Paul Has Measles is a free children's book about viruses and vaccines available in 16 languages (link). Paul Stays Home is a free children's book about COVID-19 (link).

How to End this Pandemic

by Gertrud U. Rey

As of today, SARS-CoV-2 has infected 18.7 million people and caused 700,000 deaths worldwide. The most realistic way to quickly curb the spread of the virus would require daily identification and isolation of individuals who are contagious, a process that is hampered by cumbersome sampling and testing methods with slow turnaround times. 

The predominant test for diagnosing SARS-CoV-2 infection is a highly sensitive assay called quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR). To carry out a SARS-CoV-2 qRT-PCR test, a mucus sample is processed to inactivate virus particles and extract the viral RNA. The RNA is converted to DNA (the reverse transcription step), which is then amplified during the polymerase chain reaction portion of the assay. For amplification to occur, a small piece of DNA (a primer) binds to a complementary target sequence in the SARS-CoV-2 DNA, while another piece of DNA (a probe) attaches to a sequence downstream of the primer binding site. Binding of the primer initiates amplification of the target DNA by an enzyme called polymerase, which copies the DNA in one direction towards the probe. Once the polymerase reaches the probe, it cleaves it, which activates a fluorescent marker attached to the probe. The use of this fluorescent probe allows for monitoring of the fluorescent signal quantitatively in real time rather than just detecting an accumulated end product. 

While the qRT-PCR test is very sensitive, it also has multiple limitations. It requires expensive laboratory instrumentation and trained technicians with an estimated cost of about $100 per test, meaning that most people probably only get tested once. Current testing capacities are limited and results often take days or weeks to return, meaning that individuals who don’t know they are infected can transmit the virus during this time. The high sensitivity of qRT-PCR may also be a drawback rather than an advantage, because the test often detects small fragments of RNA that don’t originate from whole virus particles and thus don’t represent transmissible virus. Such RNA fragments can persist in individuals for weeks and months. As illustrated in Figure 1, infection with SARS-CoV-2 usually results in high initial levels of viral replication that peak and begin to decline within a few days. Symptoms don’t usually appear until after that peak has already occurred, and, because most people don’t get tested until they experience symptoms, they are likely already on the downward slope of viral replication and no longer infectious at the time of testing. In the meantime, they have been unknowingly transmitting the virus to others for several days. Clearly, these people need to be identified and isolated during their period of high infectivity.

In late June, Harvard epidemiologist Michael Mina published a preprint that evaluates the effectiveness of current SARS-CoV-2 surveillance measures for reducing transmission when considering frequency of testing and delayed reporting of results. Mina and co-authors concluded that infrequent testing with an ultra-sensitive test like qRT-PCR often results in unnecessary quarantine of individuals who are no longer infectious. Notably, it also results in missing pre- or asymptomatic individuals who are at the beginning of their infection and thus highly contagious, allowing them to go about their daily routines and infect others. 

A few days after publication of the preprint, Mina co-authored an opinion article in the New York Times in which he discussed the potential for controlling the SARS-CoV-2 pandemic by widespread use of frequent, rapid at-home diagnostic tests. One example of such a diagnostic test is a lateral flow device, which is a paper strip that works similarly to a pregnancy test. The strip has a sample pad on one end and contains antibodies that recognize SARS-CoV-2 antigens. One would dip the sample pad portion of the strip into a sample of saliva and allow the saliva to wick across the strip. The presence of SARS-CoV-2 antigens in the saliva would be indicated by the appearance of a test line in addition to the control line, while a negative test would only indicate the control line (Figure 2). The test provides results in 10-15 minutes at a cost of about $1-2 per test and does not require any additional equipment. A positive result would indicate the need for self-quarantine and confirmation of test results through a doctor’s office. 

Although these rapid tests are only about half as sensitive as qRT-PCR tests, they detect the presence of viral antigen during the actual window of transmissibility when viral levels are very high. The highly sensitive qRT-PCR assays detect viral RNA for weeks after a patient is no longer transmitting virus, which is irrelevant for quarantine/isolation purposes and does nothing to curb transmission. A less sensitive test that is done on a daily basis and provides immediate results would be more valuable because it would identify individuals while they are actually infectious. This would also alleviate the need for costly contact tracing measures because most infected individuals would be aware of their status and would stay isolated during their period of transmission. 

Rapid lateral flow SARS-CoV-2 diagnostic tests are already available, but there is concern that the FDA may not approve these products because of their low sensitivity. You can help bring these products to market by writing to your elected officials (see sample letter templates here), contacting your local TV and radio stations, and telling your friends and family to do the same. Hopefully, with sufficient media attention, the FDA, CDC, and NIH will recognize the value of these tests and make them widely available to the public. This may be the ultimate solution for opening schools and workplaces, and for rebuilding the economy. 

[Michael Mina discussed rapid at-home SARS-CoV-2 testing options on TWiV 640. Tidbits of that episode were also reviewed on MedCram.]

By David Tuller, DrPH

In the UK, the National Health Service has launched a website called “Your COVID Recovery,” part of its strategy for coping with the after-effects of the coronavirus pandemic. This effort is geared toward “supporting your recovery after COVID-19.” In other words, it appears to be targeting the “long-haulers,” as those experiencing lingering symptoms after an acute bout of Covid-19 have been called. These prolonged medical complaints have been given the collective name of “post-Covid syndrome.”

[continue reading…]

Vincent visits Ohio State University (March 2020) and speaks with Shan-Lu, David, Amanda, Mark, Matt, Chris, and Qiuhong about their careers and their work on retroviruses, hepatitis C virus, coronaviruses, paramyxoviruses, and environmental viruses.

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Daniel Griffin provides a clinical report on COVID-19, followed by a review of the findings that children shed as much SARS-CoV-2 viral RNA from the respiratory tract as older patients, the lineage giving rise to SARS-CoV-2 has been circulating in bats in China for decades, and answers to listener questions.

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By David Tuller, DrPH

Massachussetts writer Rivka Solomon has had moderate* [I initially wrote “severe,” and Rivka corrected me.] ME for many years but still manages to get out there (metaphorically) and organize lots of stuff. A couple of years ago, she arranged a talk for me to give about the PACE trial debacle at a Boston-area hospital. She’s also pulled together a well-attended presentation for students, staff, clinicians and others at MGH Institute of Health Professions.* [I initially wrote “Massachusetts General Hospital.” MGH Institute for Health Professions is affiliated with Mass General but is an independent entity.] Most recently, she has written an article about the need to investigate possible links between the illness and so-called coronavirus “long haulers”—those experiencing serious symptoms after recovery from acute cases of Covid-19.

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Among the mountains of false information being peddled during the current pandemic, one of the most offensive is being used to drive opening of schools in the fall: that children do not transmit SARS-CoV-2. The results of multiple studies have shown that this assertion is incorrect. I’ll review two of them here.

One study examined 59,073 contacts of 5,706 COVID-19 patients in South Korea during January 20–March 27, 2020. The 5,706 index patients were grouped by age and the numbers of cases associated with that individual were identified. COVID-19 was detected in 11.8% of household contacts, and the rates were higher for contacts of children than for adults. The highest transmission rate, 18.6%, was observed for household contacts of school-aged children (10-19 years), and the lowest, 5.3%, for household contacts of children 0–9 years. This study was conducted in the middle of school closure; transmission rates are expected to be higher when school resumes.

A second study examined the presence of SARS-CoV-2 nucleic acids in nasopharyngeal swabs at a pediatric tertiary medical center in Chicago. The cohort, which included individuals less than a year of age to 65, all tested positive for SARS-CoV-2. Viral nucleic acid was detected by RT-PCR and the cycle threshold (CT) values for each individual were calculated. The CT value is inversely related to the quantity of nucleic acid present: the higher the number, the fewer copies of nucleic acid present in the sample.

The results show that young children (less than 5 years old) have as much or more SARS-CoV-2 nucleic acids in their upper respiratory tracts compared with older children (5-17 years old) or adults (over 18). While infectious virus was not measured, these differences mean that young children could have 10 to 100 times more infectious virus in their upper respiratory tracts.

The findings of these two studies show that young children are likely to be important drivers of SARS-CoV-2 transmission. Given the behavioral habits of young children in schools and day care centers, they will serve to efficiently amplify the virus among themselves, teachers, and their parents.

Schools may be opened only if stringent precautions are taken, including wearing of face masks, physical distancing, and most importantly, frequent testing. As discussed by Dr. Michael Mina on TWiV 640, the availability of a rapid and daily $1 test would make it possible to identify infected students and keep them at home. Unfortunately, such tests will not be widely ready for school opening this fall. Write your elected officials to demand that such tests be made available as soon as possible. There is no valid reason why we cannot achieve this goal.

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By David Tuller, DrPH

Professor Trudie Chalder is a lead investigator of a series of studies of rehabilitative interventions for so-called “medically unexplained symptoms” that have failed to meet expectations but have nevertheless been promoted as demonstrating treatment success. The piece of crap known as the PACE trial is a prime example. Most famously, Professor Chalder declared at the press conference for the first PACE results, published in 2011 in The Lancet, that twice as many people in the cognitive behavior therapy and graded exercise therapy groups “got back to normal” compared to those in the other groups. This statement was false and scientifically indefensible. [In this paragraph, I initially wrote “more than twice as many people” rather than “twice as many.” I apologize for the error, which I fixed within a couple of hours.]

[continue reading…]

Daniel Griffin provides a clinical report on COVID-19, followed by a review of the State Department document on the Wuhan BSL-4 laboratory, the report on infection of tigers and lions in the Bronx Zoo, and, answers to listener questions.

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By David Tuller, DrPH

On Thursday, Professors Vincent Racaniello and Mady Hornig, both from Columbia University, wrote to BMJ’s research integrity coordinator. I have been corresponding with BMJ, and specifically the research integrity coordinator, about the Norwegian study of cognitive behavior therapy combined with music therapy as a treatment for chronic fatigue in adolescents after acute EBV infection (known in the US as mononucleosis and elsewhere as glandular fever). BMJ Paediatrics Open published the paper a few months ago.

[continue reading…]

by Gertrud U. Rey

On July 20, 2020, Oxford University’s Jenner Institute and the pharmaceutical company AstraZeneca reported preliminary results from phase I/II clinical trials assessing the safety and efficacy of a vaccine candidate against SARS-CoV-2. 

The vaccine candidate, named AZD1222 (referred to in the publication as ChAdOx1 nCoV-19), consists of an adenovirus vector with an inserted gene that encodes the full-length SARS-CoV-2 spike protein. The notion of using a virus as a vector to deliver vaccines to humans is based on the ability of viruses to enter cells by attaching to host cell receptors and releasing their genome into the cell. Upon injection into a vaccine recipient, the vaccine vector should enter cells and serve as a code for host proteins to synthesize the SARS-CoV-2 spike protein from the inserted gene. Ideally, the spike protein will then act as an antigen to prime the immune system to recognize SARS-CoV-2 if it infects the body at a later time. As described in last week’s summary of the Moderna vaccine trial, the spike protein has been the primary antigenic choice for several SARS-CoV-2 vaccine candidates, because it mediates both binding of the virus to the ACE2 host cell receptor and fusion of the viral particle with the host cell membrane. 

Adenoviruses are particularly suitable as vectors for delivering foreign genes into cells because they have a double-stranded DNA genome that can accommodate large segments of foreign DNA, and because they infect most cell types without integrating into the host genome. However, due to the prevalence of adenovirus infections in humans, most people have adenovirus-specific antibodies that could bind and neutralize these vectors, thus rendering them less effective at stimulating antibodies to the foreign gene product. To circumvent this problem, the Oxford/AstraZeneca investigators used an adenovirus of chimpanzee origin that does not normally infect humans. Thus recipients would not likely have pre-existing antibodies to the adenovirus vector itself. They also further optimized the virus by deleting two genes. Deletion of the first gene – which regulates viral replication – ensures that the virus cannot cause an infection in human cells. Deletion of the second gene creates more space inside the vector to allow for insertion of the gene coding for the SARS-CoV-2 spike protein.  

The Oxford/AstraZeneca combined phase I/II clinical trial enrolled 1,077 healthy adult volunteers aged 18-55 who were randomly assigned to receive AZD1222 or a control vaccine. The control vaccine was a licensed vaccine against meningitis and is not viral-vector based. The trial was single-blinded, meaning that only investigators knew whether any particular subject received AZD1222 or the control vaccine, while the subject did not know. This is in contrast to double-blinded studies, where neither the investigators nor the subjects know who is receiving a particular treatment. The investigators chose the meningitis vaccine as a control to ensure that subjects remained blinded to which treatment they were receiving, because, like some vaccines, the meningitis vaccine causes a slight reaction. Use of a saline control would not have induced a reaction, causing subjects to possibly suspect that they received a placebo, which could create a subjective bias and affect experimental outcomes. The AZD1222 vaccine was administered as an intramuscular injection at a single concentration of 50 billion viral particles.

Volunteers were assigned to one of the following groups:   

Group 1  – 88 subjects who received a single dose of AZD1222 or control vaccine were assessed for both side effects and vaccine immunogenicity; 

Group 2 – 412 subjects who received a single dose of AZD1222 or control vaccine were assessed for both antibody and T cell immunity;

Group 3 – 10 subjects who received two doses of AZD1222 at a 28-day interval were assessed for both side effects and vaccine immunogenicity; and

Group 4 – 567 subjects who received a single dose of AZD1222 or control vaccine were only assessed for antibody immunity. 

The basic findings were:

  • Side effects were mild to moderate, mostly consisting of pain and tenderness at the site of injection. Participants had the option of taking acetaminophen (paracetamol) prior to vaccination, which prevented injection site pain and tenderness in at least half of those who took it, and had no effect on vaccine immunogenicity. 
  • All recipients of a single dose of AZD1222 (groups 1, 2, and 4) produced high levels of spike protein-specific total binding antibodies that were sustained to day 56 post-vaccination, and most subjects in these groups also produced neutralizing antibodies.
  • The second dose of AZD1222 boosted the levels of existing total binding antibodies and induced neutralizing antibodies in all subjects in group 3. 
  • A single dose of AZD1222 induced high levels of spike protein-specific T cell responses in all subjects through day 56 post-vaccination. The second dose given to group 3 subjects did not boost these responses. 

In general, the results of the trial are reassuring; AZD1222 seems to activate both arms of the adaptive immune response by inducing both neutralizing antibody and T cell responses specific to the SARS-CoV-2 spike protein. The study also involved a good number of subjects, a factor that is crucial for determining whether results are statistically significant for a phase I/II trial. Due to ethical implications, the efficacy of the vaccine cannot be tested by intentionally infecting (challenging) immunized subjects with SARS-CoV-2. However, results from such a challenge experiment previously done in rhesus macaques suggest that AZD1222 protected the animals against SARS-CoV-2 infection. Immunized macaques infected with SARS-CoV-2 had no signs of virus replication in the lungs, significantly lower levels of respiratory disease, and no lung damage compared to control animals. Even though macaques are not people, their immune responses often parallel those of humans and can provide important insights into human immunity.

Nevertheless, the trial also had several limitations. The vaccine was not tested in subjects over the age of 55, a group who often mount a weaker immune response and are at higher risk for severe COVID-19. The authors acknowledge the importance of a SARS-CoV-2 vaccine for this age group and note that the adenovirus vector used to make AZD1222 was previously shown to be immunogenic in individuals aged 50-78 when used to deliver an influenza virus vaccine. The majority of the volunteers were white, and it is well known that ethnic groups are disproportionately affected by COVID-19. The follow-up period was short, so we don’t know how long the observed immune responses will last and if there are any long-term side effects. It is also unclear why the study was only blinded to vaccine recipients, since double-blinded studies lead to more authentic conclusions because they reduce researcher bias.

The results obtained so far regarding the safety and efficacy of AZD1222 are only preliminary. Phase III trials aimed at assessing the vaccine’s efficacy in ethnically diverse populations as well as in older age groups with comorbidities are currently ongoing in Brazil, South Africa, and the UK, and will hopefully yield more conclusive results. 

[The Oxford/AstraZeneca phase I/II clinical trial was also discussed on TWiV 644.]