genomic Distribution of SARS-CoV-2 Mutations (April 29) – The genomic variability of SARS-CoV-2 specimens scattered across the globe can underly geographically specific etiological effects. This study gathered the 10,014 SARS-CoV-2 complete genomes currently available thanks to the collection endeavor of the GISAID consortium and thousands of contributing laboratories. The researchers analyzed and annotated all SARS-CoV-2 mutations and compared with the reference Wuhan genome NC_045512.2

The trinity of COVID-19: immunity, inflammation and intervention (April 28) – Describes the interaction of SARS-CoV-2 with the immune system and the subsequent contribution of dysfunctional immune responses to disease progression. 

SARS-CoV-2 Likely Uses Two Nose Cell Types for Entry (April 24) – The study published in Nature shows that goblet and ciliated cells in the nose have high levels of the entry proteins that SARS-CoV-2 uses to get into our cells. It further shows that cells in the eye and some other organs also contain the viral-entry proteins. It is suggested that a key entry protein is regulated with other immune system genes and reveals potential targets for the development of treatments to reduce transmission.

Renin–Angiotensin–Aldosterone System Inhibitors in Patients with Covid-19 (April 23) – The interaction between the SARS viruses and ACE2 has been proposed as a potential factor in their infectivity, The data sill limited.

Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) (April 21) – The findings could have immediate applications to SARS-CoV-2 diagnostics, public health monitoring, and therapeutic development.

SRTI, Stanford Health Launch mHealth Consortium for COVID-19 Research (April 14) – Stanford Health and the Scripps Research Translational Institute are partnering with Fitbit to aggregate data from mHealth programs that are studying how wearables can be used to tackle the Coronavirus pandemic.

UK Biobank: DNA to unlock coronavirus secrets (April 14) – The UK Biobank – which contains samples from 500,000 volunteers, as well as detailed information about their health – is now adding Covid-19 data.

How Scientists Can Volunteer to Help Fight COVID-19 (April 13) – Researchers are offering tools, equipment, time, and expertise to help alleviate COVID-19 suffering.

NIH begins study to quantify undetected cases of coronavirus infection (April 10) – In this “serosurvey,” researchers will collect and analyze blood samples from as many as 10,000 volunteers to provide critical data for epidemiological models. The results will help illuminate the extent to which the novel coronavirus has spread undetected in the United States and provide insights into which communities and populations are most affected.

Why Does Covid-19 Make Some People So Sick? Ask Their DNA (April 7) – Consumer genomics company 23andMe wants to mine its database of millions of customers for clues to why the virus hits some people harder than others.

IBM is sharing its AI tools to fight COVID-19 crisis (April 7) – The company announced the plan to share its AI tools so that researchers can better understand the virus, and fast-track the development of vaccines and anti-viral therapies to treat the disease stemming from it.

Largest Study to Date of COVID-19 Susceptibility Launched (March 31) – The new study, launched by the Hannover Medical School in Germany, is intended to identify genomic and other biological factors of patient susceptibility and is supported by a range of genomics and technology companies including Rescale, Amazon Web Services (AWS), Bionano Genomics, Genoox, and other companies associated with Tech Against Covid. The study involves 1,000 patients and controls – consisting of COVID-19 patients and their partners and first-degree relatives as controls – and will compare a variety of genomic and other biological variables between those patients who show no or mild symptoms and those who show severe illness. Partners have typically been intensely exposed to the same strain of the virus as the patients, and differences in disease severity can be caused by genetic variation.

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing (March 23) – 26 of the 29 viral proteins were cloned, tagged and expressed in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs).

Adaptive Biotechnologies and Microsoft expand partnership to decode COVID-19 immune response and provide open data access (March 20)

SARS-CoV-2_Sequencing (March 19) – The CDC has started a collection of SARS-CoV-2 sequencing and bioinformatic protocols, metadata guidance, scripts/workflows, links and best practices.

The proximal origin of SARS-CoV-2 (March 17) – Demonstrates that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.

Over 24,000 coronavirus research papers are now available in one place (March 16) – A database with over 24,000 research papers related to the coronavirus pandemic is now live. The database not only helps scientists consolidate existing research but also makes the body of literature easier to mine for insights with artificial intelligence.

The Establishment of Reference Sequence for SARS-CoV-2 and Variation Analysis (March 13) – The SARS-CoV-2 reference sequence could benefit not only biological study of this virus but also diagnosis, clinical monitoring and intervention of SARS-CoV-2 infection in the future.

Why does the coronavirus spread so easily between people? (March 6) – To infect a cell, the coronaviruses use a ‘spike’ protein that binds to the cell membrane. Its spike protein differs from those of close relatives, and suggest that the protein has a site on it which is activated by a host-cell enzyme called furin. Furin is found in liver, lung, and small intestines which explains the symptoms associated with coronavirus infection – still little is know whether this is exactly what is happening and the importance of these activation sites.

Two genome sequences of coronavirus (COVID-19) show possible internal transmission (March 4) – Scientists have published two genome sequences for severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). Coronavirus disease (COVID-19) is an infectious disease caused by SARS-CoV-2.

Coronavirus Method Development Community – This group is for the support of researchers working on coronavirus methods, intended to facilitate method-centered collaboration and sharing.

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