Virus World

The main protease, Mpro (or 3CLpro) in SARS-CoV-2 is a viable drug target because of its essential role in the cleavage of the virus polypeptide. Feline infectious peritonitis, a fatal coronavirus infection in cats, was successfully treated previously with a prodrug GC376, a dipeptide-based protease inhibitor.

Here, we show the prodrug and its parent GC373, are effective inhibitors of the Mpro from both SARS-CoV and SARS-CoV-2 with IC50 values in the nanomolar range. Crystal structures of SARS-CoV-2 Mpro with these inhibitors have a covalent modification of the nucleophilic Cys145. NMR analysis reveals that inhibition proceeds via reversible formation of a hemithioacetal. GC373 and GC376 are potent inhibitors of SARS-CoV-2 replication in cell culture. They are strong drug candidates for the treatment of human coronavirus infections because they have already been successful in animals.  The work here lays the framework for their use in human trials for the treatment of COVID-19. Coronavirus main protease is essential for viral polyprotein processing and replication. Here Vuong et al. report efficient inhibition of SARS-CoV-2 replication by the dipeptide-based protease inhibitor GC376 and its parent GC373, which were originally used to treat feline coronavirus infection.

Published in Nature Commun.  (August 27, 2020):

https://doi.org/10.1038/s41467-020-18096-2

Scientists not involved in the study seriously doubt the findings, which challenge the current consensus on where and when the virus originated. In a study not yet published in a journal, scientists have reported that the new coronavirus was present in wastewater in Barcelona, Spain in March 2019, a finding that, if confirmed, would show that the pathogen had emerged much earlier than previously thought. But independent experts who reviewed the findings said they doubted the claim. The study was flawed, they said, and other lines of evidence strongly suggest the virus emerged in China late last year. Up until now, the earliest evidence of the virus anywhere in the world has been from December 2019 in China and it was only known to have hit mainland Spain in February 2020.

“Barcelona is a city that is frequented by Chinese people, in tourism and business, so probably this happened also elsewhere, and probably at the same time,” said the lead author, Albert Bosch, a professor in the Department of Microbiology of the University of Barcelona who has been studying viruses in wastewater for more than 40 years. Several experts not involved in the research pointed out problems with the new study, which has not yet been subjected to the critical review by outside experts that occurs before publication in a scientific journal. They suggested that the tests might very well have produced false positives because of contamination or improper storage of the samples. 

“I don’t trust the results,” said Irene Xagoraraki, an environmental engineer at Michigan State University. Researchers at the University of Barcelona posted their findings online on June 13. Most of their report described research on wastewater treatments from early 2020. 

Preprint available at medRxiv (June 13, 2020):

https://doi.org/10.1101/2020.06.13.20129627

A virus is “simply a piece of bad news wrapped up in protein,” the biologists Jean and Peter Medawar wrote in 1977. In January, scientists deciphered a piece of very bad news: the genome of SARS-CoV-2, the virus that causes Covid-19. The sample came from a 41-year-old man who worked at the seafood market in Wuhan where the first cluster of cases appeared. Researchers are now racing to make sense of this viral recipe, which could inspire drugs, vaccines and other tools to fight the ongoing pandemic.

Viruses must hijack living cells to replicate and spread. When the coronavirus finds a suitable cell, it injects a strand of RNA that contains the entire coronavirus genome. The genome of the new coronavirus is less than 30,000 “letters” long. (The human genome is over 3 billion.) Scientists have identified genes for as many as 29 proteins, which carry out a range of jobs from making copies of the coronavirus to suppressing the body’s immune responses....

We extracted data regarding 1099 patients with laboratory-confirmed Covid-19 from 552 hospitals in 30 provinces, autonomous regions, and municipalities in China through January 29, 2020. The primary composite end point was admission to an intensive care unit (ICU), the use of mechanical ventilation, or death.

The median age of the patients was 47 years; 41.9% of the patients were female. The primary composite end point occurred in 67 patients (6.1%), including 5.0% who were admitted to the ICU, 2.3% who underwent invasive mechanical ventilation, and 1.4% who died. Only 1.9% of the patients had a history of direct contact with wildlife. Among nonresidents of Wuhan, 72.3% had contact with residents of Wuhan, including 31.3% who had visited the city. The most common symptoms were fever (43.8% on admission and 88.7% during hospitalization) and cough (67.8%).

Diarrhea was uncommon (3.8%). The median incubation period was 4 days (interquartile range, 2 to 7). On admission, ground-glass opacity was the most common radiologic finding on chest computed tomography (CT) (56.4%). No radiographic or CT abnormality was found in 157 of 877 patients (17.9%) with nonsevere disease and in 5 of 173 patients (2.9%) with severe disease. Lymphocytopenia was present in 83.2% of the patients on admission.....

Published in New England Journal of Medicine on Feb. 28, 2020:

https://www.nejm.org/doi/full/10.1056/NEJMoa2002032

China’s top legislature imposed a total ban on trade and consumption of wild animals, according to state-run China Central Television, a move that aims to curb activities that scientists say may have caused the deadly coronavirus to jump from animals to humans. The Standing Committee of the National People’s Congress took the decision at a meeting on Monday. The move should restrict trade and protect biodiversity, said Li Shuo, a senior global policy adviser at Greenpeace in Beijing.

The coronavirus is proliferating globally, roiling markets and business, after originating in China where more than 77,000 people have been infected and over 2,500 have died. The virus emerged in early December in Wuhan, an industrial city of 11 million in Hubei province, and early attention focused on a seafood market where live animals were sold, even though a third of the first 40 cases or so were found to have no link to it. The process of ending trade and consumption “will be a challenging exercise,” said Li. Defining what wildlife is, whether Chinese medicines are included and what counts as illegal are some of the issues that need to be tackled, he said. 

According to the People’s Daily, wild animals covered by the ban include those that the Wildlife Protection Law and other laws prohibit people from eating, terrestrial wild animals that China protects as they have “important ecological, scientific and social value” as well as other terrestrial wild animals including those bred in captivity. China issued a temporary ban on trading in wild animals shortly after the outbreak of the virus, and pressure has been mounting to make the prohibition permanent. The existing Wildlife Protection Law bans the sale of food from endangered species, but doesn’t cover all wild animals. International animal rights groups have criticized the use of exotic animal parts such as tiger bones, bear gall and pangolin scales in traditional Chinese medicine.

(Last Update March 16,  2020, 11:30 pm, Pacific Standard Time)

Global Infections:182407

Infections Outside China: 101356

Global Deaths: 7154

Countries & territories affected: 148

March 16, 2020 - Largest ever one-day drop of the U.S. stock market (3000 points). Moderna therapeutic doses its first patient, a healthy volunteer in Seattle, with an experimental mRNA vaccine. 28000 infections in Italy and 10000 in Spain. 4700 cases in U.S., where Trump releases new guidelines, including avoiding eating at restaurants and public places, and gatherings of more than 10 people. Iceland performs widespread testing of its population. Venezuela imposes nation-wide quarantine, and Philippines quarantines the entire island of Luzon (57 million). Imported cases into China continue rising. Liberia, Somalia and Tanzania report firs cases.

March 15, 2020 - For the first time global infections outside China exceed infections in China. 25000 cases and 1800 deaths in Italy. In Madrid (Spain) cases are doubling every 2 days, one of the fastest rates on record at this moment. CDC recommends to avoid gatherings of 50 or more in the U.S. NY and Washington states order restaurants and bars to close. The Federal Reserve cuts interest rates to near zero. First cases reported in Bahamas, Central African Republic, Guinea, Northern Cyprus, and Uzbekistan.

March 14, 2020 - Europe has become the center of the epidemics with over 45000 cases reported. Italy remains the country with the highest density of COVID19 cases, with over 21000 confirmed infections (0.03% population). Spain reports over 1500 new cases in 24h, despite most citizens remain at home and few are being tested. All contiguous US states and Alaska have reported COVID-19. Citizens of U.K. and Ireland added to the list of countries restricted to travel to the U.S. Lancet study suggest that fatality rates in symptomatic patients may have been largely underestimated at the peak of the outbreak. First cases reported in Equatorial Guinea, Namibia, Seychelles, Sudan, and Venezuela.

March 13, 2020 - First cases reported in Aruba, Cayman Islands, Eswatini (Swaziland), Ethiopia, Gabon, Guadeloupe, Guatemala, Kazakhstan, Kenia, Kosovo, Mauritania, Suriname, and Uruguay. U.S. and Spain declare National emergencies. U.S. releases $50 billion to fight the outbreak at a time when 46 people have already died and 22000 schools are closed. Criteria for testing in the U.S. is revised. In Spain, with over 5000 cases, everybody is asked to stay at home for 15 days. South Korea’s cases continue to lower, whereas Europe reports more daily cases than China at its peak. Apple reopens stores in China. First Chinese case of COVID-19 now tracked back to November 17...

Yunjeong Kim and Kyeong-Ok "KC" Chang, virologists in the College of Veterinary Medicine at Kansas State University, have published a study showing a possible therapeutic treatment for COVID-19. Pathogenic coronaviruses are a major threat to global public health, as shown by severe acute respiratory syndrome coronavirus, or SARS-CoV; Middle East respiratory syndrome coronavirus, known as MERS-CoV; and the newly emerged SARS-CoV-2, the virus that causes COVID-19 infection. The study, "3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice," appears in the Aug. 3 issue of the prestigious medical journal Science Translational Medicine. It reveals how small molecule protease inhibitors show potency against human coronaviruses. These coronavirus 3C-like proteases, known as 3CLpro, are strong therapeutic targets because they play vital roles in coronavirus replication. Vaccine developments and treatments are the biggest targets in COVID-19 research, and treatment is really key," said Chang, professor of diagnostic medicine and pathobiology. "This paper describes protease inhibitors targeting coronavirus 3CLpro, which is a well-known therapeutic target."

The study demonstrates that this series of optimized coronavirus 3CLpro inhibitors blocked replication of the human coronaviruses MERS-CoV and SARS-CoV-2 in cultured cells and in a mouse model for MERS. These findings suggest that this series of compounds should be investigated further as a potential therapeutic for human coronavirus infection. Chang and Kim have been using National Institutes of Health grants to develop antiviral drugs to treat MERS and human norovirus infections. Their work extends to other human viruses such as rhinoviruses and SARS-CoV-2...

Original study published in Science Translational Medicine (Aug. 3, 2020):

https://doi.org/10.1126/scitranslmed.abc5332

Far more people may have been infected with Covid-19 than have been confirmed by health officials in Santa Clara County, California, according to a study released Friday in preprint. The study used an antibody blood test to estimate how many people had been infected with Covid-19 in the past. Other tests, like those performed with nasal swabs or saliva, test for the virus' genetic material, which does not persist long after recovery, as antibodies do.

"We found that there are many, many unidentified cases of people having Covid infection that were never identified with it with a virus test," said Dr. Jay Bhattacharya, a professor of medicine at Stanford University and one of the paper's authors. "It's consistent with findings from around the world that this disease, this epidemic is further along than we thought." The study estimated that 2.49% to 4.16% of people in Santa Clara Country had been infected with Covid-19 by April 1. This represents between 48,000 and 81,000 people, which is 50 to 85 times what county officials recorded by that date: 956 confirmed cases....

If 50 times more people have had the infection, the death rate could drop by that same factor, putting it "somewhere between 'little worse than the flu' to 'twice as bad as the flu' in terms of case fatality rate," Bhattacharya said.

Preprint of Original Study (April 17, 2020):

https://www.medrxiv.org/content/10.1101/2020.04.14.20062463v1 

RetroVirox offers a menu of cell-based antiviral services to evaluate experimental therapies and vaccines against coronaviruses, including SARS-CoV-2. The company offers in vitro testing with SARS-CoV-2 pseudovirions and with  live SARS-CoV-2 viruses to evaluate entry inhibitors, neutralizing antibodies, and antivirals against the novel coronavirus causative agent of COVID-19. Multiple viral strains are available for testing, including the most recent Omicron variants of concern (XBB.1.5, XBB.1.16, XBB.2.3.2, EG.5.1 JN.1, KP.2, and KP.3).

Pseudoviruses  coated with the viral spike (S) protein of SARS-CoV-2 are also used to recapitulate the mode of entry of the novel coronavirus. Over 50 spike mutant and variants are available as pseudoviruses. These assays can be used for the following purposes:

• To determine the neutralizing activity of therapeutic antibodies and antisera
• To test experimental COVID-19 vaccines using antisera from inoculated animals or humans
• To evaluate small-molecule and other entry inhibitors targeting the S viral protein, the ACE-2 viral receptor, or host proteases and other targets involved in SARS-CoV-2 viral entry

Assays with live replicating SARS-CoV-2, and milder forms of seasonal human coronaviruses (hCoV-OC43  and 229E) allow for the evaluation of inhibitors at all stages of the coronavirus life cycle. Additional Information about the coronavirus assays and many other cell-based antiviral assays offered at RetroVirox is available here. Request additional information by email at info@retrovirox.com

Takeda announced that it has commenced the development of a plasma-derived therapy for COVID-19, a disease caused by severe SARS-CoV-2. The company will inform the members of the US Congress regarding the development of an anti-SARS-CoV-2 polyclonal hyperimmune globulin (H-IG) for the treatment of high-risk individuals with COVID-19.  Takeda will also evaluate whether the firm’s currently marketed and pipeline products serve as effective treatments for infected patients.

According to the company, the hyperimmune globulins are plasma derived-therapies that were earlier demonstrated as an effective treatment for severe acute viral respiratory infections and may serve as an option for COVID-19. The company is specialised in the research, development and manufacturing of a potential anti-SARS-CoV-2 polyclonal H-IG, which is referring to as TAK-888.

Takeda’s vaccine business unit president and company’s COVID-19 response team co-lead Dr Rajeev Venkayya said: “We have identified relevant assets and capabilities across the company and are hopeful that we can expand the treatment options for patients with COVID-19 and the providers caring for them.” Currently, the Japanese pharmaceutical firm is in negotiations with multiple national health and regulatory agencies and health care partners in the US, Asia, and Europe to rapidly advance the research of TAK-888. Initially, the company plans to produce the therapy in an isolated within its manufacturing facility in Georgia to avoid a negative impact on its other plasma-derived therapies.

A randomized, controlled clinical trial to evaluate the safety and efficacy of the investigational antiviral remdesivir in hospitalized adults diagnosed with coronavirus disease 2019 (COVID-19) has begun at the University of Nebraska Medical Center (UNMC) in Omaha. The trial regulatory sponsor is the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health. This is the first clinical trial in the United States to evaluate an experimental treatment for COVID-19, the respiratory disease first detected in December 2019 in Wuhan, Hubei Province, China.

The first trial participant is an American who was repatriated after being quarantined on the Diamond Princess cruise ship that docked in Yokohama, Japan and volunteered to participate in the study. The study can be adapted to evaluate additional investigative treatments and to enroll participants at other sites in the U.S. and worldwide. There are no specific therapeutics approved by the Food and Drug Administration (FDA) to treat people with COVID-19, the disease caused by the newly emergent SARS-CoV-2 virus (formerly known as 2019-nCoV). Infection can cause mild to severe respiratory illness, and symptoms can include fever, cough and shortness of breath. As of February 24, the World Health Organization (WHO) has reported 77,262 confirmed cases of COVID-19 and 2,595 deaths in China and 2,069 cases of COVID-19 and 23 deaths in 29 other countries. There have been 14 confirmed COVID-19 cases reported in the United States and an additional 39 cases among persons repatriated to the United States, according to the Centers for Disease Control and Prevention (CDC)

Remdesivir, developed by Gilead Sciences Inc., is an investigational broad-spectrum antiviral treatment. It was previously tested in humans with Ebola virus disease and has shown promise in animal models for treating Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS), which are caused by other coronaviruses. “We urgently need a safe and effective treatment for COVID-19. Although remdesivir has been administered to some patients with COVID-19, we do not have solid data to indicate it can improve clinical outcomes,” said NIAID Director and U.S. Coronavirus Task Force member Anthony S. Fauci, M.D. “A randomized, placebo-controlled trial is the gold standard for determining if an experimental treatment can benefit patients.”

The second notable feature of SARS-CoV-2 is a predicted polybasic cleavage site (RRAR) in the spike protein at the junction of S1 and S2, the two subunits of the spike protein (Figure 1b)8,9. In addition to two basic arginines and an alanine at the cleavage site, a leading proline is also inserted; thus, the fully inserted sequence is PRRA (Figure 1b). The strong turn created by the proline insertion is predicted to result in the addition of O-linked glycans to S673, T678, and S686 that flank the polybasic cleavage site. A polybasic cleavage site has not previously been observed in related lineage B betacoronaviruses and is a unique feature of SARS-CoV-2. Some human betacoronaviruses, including HCoV-HKU1 (lineage A), have polybasic cleavage sites, as well as predicted O-linked glycans near the S1/S2 cleavage site.

While the functional consequence of the polybasic cleavage site in SARS-CoV-2 is unknown, experiments with SARS-CoV have shown that engineering such a site at the S1/S2 junction enhances cell–cell fusion but does not affect virus entry10. Polybasic cleavage sites allow effective cleavage by furin and other proteases, and can be acquired at the junction of the two subunits of the haemagglutinin (HA) protein of avian influenza viruses in conditions that select for rapid virus replication and transmission (e.g. highly dense chicken populations). HA serves a similar function in cell-cell fusion and viral entry as the coronavirus S protein. Acquisition of a polybasic cleavage site in HA, by either insertion or recombination, converts low pathogenicity avian influenza viruses into highly pathogenic forms11-13. The acquisition of polybasic cleavage sites by the influenza virus HA has also been observed after repeated forced passage in cell culture or through animals14,15. Similarly, an avirulent isolate of Newcastle Disease virus became highly pathogenic during serial passage in chickens by incremental acquisition of a polybasic cleavage site at the junction of its fusion protein subunits....

...It is improbable that SARS-CoV-2 emerged through laboratory manipulation of an existing SARS-related coronavirus. As noted above, the RBD of SARS-CoV-2 is optimized for human ACE2 receptor binding with an efficient binding solution different to that which would have been predicted. Further, if genetic manipulation had been performed, one would expect that one of the several reverse genetic systems available for betacoronaviruses would have been used. However, this is not the case as the genetic data shows that SARS-CoV-2 is not derived from any previously used virus backbone17. Instead, we propose two scenarios that can plausibly explain the origin of SARS-CoV-2: (i) natural selection in a non-human animal host prior to zoonotic transfer, and (ii) natural selection in humans following zoonotic transfer. We also discuss whether selection during passage in culture could have given rise to the same observed features...

Mandarin version of the article available at: 

http://virological.org/uploads/short-url/dHpDmgjWKLNlBztUWteEJZq4Pvw.pdf

South Korea reported more virus cases Friday and declared a “special management zone” around Daegu after an outbreak linked to a church. South Korea reported 100 new virus cases Friday, bringing the country’s total to 204, many of them clustered around a southeastern city, and raising fears that the outbreak is getting out of control. In the capital, Seoul, officials banned major downtown rallies and shut down a big park to avoid mass public gatherings where the virus could spread. Workers in protective gear also sprayed disinfectant in the city’s subway. Most of the new cases have been reported since Wednesday. The spike, especially in and around Daegu city, has raised fears the outbreak is overwhelming the region’s medical system. Many of the cases have been linked to a church in the city.

And the first two cases were confirmed in South Korea’s 600,000-member military, a navy sailor and an army officer who had both reportedly visited Daegu recently. Prime Minister Chung Se-kyun said in a televised statement the central government will concentrate its support to the southeastern region to ease a shortage in sickbeds, medical personnel and equipment. “A month into the (COVID-19) outbreak, we have entered an emergency phase,” Chung said. “Our efforts until now had been focused on blocking the illness from entering the country. But we will now shift the focus on preventing the illness from spreading further in local communities.”

The surge of infections in Daegu and several cases in Seoul with unclear infection routes forced government officials to acknowledge Thursday for the first time that the virus was circulating in the local population. Initial cases of the illness in South Korea had been connected to China, where the virus has infected 75,000 people and caused more than 2,200 deaths. South Korea on Thursday reported its first virus-related death, one of 11 outside mainland China. Daegu Mayor Kwon Young-jin on Thursday urged the city’s 2.5 million people to stay home and wear masks even indoors if possible....