Virus World

The coronavirus is an oily membrane packed with genetic instructions to make millions of copies of itself. The instructions are encoded in 30,000 “letters” of RNA — a, c, g and u — which the infected cell reads and translates into many kinds of virus proteins. In December, a cluster of mysterious pneumonia cases appeared around a seafood market in Wuhan, China. In early January, researchers sequenced the first genome of a new coronavirus, which they isolated from a man who worked at the market. That first genome became the baseline for scientists to track the SARS-CoV-2 virus as it spreads around the world.

A cell infected by a coronavirus releases millions of new viruses, all carrying copies of the original genome. As the cell copies that genome, it sometimes makes mistakes, usually just a single wrong letter. These typos are called mutations. As coronaviruses spread from person to person, they randomly accumulate more mutations. The genome below came from another early patient in Wuhan and was identical to the first case, except for one mutation. The 186th letter of RNA was u instead of c. When researchers compared several genomes from the Wuhan cluster of cases they found only a few new mutations, suggesting that the different genomes descended from a recent common ancestor. Viruses accumulate new mutations at a roughly regular rate, so the scientists were able to estimate that the origin of the outbreak was in China sometime around November 2019.

Outside of Wuhan, that same mutation in the 186th letter of RNA has been found in only one other sample, which was collected seven weeks later and 600 miles south in Guangzhou, China. The Guangzhou sample might be a direct descendent of the first Wuhan sample. Or they might be viral cousins, sharing a common ancestor. During those seven weeks, the Guangzhou lineage jumped from person to person and went through several generations of new viruses. And along the way, it developed two new mutations: Two more letters of RNA changed to u....

The country's health care system, with its expertise in conducting clinical research, is ready to run new drug tests. But coordinating them all is another matter.  In the quarantined Chinese city of Wuhan, health workers fighting the explosive outbreak of a new coronavirus have been improvising for weeks, trying to provide whatever care they can for Covid-19 patients whose symptoms range from a cough and fever to severe pneumonia, septic shock, and organ failure. In addition to treating these symptoms with oxygen therapy, ventilators, and antibiotics, doctors there have also resorted to experimentation. With no approved treatments for any of the illnesses caused by coronaviruses, health workers have been trying everything from steroids and antibodies to drugs normally intended for HIV and influenza. But because these treatments have been dispensed on a case-by-case basis, without any rigorous, centralized tracking of results, it’s hard to know if any of them are effective against the new disease.

Now, researchers in China are racing to launch more systematic tests of these repurposed medicines. Since January 28, scientists have registered 19 clinical trials in China, and at least a few have already begun dosing patients. With initial results expected as early as April, the swift leap into clinical research is an important one for frontline health workers desperate for hard evidence about which therapies work best. The trick will be making sure that evidence stacks up. “When you have a treatment, you can measure different things in a patient,” said Marie-Paule Kieny, WHO’s assistant director general of health systems and innovation, at a press conference Wednesday. “What is important if you want to compare different treatments is that everybody measures the same.” Her remarks came at the conclusion of a two-day summit convened by the WHO that brought together major funders and more than 300 scientists to define the most pressing research priorities of the current outbreak.

For Chinese readers, the list of ongoing clinical  is available at the  Chinese Clinical Trial Registry

For English readers see this Registry in English

(Last updated April 22, 2020 - 6:00 pm, PST) 

Global Infections: 2,627,000

Global Deaths: 183,000

Countries & territories affected: 225

April 22, 2020 - More than 2.6 million cases diagnosed, 183,000 deaths globally. Several states in the US start to reopen their businesses despite lack of a 2-week trend downward of COVID-19 cases (Georgia), and at a time when over 2000 people are still dying every day in the U.S. At the same time, Trump signs an executive order to stop immigration. In Spain the lockdown will continue until the second part of May. Deaths in Spain increased overnight to 453. Germany authorizes the test of its first clinical vaccine. Vaccine trials also set to start in the UK. Two cats in New York test positive for COVID-19.

April 21, 2020 - Price of oil drops below zero for the first time on record and oil producers struggle to find places to store current production. Missouri sues the Chinese government over its handling of the coronavirus, saying China's response to the outbreak brought devastating economic losses.

April 15, 2020 - 2 million cases of COVID-19 globally.

April 11, 2020 - U.S. surpasses Italy and reaches a toll of 20,000 deaths and half a million cases. Spain reaches the highest density of confirmed cases in any large country, nearing 4 infections per 1000. The curve of cases in New York starts to flatten after more than 180,000 infections and 8600 deaths have been reported. All U.S. states are now under a federal disaster declaration. The U.S. Internal Revenue Service starts depositing the first coronavirus stimulus payments in taxpayers bank accounts. China reports 99 new cases, although near all of them are overseas travelers returning to the country.

April 10, 2020 - 100,000 deaths globally. A small clinical trial on remdesivir suggest some effect in a study where two thirds of enrolled patients were severely ill.

(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...