Pandemic – Page 2 – surfing the universe

20191230M Day -1: “Bat Woman” Shi Zhengli begins testing mysterious patient samples at Wuhan Institute of Virology

20200508F, Santa Cruz, CA: On Dec 30th, 2019, virologist Shi Zhengli began testing samples from patients who had a mysterious illness in Wuhan, China. An article by Scientific America was written about her, originally published online Mar 11, 2020: How China’s “Bat Woman” Hunted Down Viruses from SARS to the New Coronavirus.

Here are quotes of Shi Zhengli from the article:

I wondered if [the municipal health authority] got it wrong.

I had never expected this kind of thing to happen in Wuhan, in central China.

Could they have come from our lab?

Eight months of hard work seemed to have gone down the drain. [after not being able to find SARS virus in bats] We thought maybe bats had nothing to do with SARS.

The majority of them [coronaviruses] are harmless.

You don’t need to be a wildlife trader to be infected.

That really took a load off my mind. I had not slept a wink for days.

Wildlife trade and consumption are only part of problem.

Maybe we are getting used to it. The worst days are certainly over.

The Wuhan outbreak is a wake-up call.

The mission must go on.

What we have uncovered is just the tip of an iceberg.

Bat-borne coronaviruses will cause more outbreaks. We must find them before they find us.

Other quotes of Shi Zhengli:

The 2019 novel coronavirus is a punishment by nature to humans’ unsanitary life styles. I promise with my life that the virus has nothing to do with the lab. [WeChat Feb 2, 2020]

No matter how difficult things are, there will not be a ‘defector’ situation. We’ve done nothing wrong. With strong belief in science, we will see the day when the clouds disperse and the sun shines. [WeChat May 2, 2020]

I will save analysis of these quotes for another time.

20200511M: Here’s a looped photo I took on the 30th of December, 2019. I enjoy noticing the way the reflection of the light is affected by the interference of the waves on the lake. The path of the boat towards the rays of the sun is like the path we were on pre-pandemic. I imagine the portion of the lake with reflected light as representing the pandemic wormhole. The path that we take as we exit the wormhole is unknown, as is in which universe we will exit. What is more certain is that we will exit the wormhole. Personally, I’m targeting June 8th, 2020 as my exit date.

image_c84abb31-6086-4b10-9cac-deeb9e102a90.img_0960 — Edward Rendon Sr. Metropolitan Park, Austin, Texas – Dec. 30th, 2019 (Credit: SurfingTheUniverse.com)

20191231T Day 0: Pneumonia Unknown Etiology detected in Wuhan City, Hubei Province of China

image_f056e2dc-61b1-45e4-b8d7-2199e5b5247d.img_8538 — Pandemic wormhole continues to open in Wuhan (photo credit: surfingtheuniverse.com)

On Dec 31, 2019, the WHO China Country Office was informed of cases of “pneumonia of unknown etiology” detected in Wuhan City, Hubei Province of China. This was reported in the first Novel Coronavirus (2019-nCOV) Situation Report on 21 Jan 2020.

It’s 128 days later as I write this. I’m listening to the WHO report now and they are discussing the origin day of the pandemic.

The photo is from January 21st, 2019, when I was traveling through Wuhan. I’ve been self-amusingly referring to my experience of the pandemic as being in a pandemic wormhole. It’s a mental construct I’m using in order to explain all of the changes I’ve seen since I began almost daily blogging 128 days ago.

On Dec 30, 2019, the AP reported: China investigates respiratory illness outbreak sickening 27, which was referring to the city’s health commission statement on China’s 31st (different time zone). The full text of the AP report:

BEIJING (AP) — Chinese experts are investigating an outbreak of respiratory illness in the central city of Wuhan that some have likened to the 2002-2003 SARS epidemic.

The city’s health commission said in a statement Tuesday that 27 people had fallen ill with a strain of viral pneumonia, seven of whom were in serious condition.

It said most had visited a seafood market in the sprawling city, apparently pointing to a common origin of the outbreak.

Unverified information online said the illnesses were caused by Severe Acute Respiratory Syndrome, which emerged from southern China and killed more than 700 people in several countries and regions. SARS was brought under control through quarantines and other extreme measures, but not before causing a virtual shutdown to travel in China and the region and taking a severe toll on the economy.

However, the health commission said the cause of the outbreak was still unclear and called on citizens not to panic.

It’s interesting to see that at this time, the respiratory illness was already linked to the SARS-1 epidemic and that a request was made for citizens “not to panic”, which many people read as “it’s time to panic, or at least prepare before everyone else panics”.

From a news scan of Dec 31, 2019 on CIDRAP, the following related notes:

Chinese officials probe unidentified pneumonia outbreak in Wuhan

Health officials in China are investigating the cause of a pneumonia outbreak in the city of Wuhan in Hubei province that has sickened 27 people and seems to be linked to a seafood market.

Government officials in Hong Kong and Taiwan detailed what’s known from mainland sources, and infectious disease news reporting sites such as FluTrackers, Avian Flu Diary, and ProMED Mail have been tracking official and media reports.

In a statement today, Hong Kong’s Centre for Health Protection (CHP), citing provincial health commission sources, said that, of 27 patients, 7 are in serious condition and the rest are stable. The main symptom is fever, but some patients have had shortness of breath.

Wuhan health officials said the pneumonia appears to be viral and that the patients are in isolation. No obvious human-to-human transmission has been observed, and no healthcare worker infections have been reported.

So far, the cause of the outbreak is still under investigation. News of the outbreak triggered rumors of possible severe acute respiratory syndrome (SARS). Virologist Leo Poon, DPhil, a SARS expert from Hong Kong University, told Radio Television Hong Kong (RTHK), a public broadcasting service in Hong Kong, that it’s too early to say the outbreak is a SARS event. He added that the emergence of atypical pneumonia cases requires identifying the responsible pathogen and ruling out SARS or other types of coronaviruses.

and in the same scan is coincidentally a report of a new fatal MERS (which should maybe be renamed SARS-1.5, or SARS-ME) case in Saudi Arabia:

The Ministry of Health (MOH) of Saudi Arabia reported a new MERS-CoV case from earlier this month.

The case-patient was a 70-year-old man from the city of Hafar Al Batin in the northeastern part of the country. The man died from complications of his Middle East respiratory syndrome coronavirus (MERS-CoV) infection. The MOH also said the man had camel contact, a common risk factor for MERS.

This is the fourth MERS case recorded in Saudi Arabia in December. In November the MOH noted 12 cases.

The WHO said in an update earlier this month that, since MERS-CoV was first detected in humans in 2012, it has received reports of 2,484 cases, at least 857 of them fatal. The vast majority were reported from Saudi Arabia.

The government of Hong Kong issues the following press release:

CHP closely monitors cluster of pneumonia cases on Mainland

*************************************************

The Centre for Health Protection (CHP) of the Department of Health is today (December 31) closely monitoring a cluster of pneumonia cases in Wuhan, Hubei Province, and has contacted the National Health Commission for further information.

According to an announcement from the Health Commission of Hubei Province, a number of pneumonia cases related to a local seafood market was recently reported in Wuhan. The Wuhan Municipal Health Commission has commenced investigation and so far identified 27 cases. Among them, seven cases were serious and the remaining were stable. Symptoms were mainly fever while a few had presented with shortness of breath. All patients are isolated and receiving treatment. Contact tracing of close contacts and medical surveillance are ongoing.

The Wuhan Municipal Health Commission announced that assessment by relevant experts revealed that the cases were compatible with viral pneumonia. For the time being, no obvious human-to-human transmission has been observed and no healthcare workers have been infected. The causative pathogen and cause of infection are still under investigation.

Locally, while surveillance, prevention and control measures are in place, the CHP will remain vigilant and work closely with the World Health Organization and relevant health authorities to monitor the latest developments.

The CHP’s Port Health Division conducts health surveillance measures at all boundary control points. Thermal imaging systems are in place for body temperature checks on inbound travellers. Suspected cases with serious infectious diseases identified will be immediately referred to public hospitals for isolation, treatment and follow-up. The CHP has also informed the Hospital Authority about the cluster of pneumonia cases in Wuhan.

Travellers are reminded to wear surgical masks and seek medical attention if they present with respiratory symptoms, and reveal their travel history to doctors. The CHP will continue to closely monitor the latest situation of the cluster of pneumonia cases in Wuhan and update the surveillance criteria and testing strategies accordingly.

To prevent pneumonia and respiratory tract infection, members of the public should maintain good personal and environmental hygiene. They are advised to:

Perform hand hygiene frequently, especially before touching the mouth, nose or eyes; after touching public installations such as handrails or door knobs; or when hands are contaminated by respiratory secretion after coughing or sneezing.

Wash hands with liquid soap and water, and rub for at least 20 seconds. Then rinse with water and dry with a disposable paper towel or hand dryer. If hand washing facilities are not available, or when hands are not visibly soiled, hand hygiene with 70 to 80 per cent alcohol-based handrub is an effective alternative.

Cover your mouth and nose with tissue paper when sneezing or coughing. Dispose of soiled tissues into a lidded rubbish bin, then wash hands thoroughly.

When having respiratory symptoms, wear a surgical mask, refrain from work or attending class at school, avoid going to crowded places and seek medical advice promptly.

The public should take heed of the health advice below when travelling outside Hong Kong:

Avoid touching poultry/birds or their droppings, and avoid visiting wet markets, live poultry markets or farms;

Avoid making close contact with patients, especially those with symptoms of acute respiratory infections;

Adhere to food safety and hygiene rules such as avoiding consuming raw or undercooked animal products, including milk, eggs and meat, or foods which may be contaminated by animal secretions, excretions (such as urine) or contaminated products, unless they have been properly cooked, washed or peeled.

If feeling unwell when outside Hong Kong, especially if having a fever or cough, wear a surgical mask, inform the hotel staff or tour escort and seek medical advice at once.

After returning to Hong Kong, consult a doctor promptly if having a fever or other symptoms, inform the doctor of recent travel history and wear a surgical mask to help prevent spread of the disease.

Ends/Tuesday, December 31, 2019
Issued at HKT 19:06

Notice the mention of the advise to wear a surgical mask if feeling unwell and to inform doctors of recent travel history outside of Hong Kong.

The Tiawan CDC reported in a 2019-12-31 press release that there would be border control for flights incoming from Wuhan:

In response to the outbreak of pneumonia in Wuhan, Mainland China, the CDC has continued to implement border quarantine and boarding quarantine for Wuhan inbound flights

Release Date: 2019-12-31

Regarding a number of cases of pneumonia reported in Wuhan, Mainland China, the CDC has confirmed the epidemic information to the Mainland China Centers for Disease Control and Prevention and the World Health Organization (WHO) IHR window today (31). In the evening, Lu Fang sent experts to Wuhan in response. Conducted pathogen detection and investigation of the cause of infection, and provided information released by the Wuhan Municipal Health and Health Committee on December 31, stating that 27 cases of pneumonia were recently discovered in the local area and 7 cases were critically ill. All of them have been treated in isolation and 2 cases have improved. The clinical manifestations are mainly fever, a few patients have difficulty breathing, and have bilateral lung infiltrative lesions. Most of the cases were operated by South China Seafood City, Jianghan District, Wuhan City. No obvious human-to-human transmission and medical staff infection have been found. Lu indicated that if there is further information, he will inform us in time.

In response to the epidemic of pneumonia in Wuhan, Mainland China, in order to prevent cases from moving abroad, China has initiated contingency measures for border quarantine in accordance with standard operating procedures, strengthened fever screening for inbound tourists, implemented travel history, occupation type, contact history of suspected cases, Inquiries about the gathering situation, health assessment and health education, the assessment of the epidemic can be effectively prevented from overseas, but for the sake of prudence, boarding and quarantine will be carried out for flights departing directly from Wuhan, Mainland China, except for proactive assessment of passenger health In addition to this situation, relevant preventive measures were also introduced to passengers on the flight.

The Department of Disease Control will continue to monitor the epidemic situation in Wuhan, Mainland China, and adjust the prevention and control according to the epidemic situation. As the local epidemic situation is not yet clear, the public is urged to receive information on unknown or unproven epidemic situations. Do not distribute or repost it at will. Article 63 of the Law on the Prevention and Control of Infectious Diseases stipulates that the spread of rumors or false information about the epidemic situation of infectious diseases, which is caused to the public or others in full, is subject to a fine of up to NT $ 3 million; and in accordance with the Law on the Maintenance of Social Order Article 63, paragraph 5, provides that those who spread rumors enough to affect public peace may be detained for less than three days or fined less than NT $ 30,000.

The Department of Disease Control stated that in addition to the flu epidemic season, winter is also a period of pneumonia. It reminds the public to take good personal hand hygiene and cough etiquette, and try to avoid crowded and airless public places. People in the Wuhan area of mainland China who have fever or acute respiratory symptoms within 10 days of returning to China should take the initiative to report the 1922 epidemic prevention line and wear a mask to seek medical treatment as soon as possible. When seeking medical treatment, please actively inform the history of tourism activities, timely diagnosis notification and obtain a complete Medical care.

ProMED International Society for Infectious Diseases posted Undiagnosed pneumonia – China (HU): RFI:

Published Date: 2019-12-30 23:59:00
Subject: PRO/AH/EDR> Undiagnosed pneumonia – China (HU): RFI
Archive Number: 20191230.6864153

UNDIAGNOSED PNEUMONIA – CHINA (HUBEI): REQUEST FOR INFORMATION
**************************************************************
A ProMED-mail post
http://www.promedmail.org
ProMED-mail is a program of the
International Society for Infectious Diseases
http://www.isid.org

[1]
Date: 30 Dec 2019
Source: Finance Sina [machine translation]
https://finance.sina.cn/2019-12-31/detail-iihnzahk1074832.d.html?from=wap

Wuhan unexplained pneumonia has been isolated test results will be announced [as soon as available]
—————————
On the evening of [30 Dec 2019], an “urgent notice on the treatment of pneumonia of unknown cause” was issued, which was widely distributed on the Internet by the red-headed document of the Medical Administration and Medical Administration of Wuhan Municipal Health Committee.

On the morning of [31 Dec 2019], China Business News reporter called the official hotline of Wuhan Municipal Health and Health Committee 12320 and learned that the content of the document is true.

12320 hotline staff said that what type of pneumonia of unknown cause appeared in Wuhan this time remains to be determined.

According to the above documents, according to the urgent notice from the superior, some medical institutions in Wuhan have successively appeared patients with pneumonia of unknown cause. All medical institutions should strengthen the management of outpatient and emergency departments, strictly implement the first-in-patient responsibility system, and find that patients with unknown cause of pneumonia actively adjust the power to treat them on the spot, and there should be no refusal to be pushed or pushed.

The document emphasizes that medical institutions need to strengthen multidisciplinary professional forces such as respiratory, infectious diseases, and intensive medicine in a targeted manner, open green channels, make effective connections between outpatient and emergency departments, and improve emergency plans for medical treatment.

Another piece of emergency notification, entitled “City Health and Health Commission’s Report on Reporting the Treatment of Unknown Cause of Pneumonia” is also true. According to this document, according to the urgent notice from the superior, the South China Seafood Market in our city has seen patients with pneumonia of unknown cause one after another.

The so-called unexplained pneumonia cases refer to the following 4 cases of pneumonia that cannot be diagnosed at the same time: fever (greater than or equal to 38C); imaging characteristics of pneumonia or acute respiratory distress syndrome; reduced or normal white blood cells in the early stages of onset The number of lymphocytes was reduced. After treatment with antibiotics for 3 to 5 days, the condition did not improve significantly.

It is understood that the 1st patient with unexplained pneumonia that appeared in Wuhan this time came from Wuhan South China Seafood Market.

12320 hotline staff said that the Wuhan CDC went to the treatment hospital to collect patient samples as soon as possible, specifically what kind of virus is still waiting for the final test results. Patients with unexplained pneumonia have done a good job of isolation and treatment, which does not prevent other patients from going to the medical institution for medical treatment. Wuhan has the best virus research institution in the country, and the virus detection results will be released to the public as soon as they are found.

—
Communicated by:
ProMED-mail
<promed@promedmail.org>

******
[2]
Date: 31 Dec 2019
Source: Sina Finance Mobile
https://tech.sina.com.cn/roll/2019-12-31/doc-iihnzhfz9428799.shtml

Patients with unknown cause of pneumonia in Wuhan have been isolated from multiple hospitals
———————-
Whether or not it is SARS has not yet been clarified, and citizens need not panic.

On [31 Dec 2019], various hospitals in Wuhan held an emergency symposium on the topic of the treatment of patients with pneumonia of unknown cause in some medical institutions. The 21st Century Business Herald reporter learned from multiple cross-examinations that these patients have gradually appeared in the South China Seafood Market in Wuhan. At present, the patients have been isolated at the hospital where they saw them. At the scene of the South China Seafood Market, the scene has been isolated and medical staff have confirmed Preventive treatment on site. However, several hospital sources said that at present, the etiology of these patients is not clear, and it cannot be concluded that it is the SARS virus [presently] rumored online. Even if the SARS virus is eventually diagnosed, there is a mature prevention and treatment system in place, and citizens need not panic.

On [31 Dec 2019], an official report from Hubei Province said: “Following the report of the Provincial Health and Health Commission, since December [2019], Wuhan has continued to monitor influenza and related diseases, and 27 cases of viral pneumonia have been found, all of which were diagnosed with viral pneumonia / pulmonary infection. Of the 27 cases, 7 were critically ill, and the remaining cases were controllable. Two of them improved and were expected to be discharged soon. The investigation found that most of the cases were operated by South China Seafood City in Jianghan District, Wuhan. The National Health and Health Commission has decided to send an expert group to our province to guide the epidemic disposal on the morning of [31 Dec 2019]. At present, related virus typing, isolation treatment, public opinion control, and terminal disinfection are underway.

On the evening of [30 Dec 2019], an “Urgent Notice on Doing a Good Job in the Treatment of Unknown Cause of Pneumonia” issued by the Wuhan Municipal Health Commission circulated. The document was verified by cross-examination. “We are holding a special meeting on this,” said a medical worker at a famous 3rd-level hospital in Wuhan on the morning of [31 Dec 2019], but it was clear that the cause of the patient was not clear. For more detailed information, it is temporarily inconvenient to disclose. At present, Wuhan Health and Health Commission official phone 12320 and official website are busy and unable to log in respectively.

Baidu encyclopedia information shows that human diseases caused by SARS virus are mainly respiratory infections (including severe acute respiratory syndrome). The virus is sensitive to temperature and grows well at 33 C, but it is suppressed at 35 C. Because of this characteristic, winter and early spring are the epidemic seasons of the virus disease. SARS virus is one of the main pathogens of the common cold in adults. The infection rate in children is high, mainly upper respiratory tract infection, and it rarely spreads to the lower respiratory tract. In addition, it can cause acute gastroenteritis in infants and newborns. The main symptoms are watery stools, fever, and vomiting. It can be pulled more than 10 times a day. In severe cases, bloody stools can occur. In rare cases, it also causes nervous system syndrome. .

The serotype and antigenic variability of SARS virus is unknown. SARS virus can be repeatedly infected, indicating that it has multiple serotypes (at least 4 are known) and antigenic variations, and its immunity is difficult.

The SARS virus is mainly excreted through respiratory secretions, transmitted through oral fluids, sneezing, and contact, and transmitted through air droplets. The peak of infection occurs in autumn, winter, and early spring. Sensitive to heat, UV, Lysol water, 0.1% peroxyacetic acid, and 1% keliaolin [?] can kill the virus in a short time. [studies on removal of the SARS-CoV from surfaces demonstrated that the virus was rapidly killed by bleach, ethanol, acetone, and formaldehyde. http://www.cidrap.umn.edu/news-perspective/2003/05/sars-virus-can-last-2-days-surfaces-and-feces. – Mod.MPP]

There is specific prevention for SARS virus prevention, that is, targeted preventive measures, that is, prevention through vaccines, but there is no preventive vaccine against SARS. In addition, non-specific preventive measures can be taken, that is, measures to prevent respiratory infections in the spring, such as keeping warm, washing hands, ventilating, avoiding excessive fatigue and contacting patients, and going to less public places.

—
Communicated by:
ProMED-mail
<promed@promedmail.org>

[Having been involved in moderating the SARS-CoV (Severe acute respiratory syndrome – coronavirus) and the MERS-CoV (Middle Eastern Respiratory Syndrome – coronavirus), the type of social media activity that is now surrounding this event, is very reminiscent of the original “rumors” that accompanied the SARS-CoV outbreak. The exception is the transparency of the local government in responding to this currently undiagnosed outbreak. While this report does not contain the tweets, there have been numerous tweets about this as yet undiagnosed outbreak.

Returning to the rumor mill, the discussion of this outbreak (a cluster of 4 or 7 cases) involves an “atypical pneumonia”. and now additional information of apparently 27 cases, with 7 severe cases. We do not know if influenza tests were performed, or if tests for the SARS-CoV are underway (but presumably are according to section [2] media report) in addition to other known (or unknown) respiratory viruses. As one of the tweets mentioned, another unusual pneumonia could be associated with infection with the bacteria _Yersinia pestis_ (plague) which has been diagnosed in Inner Mongolia in November 2019, but presumably has already been ruled out. The most recent report refers to the outbreak as a “viral pneumonia”, suggesting bacterial agents have been ruled out. But has legionellosis been ruled out? or have viral panels been performed?

More information on this outbreak including demographics of cases, possible known common contacts, and a clinical description of the illness would be greatly appreciated. And if results of testing are released.

According to Wikipedia, Wuhan city is the capital city of Hubei province. It has an estimated population over 11 million inhabitants and is the largest city in central China, and the 7th largest city in all of China. Geographically it is located in the eastern Jianghan Plain, on the Yangtze river’s intersection with the Han river.

A map of China showing locations of major cities in China can be found at https://www.chinadiscovery.com/china-maps/city-maps.html.
The HealthMap/ProMED map of China: http://healthmap.org/promed/p/155.
– Mod.MPP]

In flutrackers.com, there is this alert by “alert”, a Senior Moderator with 8747 posts who joined Apr 2009. Notice the “seems incredibly unlikely, unless a laboratory accident has occurred.”

December 31st, 2019, 10:00 AM

SARS (or a related animal coronavirus) seems incredibly unlikely, unless a laboratory accident has occurred. Nevertheless:

https://news.rthk.hk/rthk/en/compone…1-20191231.htm

Some mainland media have also quoted sources from Shanghai’s Tongji University as saying the new cases of pneumonia and the Sars virus appear to be very similar, with both belonging to the coronavirus category.

(It should take very little time, perhaps less than 24 hours, to confirm or rule out SARS and influenza A. – alert)

The original Wuhan city health briefing on 31 Dec 2019 is no longer available at the originally posted link. Here is an English translation:

Wuhan Municipal Health and Health Commission’s briefing on the current pneumonia epidemic situation in our city

Issuing authority: Wuhan City health committee | Published: 2019-12-31 13:38:05 | Hits: 48254 |

Recently, some medical institutions found that many of the pneumonia cases received were related to South China Seafood City. After receiving the report, the Municipal Health and Health Commission immediately launched a case search and retrospective investigation related to South China Seafood City in the city’s medical and health institutions. Twenty-seven cases have been found , of which 7 are in serious condition, and the remaining cases are stable and controllable. Two patients are expected to be discharged in the near future. The clinical manifestations of the cases were mainly fever, a few patients had difficulty breathing, and chest radiographs showed bilateral lung infiltrative lesions. At present, all cases have been isolated for treatment, follow-up investigations and medical observations of close contacts are ongoing, and hygiene investigations and environmental sanitation disposals for South China Seafood City are ongoing.

Wuhan organized consultations with clinical medical, epidemiological, and virological experts from Tongji Hospital, Provincial CDC, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan Infectious Diseases Hospital, and Wuhan CDC. According to the analysis of epidemiological investigations and preliminary laboratory tests, the above cases are considered to be viral pneumonia. Investigations so far have not revealed any apparent human-to-human transmission or infection by medical staff. Detection of the pathogen and investigation of the cause of the infection are ongoing.

Viral pneumonia is more common in winter and spring, and can be spread or outbreak. The clinical manifestations are fever, soreness, dyspnea in a small part, and lung infiltration. Viral pneumonia is related to the virulence of the virus, the route of infection, and the age and immune status of the host. Viruses that cause viral pneumonia are common with influenza viruses, others are parainfluenza virus, cytomegalovirus, adenovirus, rhinovirus, and coronavirus. Confirmation depends on pathogenic tests, including virus isolation, serological tests, and viral antigen and nucleic acid tests. The disease can be prevented and controlled, and indoor air circulation can be prevented to prevent the public places and crowded places where there is no air circulation. People can wear masks when going out. Symptomatic treatment is the main clinical practice, and bed rest is required. If you have the above symptoms, especially the persistent fever, you should go to the medical institution in time.

December 31, 2019

20200506W Day 127: Immunology of COVID-19

2020_Immunology_of_COVID19 — Figure 6: Mechanism of Action for Potential Drug Therapies (reference: https://doi.org/10.1016/j.immuni.2020.05.002)

Today, the randomness of the universe brought an interesting research paper into my sights, Immunology of COVID-19: current state of the science, and so I thought I’d read through it and take notes for the future. It is a critical review of both preprint and peer-reviewed articles by trainees and faculty members of the Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai (PrIISM).

I’ll quote part of the abstract so that you know what you are getting into if you continue reading:

In this review, we summarize the current state of knowledge of innate and adaptive immune responses elicited by SARS-CoV-2 infection and the immunological pathways that likely contribute to disease severity and death. We also discuss the rationale and clinical outcome of current therapeutic strategies as well as prospective clinical trials to prevent or treat SARS- CoV-2 infection.

I’ll be taking various quotes of interest from the paper and giving my thoughts along the way.

China reported this outbreak to the WHO on December 31st, 2019 and soon after identified the causative pathogen as a betacoronavirus with high sequence homology to bat coronaviruses using angiotensin-converting enzyme 2 (ACE2) receptor as the dominant mechanism of cell entry.

The following day, I felt a universe shift and decided to begin blogging about it using this blog which I have used on a very irregular basis. In 2020 Day 9: New Strain of Coronavirus found in Wuhan, China, I was drawn into this story to the point that I researched coronaviruses and wrote the following:

Four identified coronaviruses (HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1) are endemic in humans and cause up to 30% of respiratory tract infections worldwide each year. HCoV-NL63 has been associated with acute laryngotracheitis (croup). Coronoviruses have different tolerances to genetic variability with some (i.e. HCoV-229E) having little genetic variability worldwide and primarily isolated in humans and others (i.e. HCoV-OC43) showing high genetic variability across time and location. Most cases of coronavirus infection are self-limiting and will naturally run its course.

and perhaps because I had also been sick for two weeks, had purchased some Chinese herbs at an Acupuncturist, and had been dissolving zinc under my tongue with OJ as my grandmother had taught me.

Back to the review paper, which begins by discussing our first line of defense against viruses – innate immune sensing. Since SARS-CoV-2 is an RNA virus, the standard innate immune sensing pathways for RNA viruses are identified. Rather than quote from the paper, I’ll list the “characters” involved to familiarize myself with the acronyms:

Pattern Recognition Receptor (PRR) – upon activation, PRRs trigger the secretion of cytokines via a downstream signaling cascade
Retinoic Acid-Inducible Gene I (RIG-I) – a cytosolic PRR that recognizes short viral double-stranded RNA (dsRNA) and other irregular RNAs
RIG-I Like Receptor (RLR) – a type of cytosolic PRR that detect a broad range of viral RNA and activate the Inflammosome.
Toll-Like Receptor (TLR) – a type of PRR, a single-pass membrane-spanning protein often found on sentinel cells (e.g. macrophages, dendritic cells) that recognize PAMPs (e.g. di/triacylated lipopeptides, LPS, Profilin, Flagellin, CpG DNA, ssRNA, dsRNA, 23s rRNA)
Pathogen-Associated Molecular Pattern (PAMP) – a conserved microbial structure of a pathogen
Cytokines
Interferon I (IFN-I)
Interferon III (IFN-III)
Proinflammatory tumor necrosis factor alpha (TNF-α)
Interleukin-1 (IL-1)
Interleukin-6 (IL-6)
Interleukin-18 (IL-18)
Lymphocyte antigen 6 complex locus E (LY6E) – shown to interfere with SARS-CoV-2 spike (S) protein-mediated membrane fusion
Melanoma Differentiation-Associated protein 5 (MDA5) – a RIG-I-like receptor

The paper then continues with techniques that coronaviruses have evolved in order to evade out innate immune system. Studies have found that:

SARS-CoV-1 suppresses IFN release in vitro and in vivo;
Patients with severe COVID-19 have “remarkably impaired IFN-I signatures as compared to mild or moderate cases”;
Coronaviruses encode an endoribonuclease, NSP15, that cleaves 5′ polyuridine byproducts of viral replication, thereby avoiding detection by MDA5;
SARS-CoV-1 N-protein inhibits TRIM25 activation of RIG-I;
MERS-CoV proteins NS4a and NS4b also inhibit RLRs;
SARS-CoV-1 ORF9b suppresses MAVS signaling and SARS-CoV-2 ORF9b interacts, via Tom70, with the signaling adaptor MAVS;
SARS-CoV-1 M protein and MERS-CoV ORF4b inhibit the TBK1 signaling complex and SARS-CoV-2 NSP13 interacts with TBK1 and SARS-CoV-2 NSP14 interacts with an activator of TBK1;
SARS-CoV-1 proteins PLP, N, ORF3b and ORF6 block IRF3 phosphorylation and nuclear translocation;
SARS-CoV-1 PLP and MERS-CoV ORF4b and ORF5 inhibit NF-kB;
SARS-CoV-1 and MERS-CoV NSP1 generally inhibit host transcription and translation;
SARS-CoV-1 ORF6 antagonizes STAT1 nuclear translocation;
SARS-CoV-2 ORF6 shares only 69% sequence homology with SARS-CoV-1 and appears to not antagonize STAT1 nuclear translocation since COVID-19 fails to limit STAT1 phosphorylation as happens with SARS-1;
“Animal models of SARS-CoV-1 and MERS-CoV infection indicate that failure to elicit an early IFN-I response correlates with the severity of disease. Perhaps more importantly, these models demonstrate that timing is key, as IFN is protective early in disease but later becomes pathologic. Perhaps, interferon-induced upregulation of ACE2 in airway epithelia may contribute to this effect. Furthermore, while pathogenic CoVs block IFN signaling, they may actively promote other inflammatory pathways contributing to pathology.”
“SARS-CoV-1 ORF3a, ORF8b, and E proteins enhance inflammasome activation, leading to secretion of IL-1β and IL-18, which are likely to contribute to pathological inflammation. Similarly, SARS-CoV-2 NSP9 and NSP10 might induce IL-6 and IL-8 production, potentially by inhibition of NKRF, an endogenous NF-kB repressor. Collectively, these pro-inflammatory processes likely contribute to the ‘cytokine storm’ observed in COVID-19 patients and substantiate a role for targeted immunosuppressive treatment regimens.”

The paper discusses the roll in COVID-19 of myeloid cells, innate lymphoid cells, and T cells. It then discusses the B Cell response:

The humoral immune response is critical for the clearance of cytopathic viruses and is a major part of the memory response that prevents reinfection. SARS-CoV-2 elicits a robust B cell response, as evidenced by the rapid and near-universal detection of virus- specific IgM, IgG and IgA, and neutralizing IgG antibodies (nAbs) in the days following infection. The kinetics of the antibody response to SARS-Cov-2 are now reasonably well described (Huang et al., 2020a).

Similar to SARS-CoV-1 infection, seroconversion occurs in most COVID-19 patients between 7 and 14 days after the onset of symptoms, and antibody titers persist in the weeks following virus clearance.

Antibodies binding the SARS-CoV-2 internal N protein and the external S glycoprotein are commonly detected.

The receptor binding domain (RBD) of the S protein is highly immunogenic and antibodies binding this domain can be potently neutralizing, blocking virus interactions with the host entry receptor, ACE2.

Anti-RBD nAbs are detected in most tested patients.

Although cross-reactivity to SARS-CoV-1 S and N proteins and to MERS- CoV S protein was detected in plasma from COVID-19 patients, no cross-reactivity was found to the RBD from SARS-CoV-1 or MERS-CoV. In addition, plasma from COVID-19 patients did not neutralize SARS-CoV-1 or MERS-CoV

Regarding long-term protection of antibodies, which would also likely be true of a vaccine that induced antibodies:

Studies of common coronaviruses, SARS-CoV-1 and MERS-CoV indicate that virus specific antibody responses wane over time, and, in the case of common coronaviruses, result in only partial protection from reinfection. These data suggest that immunity to SARS-CoV-2 may diminish following a primary infection and further studies will be required to determine the degree of long-term protection.

But maybe having antibodies is not necessarily a good thing:

Several studies have demonstrated that high virus-specific antibody titers to SARS- CoV-2 are correlated with greater neutralization of virus in vitro and are inversely correlated with viral load in patients (Figure 4) (Okba et al., 2020; Wölfel et al., 2020; Zhao et al., 2020a). Despite these indications of a successful neutralizing response in the majority of individuals, higher titers are also associated with more severe clinical cases (Li et al., 2020b; Okba et al., 2020; Zhao et al., 2020a; Zhou et al., 2020a), suggesting that a robust antibody response alone is insufficient to avoid severe disease.

This was also observed in the previous SARS-CoV-1 epidemic, where neutralizing titers were found to be significantly higher in deceased patients compared to patients who had recovered (Zhang et al., 2006). This has led to concerns that antibody responses to these viruses may contribute to pulmonary pathology, via antibody-dependent enhancement (ADE) (Figure 4).

The authors specifically mention vaccine development:

Vaccine trials will need to consider the possibility of antibody-driven pathology upon antigen re-challenge; strategies using F(ab) fragments or engineered Fc monoclonal antibodies may prove particularly beneficial in this setting (Amanat and Krammer, 2020).

They then continue with a discussion of predictors of COVID-19 disease risk and severity. Some associations that have been found:

Blood group A is associated with a higher risk of acquiring COVID-19 than non-A blood groups. Blood group O is associated with a lower risk of acquiring COVID-19 than non-O blood groups. Similar results were found for SARS-1.
“The most consistent findings across the different studies were elevated levels of CRP, LDH and D-dimer, as well as decreased blood platelet and lymphocyte counts (Yan et al., 2020b; Zhou et al., 2020d).”
“elevated IL-6 levels were detected in hospitalized patients, especially critically ill patients, in several studies, and are associated with ICU admission, respiratory failure, and poor prognosis (Chen et al., 2020f; Huang et al., 2020b; Liu et al., 2020f)”
“Total T cell, helper T cell, and suppressor T cell counts were significantly lower, and the TH/TS ratio was significantly higher in patients who died from infection, as compared to patients who were discharged.”
“direct correlation with patient viral load will be important to provide a greater understanding of underlying causes of morbidity and mortality in COVID-19 and the contribution of viral infectivity, hyper-inflammation and host tolerance (Medzhitov et al., 2012).”
“lymphopenia, increases in proinflammatory markers and cytokines and potential blood hypercoagulability characterize severe COVID-19 cases with features reminiscent of cytokine release syndromes. This correlates with a diverse clinical spectrum ranging from asymptomatic to severe and critical cases. During the incubation period and early phase of the disease, leukocyte and lymphocyte counts are normal or slightly reduced. After SARS-CoV-2 binds to ACE2 overexpressing organs, such as the gastrointestinal tracts and kidneys, increases in non-specific inflammation markers are observed. In more severe cases, a marked systemic release of inflammatory mediators and cytokines occurs, with corresponding worsening of lymphopenia and potential atrophy of lymphoid organs, impairing lymphocyte turnover (Terpos et al., 2020).“

Next, the authors discuss small molecules that inhibit one or more stages of the virus life cycle. Antivirals for SARS-CoV-1, MERS-CoV, and other viruses have been tested against SARS-CoV-2. These fall into three categories: broad spectrum, protease inhibitors, and RdRp inhibitors.

Broad spectrum antivirals that work against other RNA viruses have been evaluated with SARS-CoV-2. Quoting the paper:

A number of small molecules with known antiviral activity against other human RNA viruses are being evaluated for efficacy in treating SARS-CoV-2. The ribonucleoside analog β-D-N4-hydroxycytidine (NHC) reduced viral titers and lung injury in mice infected with SARS-CoV-2 via introduction of mutations in viral RNA (Sheahan et al., 2017). Further, an inhibitor of host DHODH, a rate-limiting enzyme in pyrimidine synthesis, was able to inhibit SARS-CoV-2 growth in vitro with greater efficacy than remdesivir or chloroquine (Wang et al., 2020e; Xiong et al., 2020). Merimepodib, a non-competitive inhibitor of the enzyme Inosine-5′-monophosphate dehydrogenase (IMPDH), involved in host guanosine biosynthesis, is able to suppress SARS-CoV-2 replication in vitro (Bukreyeva et al., 2020). Finally, N-(2-hydroxypropyl)-3-trimethylammonium chitosan chloride (HTCC), which was previously shown to efficiently reduce infection by the less pathogenic human coronavirus HCoV-NL63, was also found to inhibit MERS-CoV and pseudotyped SARS-CoV-2 in human airway epithelial cells (Milewska et al., 2020).

Of nine existing HIV protease inhibitors (nelfinavir, lopinavir, ritonavir, saquinavir, atazanavir, tipranavir, amprenavir, darunavir, and indinavir), the most potent inhibitor in SARS-CoV-2 infected Vero cells was found to be nelfinavir.

RdRP is the coronavirus RNA-dependent RNA polymerase. It catalyzes the synthesis of viral RNA. As an adenosine triphosphate analog, Remdesivir binds to RNA strands and prevents additional nucleotides from being added, causing the termination of viral RNA transcription. Remdesivir has already been shown to be effective against SARS-1 and MERS in animal models. A study on 12 rhesus macaques infected with SARS-CoV-2 showed “a reduction in lung viral loads and pneumonia symptoms, but no reduction in virus shedding”. It also provided “evidence that if administered early enough, Remdesivir may be effective at treating SARS-CoV-2 infections.”

Antiviral clinal trials were discussed and a random control trial of Remdesivir is worth mentioning:

Preliminary results from a larger NIAID RCT with more than 1000 patients were announced with remdesevir to be associated with quicker time to recovery: 11 days compared with 15 days (Ledford, 2020). A non-significant benefit in mortality was also noted and the trial was stopped early to allow access to remdesivir in the placebo arm. Complete safety data and full publication are awaited but this study offers encouraging results and have resulted in an FDA Emergency Use Authorization for remdesivir in hospitalized COVID-19 patients.

One of the most controversial treatments, hydroxychloroquine, was discussed under the heading “Therapeutic Immunomodulation for COVID-19 Treatment”. To avoid missing or misinterpreting anything here, I am including the full quote from the paper on modes of action and immunological impact:

Chloroquine (CQ) and its derivative hydroxychloroquine (HCQ) have gained traction as possible therapeutics for COVID-19. Both drugs are used as antimalarial agents and as immunomodulatory therapies for rheumatologic diseases. However, the application of CQ and HCQ to COVID-19 stems for their past use as antivirals (Savarino et al., 2003), including for SARS-CoV-1 (Keyaerts et al., 2004; Vincent et al., 2005). CQ and HCQ interfere with lysosomal activity and have been reported to have immuno-modulatory effects. CQ augments antigen processing for MHC class I and II presentation, directly inhibits endosomal TLR7 and TLR9, and enhances the activity of regulatory T cells (Garulli et al., 2008; Lo et al., 2015; Schrezenmeier and Dörner, 2020; Thomé et al., 2013a, 2013b). Early studies involving in vitro infection of host cells with SARS-CoV-2 demonstrated that both CQ and HCQ significantly impact endosomal maturation, resulting in increased sequestration of virion particles within endolysosomes. However, there has been conflicting evidence whether CQ is more potent than HCQ in reducing viral load (Liu et al., 2020d; Wang et al., 2020b; Yao et al., 2020a). Notably, one group reported that treatment of infected cells with HCQ before and during infection significantly reduced viral load, suggesting that combined prophylactic and therapeutic HCQ use yields maximum efficacy (Clementi et al., 2020). To better understand host immune responses to treatment, one group compared bulk transcriptomic changes in primary PBMCs treated with HCQ for 24 hours to PBMCs from confirmed SARS-CoV-2 positive patients and controls, followed by a comparison of HCQ treated primary macrophages to BAL and postmortem lung biopsies from COVID-19 patients (Corley et al., 2020). Across all comparisons, there was minimal overlap between host differential gene expression and genes altered by in vitro HCQ treatment. Thus, the potential mechanistic action of HCQ in the context of SARS-CoV-2 remains poorly defined.

and also on evaluation of HCQ efficacy in clinical trials:

Despite the apparent widespread use of HCQ and CQ to treat COVID-19 (Figure 6B), few controlled clinical trials have been performed so far and thus the potential benefits of these drugs for COVID-19 remains controversial. One of the earliest trials (2020- 000890-25) was a single-arm, open label trial of 600mg daily HCQ in 20 COVID-19 patients. They reported that HCQ alone, or in combination with the antibiotic azithromycin (AZ), reduced viral load by day 6 (Gautret et al., 2020a). A follow up trial in 80 patients treated with HCQ + AZ reported that 93% of patients had a negative PCR result on day 8 of treatment, and 81.3% were discharged within 10 days of treatment. However, it is important to note that both trials had no control arms (Gautret et al., 2020b). Rigorous statistical analyses by others that accounted for the patients excluded from the original analysis found limited evidence for HCQ monotherapy (Hulme et al., 2020; Lover, 2020). A double blind rRCT assessed HCQ monotherapy in the treatment of mild COVID-19 (ChiCTR2000029559) (Chen et al., 2020h). A total of 62 patients were enrolled; the treatment arm received 400 mg HCQ daily over 5 days. By day 6, patients who received HCQ had clinical resolution on average one day earlier than controls; no patients progressed to severe disease compared to 4 patients in the control arm. In a smaller RCT treated 30 patients with mild COVID-19 (NCT04261517) with 400 mg HCQ for 7 days, there were no significant differences in the number of patients with negative PCR results on day 7 (all but one positive), median duration of hospitalization, time to fever resolution, or progression of disease on chest CT (Chen et al., 2020c). The largest RCT to date enrolled 150 patients with mild COVID-19 across 16 centers in an open label trial of HCQ + standard of care (ChiCTR2000029868). There were no significant differences between groups in conversion to negative SARS-CoV-2 RT-PCR result on day 28 or rate of symptom resolution; there were significantly more adverse events in the HCQ arm, though largely non-serious; they reported some evidence for faster normalization of C-reactive protein in the patients who received HCQ plus standard of care, but this finding was not significant (Tang et al., 2020b). A meta- analysis including most of the studies described here found no clinical benefits to patients receiving standard of care plus an HCQ regimen (Shamshirian et al., 2020).

Two studies have assessed HCQ efficacy in severe COVID-19. In a prospective study of 11 patients who had received 600 mg HCQ over 10 days with AZ on days 1-5, there were several patients with worsening clinical status and one death; 8/10 patients had a positive PCR result on day 10 (Molina et al., 2020). An ongoing double blind RCT of patients with severe COVID-19 (NCT04323527) randomized 81 patients into high dose HCQ (600 mg 2x/d for 10 days) or low dose (450 mg/day for 5 days) treatment groups (Borba et al., 2020). Recruitment into the high dose arm was halted prematurely due to poor safety outcomes. There was no significant difference in negative PCR results on day 4 or need for mechanical ventilation on day 6. Taken together, the clinical trials performed thus far to evaluate the efficacy of HCQ ± AZ for COVID-19 have not demonstrated clear evidence of clinical benefit in patients with severe disease. A search of ClinicalTrials.gov on April 27, 2020 found 140 clinical trials investigating HCQ. This number is rapidly growing, indicating the heightened interest in this therapeutic and pressing need for evidence-based recommendations.

I’ve asked a number of questions about corticosteroids online and have gotten conflicting responses. My partner, who got sick after flying from the Bay Area in mid February, was prescribed prednisone after developing shortness of breath. She was tested twice for the flu. The first time came back negative and the second time, 5 days later, came back positive for Flu A (H1N1). I have been wondering whether people with COVID-19 are being treated with corticosteroids – possibly without having a confirmed COVID-19 diagnosis. To avoid missing or misinterpreting, the full quote from the paper follows:

Because of their anti-inflammatory activity, corticosteroids (CS) are an adjuvant therapy for ARDS and cytokine storm. However, the broad immunosuppression mediated by CS does raise the possibility that treatment could interfere with the development of a proper immune response against the virus. A meta-analysis of 5,270 patients with MERS-CoV, SARS-CoV-1, or SARS-CoV-2 infection found that CS treatment was associated with higher mortality (Yang et al., 2020c). A more recent meta-analysis of only SARS-CoV-2 infection assessed 2,636 patients and found no mortality difference associated with CS treatment, including in a subset of patients with ARDS (Gangopadhyay et al., 2020). Other studies have reported associations with delayed viral clearance and increased complications in SARS and MERS patients (Sanders et al., 2020). In fact, the interim guidelines updated by the WHO on March 13, 2020 advise against giving systemic corticosteroids for COVID-19 (World Health Organization, 2020a). Yet, new data from COVID-19 are conflicting.

One group reported no significant difference in time to viral clearance between patients who received methylprednisolone orally (mild disease) or IV (severe) and those who did not (Fang et al., 2020). Retrospective studies from groups in China report that patients who were transferred to the ICU were less likely to have received CS (Wang et al., 2020b) and that patients with ARDS who received methylprednisolone had reduced mortality risk (Wu et al., 2020a). In contrast, another retrospective analysis found that patients who received CS were more likely to have either been admitted to the ICU or perished, although the CS treated group also had significantly more comorbidities

(Wang et al., 2020c). A smaller observational study of 31 patients found no association between corticosteroid treatment and time to viral clearance, length of hospital stay, or symptom duration (Zha et al., 2020). A larger study of adjuvant CS in 244 patients with critical COVID-19 found no association with 28-day mortality; subgroup analysis of patients with ARDS found no association between treatment with CS and clinical outcomes (Lu et al., 2020b). They also found that increased dosage was significantly associated with increased mortality risk. A retrospective review of 46 patients, of whom 26 received IV methylprednisolone, found that early, low-dose administration significantly improved SpO2 and chest CT, time to fever resolution, and time on supplemental oxygen therapy (Wang et al., 2020h). Others have published perspectives in support of early (Lee et al., 2020) and short-term, low dose administration (Shang et al., 2020) based on anecdotal evidence, but not clinical trials. Most of the current data on CS use in COVID-19 are from observational studies, and support either modest clinical benefit or no meaningful effects. Larger RCTs are necessary to understand the risks and benefits of CS for these patients; there are 22 trials evaluating various corticosteroids registered on ClinicalTrials.gov as of April 27, 2020.

The authors next discussed therapies directed at cytokines and discussed cytokine blockade. Some interesting quotes:

Hyperinflammatory responses and elevated levels of inflammatory cytokines, including interleukins (IL)-6, 8, and 10, have been shown to correlate with COVID-19 severity.

The drivers of this cytokine storm remain to be established, but they are likely triggered initially by a combination of viral PAMPs and host danger signals.

The heterogeneous response between patients suggests other factors are involved, possibly including the SARS-CoV-2 receptor, ACE2.

Regarding clinical trials:

The commercial anti-IL-6R antibodies tocilizumab (Actemra) and sarilumab (Kevzara), and the anti-IL-6 antibody siltuximab (Sylvant), are now being tested for efficacy in managing COVID-19 CRS and pneumonia in 13 ongoing clinical trials.

To date, only one group has reported preliminary results from a cohort of 20 COVID- 19 patients treated with a single administration of tocilizumab (400 mg, IV), along with Lopinavir, methylprednisolone, and oxygen therapy (ChiCTR2000029765).

A second report described an association between use of tocilizumab and reduced likelihood of ICU admission and mechanical ventilation.

Other therapies discussed are neutralizing antibodies and convalescent plasma therapy. A SARS-CoV-2 neutralizing antibody was found out of 25 different antibodies isolated from the memory B cells of a survivor of SARS-1. Seven additional of the 25 were found to bind, but not neutralize. Regarding convalescent plasma (CP) therapy:

Despite the current lack of appropriately controlled trials, CP therapy has been previously used and shown to be beneficial in several infectious diseases such as the 1918 influenza pandemic (Luke et al., 2006), H1N1 influenza (Hung et al., 2011), and SARS-CoV-1 (Arabi et al., 2016).

CP therapy has also been proposed for prophylactic use in at-risk individuals, such as those with underlying health conditions or health care workers exposed to COVID-19 patients. The FDA has approved the use of CP to treat critically ill patients (Tanne, 2020). Determining when to administer the CP is also of great importance, as a study in SARS-CoV-1 patients showed that CP was much more efficient when given to patients before day 14 day of illness (Cheng et al., 2005b), as previously shown in influenza (Luke et al., 2006). This study also showed that CP therapy was more efficient in PCR positive, seronegative patients.

Finally, the authors discussed vaccine development. Some key points from this discussion are:

Although vaccination has a long and successful history as an effective global health strategy, there are currently no approved vaccines to protect humans against coronaviruses (André, 2003).

Previous work after the SARS-CoV-1 and MERS- CoV epidemics has provided a foundation on which many current efforts are currently building upon, including the importance of the S protein as a potential vaccine.

While the S protein has been found to be the most immunodominant protein in SARS- CoV-2, the M and N proteins also contain B and T cell epitopes, including some with high conservation with SARS-CoV-1 epitopes (Grifoni et al., 2020).

Regarding the vaccine pipeline:

For SARS-CoV-1 and MERS-CoV, animal studies and phase I clinical trials of potential vaccines targeting the S protein had encouraging results, with evidence of nAb induction and induction of cellular immunity (Lin et al., 2007; Martin et al., 2008; Modjarrad et al., 2019).

These findings are being translated into SARS-CoV-2 vaccine development efforts, hastening the progress drastically.

The University of Pittsburgh is also looking to move their microneedle array vaccine candidate containing a codon-optimized S1 subunit protein into clinical trials (Kim et al., 2020).

Although some of these vaccine candidates are based on platforms that have been used or tested for other purposes, there remain questions regarding their safety and immunogenicity, including the longevity of any induced responses, that will require continual evaluation.

Challenges and concerns regarding vaccine development:

One such concern involves the accumulating data supporting the initial assessment that COVID-19 is disproportionately severe in older adults. In conjunction with the large body of work related to immune-senescence, these findings indicate that vaccine design should take into consideration the impact of aging on vaccine efficacy (Nikolich-Žugich, 2018).

Furthermore, questions remain regarding the possibility of antibody-dependent enhancement of COVID-19, with in vitro experiments, animal studies, and two studies of COVID-19 patients supporting this possibility (Cao, 2020; Tetro, 2020; Zhang et al., 2020a; Zhao et al., 2020a).

Assuming vaccine candidates are identified that can safely induce protective immune responses, additional major hurdles will be the production and dissemination of a vaccine.

The concluding remarks of the authors include these notable ones:

The pathology of severe cases of COVID-19 do indeed resemble certain immunopathologies seen in SARS-CoV-1 and MERS-CoV infections, like CRS.

However, in many other ways, immune responses to SARS-CoV-2 are distinct from those seen with other coronavirus infections.

Significant proportions of individuals are asymptomatic despite infection.

SARS-CoV-2 has a longer incubation period and higher rate of transmission than other coronaviruses.

It is imperative that immune responses against SARS-Cov-2 and mechanisms of hyperinflammation-driven pathology are further elucidated to better define therapeutic strategies for COVID-19.

Since Figure 6 was used above, here is the description from the paper for Figure 6:

Figure 6. Available therapeutic options to manage COVID-19 immunopathology and to deter viral propagation.
A. Rdrp inhibitors (Remdesivir, Favipiravir), protease inhibitors (Lopinavir/Ritonavir), and anti-fusion inhibitors (Arbidol) are currently being investigated in their efficacy in controlling SARS-CoV-2 infections. B. CQ and HCQ increase the pH within lysosomes, impairing viral transit through the endolysosomal pathway. Reduced proteolytic function within lysosomes augments antigen processing for presentation on MHC complexes and increases CTLA4 expression on Tregs. C. Antagonism of IL-6 signaling pathway and of other cytokine-/chemokine-associated targets has been proposed to control COVID-19 CRS. These include secreted factors like GM-CSF that contribute to the recruitment of inflammatory monocytes and macrophages. D. Several potential sources of SARS-CoV-2 neutralizing antibodies are currently under investigation, including monoclonal antibodies, polyclonal antibodies, and convalescent plasma from recovered COVID-19 patients.
Abbreviations: GM-CSF, granulocyte-macrophage colony-stimulating factor; CQ, chloroquine; HCQ, hydroxychloroquine; RdRp, RNA-dependent RNA polymerase.

20200501F Day 122: El Salchichero Meat Market, Kim Jong Un alive, and Biden’s #MeToo moment felt 27 yrs ago

Meat selection at El Salchichero, Santa Cruz, CA – May 1st, 2020

Santa Cruz, CA: A few days ago, President Trump issued an executive order to protect meat supplies. At El Salchichero in Santa Cruz, CA, there was still a good selection of meat, including steak cuts and a great variety of chicken and pork sausages.

On the entrance was posted signs saying everyone over age 12 must wear a face covering, which could be a bandana, neck gaiter, or home made mask.

El Salchichero, Santa Cruz, CA – May 1st, 2020

Today, I moved out of the studio room that I rented the last few weeks. I can feel a universe in which I was quarantined there, because that’s how it felt. Even though the studio was in the back of a house, I didn’t engage with the other housemates. The door to the house was even duct taped to minimize air flow between the house and the studio. I am now back to living in a community house and feeling the universes in which I’m back in Texas.

The stock market was down almost 3% today.

North Korean leader Kim Jong Un made his first public appearance in weeks. Four days ago, when asked about rumors of Kim Jong Un’s death, Trump said that he knew of Kim Jong Un’s condition, but couldn’t talk about it. Today, Trump said that he make talk to Kim Jong Un this weekend.

Joe Biden and Tara Reade are in the news regarding her accusation that he sexual assault ed her 27 years ago. She has given a detailed account of the assault, to which Biden has replied “I am saying unequivocally. It never, never happened, and it didn’t.” Biden also said today “I am absolutely positive that nobody that I am aware of has been made aware of any complaint — a formal complaint — or complaint — made by Tara Reade against me at the time this allegedly happened 27 years ago until I announced for — I guess it was of April or May of this year.”

There are interesting parallel universes around the Biden/Reade story. One is that Reade has changed her name and so in some universes is known by a different name. The other is Reade’s mother called into Larry King Live and asked for help. There is now videos of this episode, from 27 years ago, posted on YouTube. It amazes me how 27 years ago, Tara Reade’s Mom felt the universe today and made the decision to call into Larry King Live.

20200430h Day 121: Last day at the beach in some universes

Capitola Beach, Capitola CA – April 30, 2020

Universes continue to collide. In many universes, today is the last day that beaches are open in California. NPR published a story about this today (Calif. Governor Expected To Order Closure Of All Beaches And State Parks). The story was about a memo sent on Wednesday to the California Police Chiefs Association. The memo read:

After the well-publicized media coverage of overcrowded beaches this past weekend, in violation of Governor Newsom’s Shelter in Place Order, the Governor will be announcing [Thursday] that ALL beaches and all state parks in California will be closed, effective Friday, May 1st.

Also Today, NPR published another story – this time without ALL emphasize, and instead referencing only Orange County (Governor Temporarily Closes All Beaches And State Parks in Orange County, Calif.):

“We’re gonna do a hard close in that part of the state, just in the Orange County area. We’re working with the county,” the governor announced Thursday.

In Santa Cruz County, a new shelter-in-place order is in place starting May 1st. Regarding beaches, the new order is more specific:

What does the modified SIP order say about beaches?

Beaches will be closed 11-5 but may be traversed during these hours for the purposes of water sports.

Beach parkways will remain open for use during these hours, as will the water.

Outside of these hours, beaches are only open for recreational activities to promote physical and mental health, such as walking, running, cycling and water sports.

At no time will sitting, lying, standing, sunbathing, sightseeing, and other non-exercise activities be allowed at beaches. No umbrellas, shade structures, tents, barbeques and grills, coolers, beach chairs, or other conveyances for sitting or lying will be allowed on the beaches.

The differences in the new order are:

What is different in the April 30th Santa Cruz County order from the March 31ST order?

All essential businesses will be required to follow minimum basic safety precautions, including physical distancing and face covering requirements, and post health and safety information (Appendix A).

Allows non-emergent healthcare services in accordance with State directives and guidance, including elective surgeries and other services which may have been delayed. Healthcare facilities must comply with State guidance around Personal Protective Equipment and other measures.

Permits construction in accordance with State directives and guidance, with proper physical distancing protocols (Appendix B).

Permits real estate transactions in accordance with State directives and guidance.

Permits individuals to move to a new residence; however, if moving into or out of Santa Cruz County, individuals are strongly encouraged to self-quarantine in their new residence for 14 days.

Permits landscaping and gardening, tree trimming, and other outdoor services.

Permits wholesale and retail nurseries, and other businesses that support outdoor services.

Allows the use of golf courses and driving ranges with documented protocols that are outlined Appendix C of the revised order.

Allows stable groups of 12 or fewer children for recreational or educational purposes. Such activities must be carried out in stable, “closed” groups of 12 of fewer, as described in the Order.

Outdoor recreational areas and activities with high-touch equipment or that encourage gathering such as team sports, pools and playgrounds will not be permitted to return at this time.

Adds those who manufacture, distribute, sell, rent, lease, repair or maintain vehicles and other transportation equipment as essential businesses, with social distancing requirements.

Includes fabric and craft stores as an essential business for purposes of supplying materials to create face coverings and other personal protective equipment (PPE).

20200426u Day 117: I can see the beach waves at the end of the wormhole

Santa Cruz, CA: Today, I wanted to make it into the water, so I drove to Bonny Doon Beach. The parking lot there was full. It was one of the few open roadside parking lots I saw. The rest of the parking lots were closed and people were parking along the side of the road. At the beaches, it almost felt like pre-pandemic. While there were a few people wearing face masks, most did not. People did try to maintain six foot distance between one another for the most part. There didn’t seem to be any concern when passing each other on the trails.

I hear from my Mom that masks are going to be mandatory in her county in Texas tomorrow – two days after masks were required here.

20200425S Day 116: Everyone Must Wear a Face Mask

Farmers Markets in Santa Cruz, CA on April 25, 2020 – First day of Santa Cruz County order requiring the wearing of face masks while in public

Today, everyone was wearing masks at the Farmers Markets. There were one way lines with people separated by six feet. Later, in the afternoon, I rode up highway 1 and the cars were also social distancing at six feet between automobiles – it was packed! Since the park parking lots were closed, everyone was parking on the side of the road. It felt like the 4th of July. You could tell that everyone is done with sheltering in place and ready to return to normal activities, especially when they can head to a sunny beach. Everything is still feeling to me that I will be out of this pandemic wormhole by June 8th. I’m still curious how life will be different in the new universe I’m surfing to.

20200422W Day 113: No Unnecessary Physical Contact on Aptos Street

20200422_AptosStBBQ

Aptos, CA: Social distancing guidelines at Aptos Street BBQ include guidelines that:

EMPLOYEES and CUSTOMERS SHOULD: Not shake hands or engage in any unnecessary physical contact

As I surf back to a universe in which I can eat BBQ inside a restaurant, like Black’s BBQ in Austin, Texas, I thought I’d check to see how things were at Aptos Street BBQ. You can no longer drink a beer inside and the selection of beers on tap is reduced. You can buy bottles and cans of beer and purchase BBQ-to-go.

Face coverings are now required in order to enter the restaurant. And no more horsin’ around with “unnecessary physical contact”.

In RV news, the water on the floor of my RV appears to be coming from the AC unit.

20200422_RV_AC_leak

20200419u Day 110: Almost 2.5M confirmed COVID-19 Cases Worldwide

Two days ago in 20200417F Day 108: Surfing the Multiverse back through a Pandemic Wormhole, I noted:

It is looking now that the 10x/month rate is still on track from March 19 and the confirmed COVID-19 cases are expected to hit 2.5M by April 19.

and data from https://www.worldometers.info/coronavirus/ shows 2,406,575 worldwide confirmed cases of COVID-19. I’m happy to see that the number of total cases is leveling off. One warning sign is the growing number of cases in Russia. If COVID-19 outbreaks are not contained quickly in Russia, then there could be 10x the number of cases in Russia by May 19th. As I continue surfing to a universe where SARS-CoV-2 returns to the wild, then something needs to change in Russia because the number of cases and deaths are currently increasing rapidly.

Screen Shot 2020-04-20 at 9.51.50 AM — Data for April 19, 2020, from https://www.worldometers.info/coronavirus/

In local news, I went on a bike ride with my brother. There were quite a few other bikers and life is beginning to return to normal in Santa Cruz. The beaches and walk along the beach were also full. Santa Cruz County has 104 cases and 2 deaths confirmed for COVID-19 out of a population of 300,000. It will be interesting to see what the serological testing shows in the county. New York plans to begin serological testing on Monday.

20200418S Day 109: Review of Recent COVID-19 Related Research

Santa Cruz, CA: Today has been a slow day, like all days under shelter-in-place seem to be. I walked to the farmer’s market and the grocery store. Both places had a much larger number of people wearing masks – about 60%. Social distancing was enforced through one-way aisles and tape markers on the ground.

It is still very difficult for me to be productive. Twitter is my main time suck at the moment. There is so much posting of what appears to me as misinformation. I think it’s time to educate myself and at least see what people are saying who have taken the time to write up and submit research papers.

The first paper I’d like to review is Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates. The authors of this paper are trying to determine the structural similarity of ACE2, specifically the part of ACE2 involved in binding to SARS-CoV-2, across mammals and vertebrates. The first thing I notice is that the authors are from a diverse group of worldwide top-notch universities and organizations. Some points of interest to me are:

There are 25 amino acids at the ACE2 binding site which are important for binding to SARA-CoV-2.
Molecular phylogenetics shows that at least one human coronavirus (HCov-OC43) may have originated in cattle or swine. HCov-OC43 is a beta coronavirus that is now believed to have been the cause of an influenza pandemic in 1889-90.
18 out of 19 catarrhine primates analyzed scored “very high” and also had 25/25 identical binding residues for binding; and the 19th, the Angola colobus, scored “high” with at least 20/25 identical binding residues.
3/3 species of Cervid deer and 12/14 cetacean species also scored “high”.
Camels and pigs both scored “low”.
9/9 species of Felids scored “medium” – there have been reports that a domestic cat became infected with SARS-CoV-2.
3/3 species of pangolins scored “low” or “very low” for ACE2 binding.
The ACE2 RBD residues critical for effective binding to SARS-CoV-2 S protein are S19, Q24, T27, F28, D30, K31, H34, E35, E37, D38, Y41, Q42, L45, L79, M82, Y83, N330, K353, G354, D355, R357, and R393. The ACE2 RBD glycosylation sites N53, N90 and N322 were also included.
“Very High” scores have at least 23/25 matching residues, and 7/7 of the residues K353, K31, E35, M82, N53, N90 and N322, and do not have N79, and the up to 2 non-matching residues have conservative substitutions.
“High” scores have at least 20/25 matching residues, have K353, have only conservative substitutions at K31 and E35, do not have N79, and up to one non-conservative substitutions among the up to 5 non-identical residues.
“Medium” scores have at least 20/25 matching residues, only conservative substitutions at K353, K31, and E35, and up to two non-conservative substitutions in the 5 non-identical residues.

The second paper I noticed was Comparative dynamic aerosol efficiencies of three emergent coronaviruses and the unusual persistence of SARS-CoV-2 in aerosol suspensions. The title says it all – the researches found that SARS-CoV-2 “generally maintains infectivity when airborne over short distances, in contrast to either comparator betacoronavirus”.

A third paper, Regulation of angiotensin converting enzyme 2 (ACE2) in obesity: implications for COVID-19, found increased expression of lung ACE2 in obese mice.

A fourth paper, Transcriptional Difference between SARS-COV-2 and other Human Coronaviruses Revealed by Sub-genomic RNA Profiling, found that “SARS-COV-2 has significantly elevated expression of the Spike gene, which may contribute to its high transmissibility.”

In a fifth paper, COVID-19 pandemic: A Hill type mathematical model predicts the US death number and the reopening date, the author predicts that “by the mid June or early July 2020, the outbreak will strongly decay and the US will have about 800K confirmed cases and less than 50K deaths.”

In a sixth paper, Delayed clearance of SARS-CoV-2 in male compared to female patients: High ACE2 expression in testes suggests possible existence of gender-specific viral reservoirs, the authors find that males have delayed viral clearance after infection (by 2 days) and that the testes was one of the highest tissue sites of ACE2 expression.

And finally, a seventh paper which seems like a good one to stop with for now: Revealing variants in SARS-CoV-2 interaction domain of ACE2 and loss of function intolerance through analysis of >200,000 exomes. This one has a lay summary which sounds significantly enough to me on first reading to quote in entirety here:

Lay summary: Our researchers took a look at a sequence of DNA known as the ACE2 gene. This gene is most well known for its role in regulating blood pressure. But in recent times, it’s drawn a lot of attention from the scientific community because it may also serve as a doorway of sorts, enabling viruses like SARS-CoV-2 to infect cells. Our researchers looked at the ACE2 gene in more than 200,000 people, comparing their exact DNA sequences to see where there are differences among people. Variation in the DNA sequence of a gene is common and is sometimes meaningless. But other times, small changes in the DNA sequence can alter the protein that is made from that gene. In this case the ACE2 gene makes the ACE2 protein, which is what the SARS-CoV-2 virus interacts with. We found a lot of variation between individuals and checked to see if that variation coincided with any traits (i.e., people with variant X tend to have high blood pressure more often than people without variant X). All of the traits we looked at were non-COVID-19-related traits, meaning we haven’t asked these people anything about COVID-19 yet (this is because these DNA sequences were collected before the pandemic). We found that there are a number of variations observed among people in a specific part of the ACE2 gene. These variations are expected to alter the shape or functionality of a specific part of the ACE2 protein: The part that interacts with the SARS-CoV-2 virus. We don’t yet know what the real-life significance of this variation is, but it’s possible that these variants decrease the protein’s ability to interact with the SARS-CoV-2 virus, thus decreasing the person’s likelihood of being infected. We can speculate that there will be a spectrum of vulnerability to COVID-19 among people, where some people are more vulnerable than others, and that variants in this part of the ACE2 gene may be one of the reasons. The research we presented here shines a light on this part of the ACE2 gene and may give future researchers a direction to go in as they try to figure out what makes people vulnerable to COVID-19 and similar viruses.

Some key points mentioned in this paper:

ACE2 is on the X chromosome and because males have only one X chromosome, males carry only one copy of the ACE2 gene.
332 coding variants were found that affected the ACE2 coding sequence. 16 of these were loss of function mutations. 11 coding variants changed specific amino acids that interact with SARS-CoV-2. 29 coding variants were nearby, within two amino acids.
Two of the most found alleles are chrX:15600835:T:C / p.K26R (allele frequency 0.5%), chrX:15600857:A:G / p.S19P (very rare except in African ancestry with allele freq of 0.1-0.2%)
A few more residues of interest that I saw were G352V, D355N, A396T, N397D, F400L, T27A, E35K, E37K, L39P, F40L, S43N, A80G, M82I, P84A, and L27F (male only).