The Garden Route – 9 to 16 June 2021 – South Africa

Editor note:

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By Tom Allin

The Garden Route is probably in the Top Five places known or gone to by tourists in South Africa.  The route is made up of towns, national parks and reserves, hiking trails, rivers, beaches, the ocean, paved highways and roads and dirt tracks, and more.  It begins in Mossel Bay and continues to Tsitsikamma Park and includes the towns of Wilderness (4 nights), Knysna (2 nights) and Storm River Camp (1 night).

We began our stay in Knysna.  The Booking.com I chose was not by far my best lodging choice I have made in the last half dozen years.  Making a quick check of the 60 Airbnb and 40 Booking.com (includes apartments, guest houses and hotels) this is the lowest rating – a 3 out of 10 – that I have given any place we have stayed.  We booked for four nights and left after two.  Not everything goes as well as it is planned in my head.

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Robberg Nature Reserve and Marine Protected Area – 10 June 2021 – Garden Route, South Africa

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By Tom Allin

We left our Airbnb and drove down the hill to have breakfast at East Head Café.  The café overlooks the ocean and the food was very good.  Good enough that we had breakfast at the café the following day.

We were headed towards Robberg Nature Reserve but first we came to a detour.  The officer explained to us that there was a civil protest ahead blocking the road.  OK, so we drove through the community of Plettenberg Bay.  As we drove by very pretty landscaped houses it didn’t take long to understand why Plettenberg Bay, population of close to 40,000, is consider a resort city.

The Nature Reserve has three different trails of varying lengths: 1) The Gap 2.1km, 2) Witsand 5.5 km and The Point 9.2 km/5.5 miles.  We opted for The Point trail.

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CORONAVIRUS INFO PROVIDED BY DR. JIM HARRIS – 6/28/2022

THIS IS A GOOD TIME TO PLAY IT COOL, MAN. EAST TEXAS COVID COUNTS ARE HIGH, BUT NOT HOSPITAL NUMBERS, YET.

FROM THE MNM AND JUDGE SIMS:

FROM JAMA

Olfactory Dysfunction in Patients With Mild COVID-19 During Gamma, Delta, and Omicron Waves in Rio de Janeiro, Brazil

”…Olfactory dysfunction is a common symptom of COVID-19, with reported rates as high as 70%. This symptom can be associated with mild COVID-19, mostly occurs within 5 days after symptom onset, and can persist for a few days to several months after infection resolution.1 The mechanism of SARS-CoV-2–related olfactory dysfunction is not completely understood…Host genetics,2 acute inflammation in the olfactory epithelium,3 local ACE2 expression,4 and downregulation of olfactory receptors5 seem to play a role; however, the viral contribution remains to be explored. We conducted a retrospective analysis of individuals with mild COVID-19 during different SARS-CoV-2 variant waves to assess the prevalence of self-reported olfactory dysfunction.

This study found that individuals with mild COVID-19 infected during the Gamma and Omicron waves had lower odds of reporting olfactory dysfunction than individuals infected during the period of the original lineages. These results suggest that the type of SARS-CoV-2 variant might be a risk factor for olfactory dysfunction, along with host genetic susceptibility. The association with Omicron also was observed after controlling for vaccination status, supporting its independence of host immunologic factors…”

FROM HOPKINS SELECTIONS:

1. FROM HOPKINS:

1. Covid-19 Vaccines Prevented Nearly 20 Million Deaths in a Year, Study Estimates (STAT News) Covid-19 vaccines cut the potential global death toll by more than half in the first year they were available, according to a study published Thursday in The Lancet Infectious Diseases. The study modeled the spread of the disease in 185 territories and countries and found that without Covid vaccines, 31.4 million people would have died of the disease between December 2020 and 2021. While the pandemic has taken a devastating toll around the globe, with more than 3.5 million deaths since the first vaccine was administered in December 2020, the study estimated that vaccinations also prevented 19.8 million deaths.

2. Hospitalization and Emergency Department Encounters for COVID-19 After Paxlovid Treatment — California, December 2021–May 2022 (CDC MMWR) COVID-19–related hospital admissions and emergency department (ED) encounters occurring 5–15 days after Paxlovid treatment were described using data from a large integrated health care system. Reports of such hospitalizations or ED encounters occurred infrequently, representing <1% of Paxlovid-treated patients over the study period. When administered as an early-stage treatment, Paxlovid might prevent COVID-19–related hospitalization among persons with mild-to-moderate COVID-19 who are at risk for progression to severe disease.

3. Association of Kidney Comorbidities and Acute Kidney Failure With Unfavorable Outcomes After COVID-19 in Individuals With the Sickle Cell Trait (JAMA Internal Medicine) In this genetic association study of 2729 persons with SCT and 129 848 who were SCT negative, individuals with SCT had a number of preexisting kidney conditions that were associated with unfavorable outcomes following COVID-19. The presence of SCT was associated with increased risk of mortality and acute kidney failure following COVID-19. Results strongly support the inclusion of SCT as an adverse prognostic factor for COVID-19.

THREE VACCINE ARTICLES AND MORE NEWS TO COME TODAY:

 Pfizer and BioNTech Announce Omicron-Adapted COVID-19 Vaccine Candidates Demonstrate High Immune Response Against Omicron (Pfizer) Pfizer Inc. and BioNTech announced positive data evaluating the safety, tolerability, and immunogenicity of two Omicron-adapted COVID-19 vaccine candidates: one monovalent and the other bivalent, a combination of the Pfizer-BioNTech COVID-19 Vaccine and a vaccine candidate targeting the spike protein of the Omicron BA.1 variant of concern. Data from the Phase 2/3 trial found that a booster dose of both Omicron-adapted vaccine candidates elicited a substantially higher immune response against Omicron BA.1 as compared to the companies’ current COVID-19 vaccine. The robust immune response was seen across two investigational dose levels, 30 µg and 60 µg.

 Sanofi, GSK Variant-specific COVID Shot Found Effective Against Omicron (Reuters) Late-stage data on an experimental COVID-19 vaccine from Sanofi and GSK has showed the shot confers protection against the Omicron variant of the virus, the companies said on Friday. The so-called bivalent vaccine targets the Beta variant – first identified in South Africa – as well as the original Wuhan strain of the virus. In a trial involving 13,000 adults, the vaccine demonstrated an efficacy rate of 64.7% against symptomatic COVID, and 72% efficacy against infections specifically caused by the Omicron variant. When used in people who previously had COVID, the results were stronger. The vaccine generated an efficacy rate of 75.1% against symptomatic COVID and 93.2% in Omicron-confirmed symptomatic cases, the companies said.

 China’s First mRNA Vaccine is Close — Will That Solve Its COVID Woes? (Nature) China is getting closer to approving its first mRNA vaccine to protect people against COVID-19. In a small clinical trial, the Chinese vaccine candidate triggered a stronger antibody response in vaccinated adults when given as a booster shot than did a jab containing inactivated SARS-CoV-2, the vaccine platform that the country has mostly relied on so far. The experimental jab, called ArCoV, is a strong candidate to become China’s first approved mRNA vaccine. But what it would mean for the government’s handling of the pandemic is hard to know, say researchers. A highly effective mRNA vaccine would reduce the chances of widespread serious infections that could overwhelm hospitals. However, it is unlikely to bring an end to the country’s strict ‘zero COVID’ strategy, which uses mass testing and lockdowns to quash all infections.

FROM A CERTAIN NORWEGIAN:

WHO official says the more times a person gets COVID-19, the more likely they are to be ‘unlucky’ and get long COVID

AND LAST BUT NOT LEASED:

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Klipgat Cave/Walker Bay Nature Reserve – 7 June 2021 – Western Cape, South Africa

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By Tom Allin

My guess is unless you live in South Africa you don’t know Walker Bay Nature Reserve much less have ever visited here.

I have no recollection as to why I thought this was a good stop but most likely it was noted in Lonely Planet and was on our route to our next stop, Cape Auglhas.  One of the advantages of our slow travel is we can stop when and where we want to, and Walker Bay Nature Reserve was a great stop to stretch the legs.

But first things first, we had to leave Hermanus.  We were up and on the road before ten, heck it may have been by 9:00 am.  I don’t keep track of our time on the road but I know we got off at a reasonable time for us.

We left the hotel and headed towards Rotary Way for its view.

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CORONAVIRUS INFO PROVIDED BY DR. JIM HARRIS – 6/24/2022

HELLO, 

YOU CAN HAVE A GOOD TIME WHILE BEING VERY CAREFUL AND WEARING YOUR MASK. 

FROM THE NYT today:

(J. Harris: Notice the recent Covid counts in East Texas are markedly elevated. Fortunately, most of these folks do not require hospitilization — which means most likly that we now have the Omicron subvariants BA .4-.5  making a visit. I personally know several local and Texas people who have become ill this week.)

FROM THE NEJM: 

Neutralization Escape by SARS-CoV-2 Omicron Subvariants BA.2.12.1, BA.4, and BA.5

”…These data show that the BA.2.12.1, BA.4, and BA.5 subvariants substantially escape neutralizing antibodies induced by both vaccination and infection. Moreover, neutralizing antibody titers against the BA.4 or BA.5 subvariant and (to a lesser extent) against the BA.2.12.1 subvariant were lower than titers against the BA.1 and BA.2 subvariants, which suggests that the SARS-CoV-2 omicron variant has continued to evolve with increasing neutralization escape. These findings provide immunologic context for the current surges caused by the BA.2.12.1, BA.4, and BA.5 subvariants in populations with high frequencies of vaccination and BA.1 or BA.2 infection…”

FROM HOPKINS SELECTIONS”

1. Hospitalized Patients with Severe COVID-19 During the Omicron Wave in Israel – Benefits of a Fourth Vaccine Dose (Clinical Infectious Diseases) Among hospitalized patients with severe/critical breakthrough COVID-19, a recent fourth dose was associated with significant protection against mechanical ventilation or death, compared to three doses.

2. SARS-COV-2 REINFECTION The newest Omicron subvariants of BA.4 and BA.5 are driving increases in new SARS-CoV-2 infections in several regions, with many people experiencing reinfections despite immunity from prior infection or vaccination (1+ shots). These subvariants appear to be able to evade antibodies more easily than their predecessors, possibly due to new and different spike proteins. Though global COVID-19-associated mortality appears to be decreasing, a new preprint study posted on Research Square cautions that reinfections pose an increased risk of hospitalization (HR 2.98), all-cause mortality (HR 2.14), and sequelae in pulmonary and other organ systems. The risk of these adverse outcomes—including those impacting the heart, blood, kidneys, lungs, and brain—were most pronounced in the acute phase of infection but persisted throughout the 6-month follow up. Additionally, for every reinfection (1, 2, 3+) there was a stepwise increase in risk for all sequelae evaluated, including hospitalization. Although not yet peer-reviewed, the study serves as a signal that the COVID-19 pandemic remains a threat to the health of the world’s population, and individuals must continue to take precautions to prevent infection.

FROM BECKERS:

1. Pending approval, Moderna aims to deploy subvariant vaccine in August

Moderna expects to distribute its bivalent booster vaccine candidate by August and has already produced the doses as it awaits approval.

“We’ve been producing millions of doses over the last couple of months,” Moderna’s president, Stephen Hoge, MD, told the Financial Times. “We would hope to have tens of millions to hundreds of millions of doses available in August, September and October to support boosting prior to the fall respiratory virus season.”

The candidate boosted antibodies “5.4-fold above baseline” against omicron subvariants BA.4 and BA.5 among the phase 2/3 trial’s 800 participants, according to a June 22 press release. Moderna said it has “already shared these data” with regulators and, if authorized by the CDC and FDA, expects rollout to be this fall.

The subvariants accounted for almost 35 percent of COVID-19 cases as of June 18, according to CDC data. The week earlier, they caused 21.6 percent of cases.

FROM JAMA

Experimental Open-source Low-cost Ventilator Could Meet Critical Need

FROM SCIENCE:

What causes Long Covid? Here are the three leading theories

(J. Harris: This is a very readable article of importance.)

FROM REUTERS:

Mexico records most daily COVID-19 cases since February, signaling 5th wave

Mexico reported 16,133 new COVID-19 cases in the country on Thursday, the highest daily number reported since late February, according to data released by the Health Ministry.

FROM THE LANCET:

1. How to interpret the total number of SARS-CoV-2 infections

”…since the beginning, it has been clear that reported cases represent only a fraction of all SARS-CoV-2 infections….According to COVID-19 Cumulative Infection Collaborators findings, a staggering number of people, 3·39 billion (95% uncertainty interval 3·08–3·63) or 43·9% (39·9–46·9) of the global population, are estimated to have been infected one or more times between March, 2020, and November, 2021. Remarkably, this was before the highly transmissible omicron (B.1.1.529) variant swept the globe. These estimates of total infections are wildly different from the number of reported cases, which stood at 254 million as of Nov 14, 2021.3..COVID-19 Cumulative Infection Collaborators study also highlights vast regional discrepancies, painting a very different picture from that provided by reported cases. From case reports, one would conclude that the highest cumulative incidence was observed in Europe and North America and the lowest in Africa. However, this study estimated that 70·5% (61·6–75·9) of the population in sub-Saharan Africa has been infected with SARS-CoV-2, compared with 30·9% (28·8–32·8) of the population in high-income North America. Underlying this apparent reversal of patterns are stark differences in case detection; fewer than 1% of infections were reported as cases in sub-Saharan Africa whereas nearly half were reported in high-income North America. It is crucial that this underreporting is considered when we compare the impact of the pandemic and the effectiveness of responses among nations…..one could argue that the proportion of the population ever infected is no longer a meaningful metric of population immunity… how do layers of vaccine-induced and virus-induced immunity combine to confer protection to the population? Perhaps most importantly at this moment in the pandemic, we need to identify the sub-populations that remain susceptible to severe disease and death. Serosurveys combined with morbidity and mortality surveillance and detailed monitoring of vaccine coverage are essential to identify the groups lacking immunity from vaccination or previous infection.5,  6,  7 Integrating data enables the kinds of insights offered by COVID-19 Cumulative Infection Collaborators to inform the next phase of the pandemic response, and we should sustain this effort…”

(J. Harris: This Comment in Lancet is very readable and very sobering. It seem “the fat lady” hasn’t sung yet — if fact, she doesn’t even have the musical score yet. Hell.)

2. COVID-19 in North Korea

AND LASTLY:

1. MILTON TOMATO wishes to announce that yesterday he used his personal influence and got 0.2 inches of rain!

2. Tom Allin sends out good jokes as he travels the world:

(Norweigan?)

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Hermanus – 5 to 7 June 2021 – Western Cape, South Africa

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By Tom Allin

We left the Porter Botanical Gardens late in the afternoon but I knew we had a relatively short drive to Hermanus and I had already selected a place to stay.  Google maps took us straight to the B & B I had selected the night before.  Drove up to the gate and went to the entrance speaker and spoke, then spoke again and again.  OK, I will use my phone and call – no answer.

The sun is beginning to set, in a new town for us, no place to stay – situation almost normal.

A couple blocks back from the B & B we are sitting in front of with the locked gate I saw a sign advertising a hotel.  Back to the sign, put the name of the hotel in Google maps, hit directions and we are on our way.

This was a situation that began semi-badly and ended up GREAT.  The 7 on Marine Hotel is one of our favorite hotels in all our travels.  We had the place to ourselves (thank you Covid) the next day after the only other guests checked out and what a beautiful place it is.

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CORONAVIRUS INFO PROVIDED BY DR. JIM HARRIS – 6/22/2022

THE HONEYMOON IS OVER AND THE COUNTS ARE SIGNIFICANTLY ELEVATED IN TEXAS, ESPECIALLY EAST TEXAS:

FROM BECKERS:

1. Mark Cuban’s generic drug prices would save Medicare billions of dollars: Harvard study

FROM DR. KATLINE JETELINA, YOUR LOCAL EPIDEMIOLOGIST:

BA.4/5 is sweeping the globe

”…The newest Omicron variant, BA.4/5, is gaining traction, causing case, hospitalization, and death curves to trend upwards in many countries. This variant was first detected in South Africa in early 2022 and caught our attention because it had several mutations on the spike protein…..In the lab, we see that Omicron is getting better at escaping our first line of defense—neutralizing antibodies. ..BA.4/5 does not fully escape immunity. This means, in the short-term, boosters help prevent infection and thus transmission…. BA.4/5 drove a substantial case wave in South Africa regardless of their high level of immunity. Case waves across Europe are now well on their way, too. In the U.K., reinfections are on the rise, even among 60+ year olds.

..We don’t have epidemiological data on duration of booster effectiveness against BA.4/5. Data from the U.K. showed that boosters provided strong initial protection against BA.1 or BA.2 infection but quickly diminished to 0% five months later. We expect BA.4/5 to shorten this timeline even more…..

In Europe, Portugal is the BA.4/5 leader, with 70% of COVID-19 cases accounting for this new variant. With one of the highest vaccination rates in the world, they largely escaped death from Delta. However, now, after recently reaching their BA.4/5 case peak, excess mortality hit the highest level since their vaccination campaign began…In Portugal, increase in hospitalizations is occurring mainly in people over 60 years old. In fact, in a recent analysis, unvaccinated people over 80 had a case fatality rate (CFR) of 9.5% … Among those with only the primary vaccine series, CFR [CASE FATALITY RATE] is 5%; among those with a booster, it is 1.7%….. While Portugal does have a higher booster rate than the U.S., it isn’t perfect. . Vaccines are not perfect, and if we have a virus burning through a population, it can still cause high levels of death among vulnerable pockets, like the elderly….BA.4/5 hospitalizations are now making headway in other European countries…[WITH] the global upswing in hospitalizations as BA.4/5 entered the scene. But, so far, remains much lower than previous peaks….Bottom line:This virus continues to mutate to escape our first line of defense causing (re)infections. If you don’t want to get sick, it’s time to leverage other layers of protection, like masking. Thankfully, other immune system mechanisms continue to work to reduce severe disease. The transmissibility of the virus is causing upswings of hospitalizations and deaths among the most vulnerable of our populations. We aren’t out of the woods yet but we are inching closer and closer to a manageable virus…”

(J. Harris: Dr. Jetelina is a PhD epidemiologist who has a day job and writes this blog at night. She has small children and accepts contributions. I have found her to be well-informed and to have the ability to explain pertinent  basic and new information to laymen and old Internists. The above article is worth reading in its entirety. I subscribed to her efforts.)

AND LASTLY:

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CORONAVIRUS INFO PROVIDED BY DR. JIM HARRIS – 6/21/2022

From Judge Sims and THE MNM:

FROM THE NYT TODAY:

1. A Chinese Omicron study finds a low risk of severe illness, renewing debate over the ‘zero Covid’ policy.

2. Deaths stay near pandemic lows, despite another virus surge.

3. CALL TO OVERHAUL THE US PUBLICK HEALTH SYSTEM

”…While other countries have centralized public health authorities, public health in the United States is largely managed at the state and local level. The Centers for Disease Control and Prevention, the federal public health agency, does not have the authority to compel states to act — it cannot, for example, investigate outbreaks of infectious disease in a particular state unless it has an invitation from state officials to do so….State health agencies and the C.D.C. have a long history of working collaboratively, but throughout the pandemic, elected state officials — particularly those in red states — have been reluctant to cede control. When the C.D.C. asked states to sign agreements to share vaccination data with the federal government, for example, a number of states balked….The Senate health committee has passed a bipartisan measure that would require the C.D.C. director to be confirmed by the Senate, and that calls for additional steps to improve coordination among the nation’s public health agencies....The commission’s recommendations are more sweeping. The panel… calls for the creation of a new position — Under Secretary for Public Health — within the Department of Health and Human Services, to oversee the national public health system…The under secretary would coordinate the work of more than a dozen federal agencies that play a role in public health, and would have the power to set minimum health standards for the states…“Our system of public health is a federalist system with states and localities having considerable autonomy — and appropriately so, as they adapt to the needs of their states and communities,” Dr. Hamburg said in an interview. “However, the public health protections that individuals receive shouldn’t be wholly dependent on where you live. There should be a core set of expectations.”

(J. Harris: We need to make significant changes in the US Public Health System, from top to bottom, in my opinion. The system seems rudderless and politically hindered at the top and poorly functional in many locales — including and especially in rural areas. Local public health systems, medically, could be more efficient with more guidance and supervision by well-trained public health experts and physicians with mandates and necessary follow-up audits, especially when future medical epidemics arise as they will. …..It appears to me that the Texas Department of Health Services has functioned very well during the Covid Pandemic and has improved as the crisis deepened, especially in the dissemination of general information and data to medical practitioners, institutions, and the public. Unfortunately, like many other rural, “red” and undereducated areas, the vaccination rates in most Texas Counties are absolutely pitiful, The Marshall-Harrison Department of Health is fortunate to have a well-educated, highly motivated leader, but we don’t seem to have a good local system of information dissemination (broadband???). Also, it would be nice if there were more state and national solution programs available for epidemiological control in times of crisis. Need I say that I would have approved of the incarceration and isolation of “Typhoid Mary” way back when?)

FROM HOPKINS SELECTIONS:

1. Covid Vaccine Hesitancy Threatens Flu Vaccine Uptake (CIDRAP) Polarized views and worries about COVID-19 vaccination had spillover effects on flu vaccination in adults, according to researchers who examined data over two pandemic years on both vaccines by state. The authors of the study say the findings are a warning of declining trust in public heath, which comes at a vulnerable time as eased COVID-19 measures put populations at risk for the return of disease threats such as flu. Late-season flu activity is still under way in some parts of the United States, and health officials are closely watching Australia, where an early-season surge is already worse than some of the country’s pre–COVID pandemic flu seasons. The group, based at University of California-Los Angeles Health Services, published its findings yesterday in a letter to the New England Journal of Medicine.

FROM THE NYT:

C.D.C.’s science advisers grapple with assessing two very different vaccines for the youngest Americans.

”…Unvaccinated people aged 5 and older had 10 times the risk of dying of Covid-19, compared with those who received at least two shots of the vaccine,…. The figures “provide real world-evidence that most deaths from Covid-19 are preventable through vaccination…”

The two vaccines[for young children] differ in almost every aspect. For young children receiving the Moderna vaccine, the Food and Drug Administration has authorized two doses of 25 micrograms each, one-fourth the amount used for adults, spaced four weeks apart…But according to the data presented on Friday, two doses of the Pfizer vaccine — each just three micrograms, or one-tenth of the adult dose — fell short of producing strong immunity against the virus in young children…To be effective, the Pfizer-BioNTech vaccine will need to be administered in three doses: the first two spaced three weeks apart, and a third at least two months after that…Pfizer has reported that three doses of its vaccine has an effectiveness of about 80 percent against symptomatic illness. But that estimate is based on infections in just three children who were immunized in the company’s trials, the C.D.C. committee members noted.

(J. Harris: Pediatricians will ”call the shot” and tell you which and when to vaccinate young children. At this time, Moderna might be the best choice?)

FOLLOW TEXAS COVID VARIANTS

(J. Harris: This is a good site to play with as the variants come and go.)

COVID-19 vaccine info for trusted messengers: Kids <5 years My Toddlers Already Had COVID-19. I’m Still Getting Them Vaccinated Right Away

(J. Harris: written by a young female epidemiologist who puts out a nice email frequently.)

Rapid, scalable assessment of SARS-CoV-2 cellular immunity by whole-blood PCR

”…As the deployment of vaccines attenuates the pandemic3, vaccine effectiveness and the duration of protective immunity will need to be systematically assessed and monitored at a global level. Long-term protection from viral infection is mediated by both humoral (antibodies) and cellular immunity4. Quantification of SARS-CoV-2-specific IgG and neutralizing antibodies is often used as a marker of immune protection5, but measurement of T cell responses is rarely performed because of the associated technical challenges. ...Fast, high-throughput methods for measuring the level and duration of protective immune responses to SARS-CoV-2 are needed to anticipate the risk of breakthrough infections. Here we report the development of two quantitative PCR assays for SARS-CoV-2-specific T cell activation. …”

(J. Harris: I have a few readers that might understand this article. I can follow some of it. The article below helps.)

A New Test Can Help Reveal If You’re Immune to COVID-

(J.Harris: FROM TIME 

”…But an international group of researchers recently developed a different tool to help assess COVID-19 immunity: a blood test that can measure T cells, white blood cells that work alongside virus-fighting antibodies to mount an immune response. Their work is described in a new study published in Nature Biotechnology….Testing for antibodies only tells part of the story, since T cells are also a critical piece of the body’s immune response. And while antibody levels drop off significantly within a few months of vaccination or infection, cellular immunity can last up to a year, Guccione says. “Monitoring both will give us a much clearer picture [of immunity] and will hopefully inform our re-vaccination strategies,” Guccione says. The wide use of this test could help define how long protection lasts and how often booster doses are needed.

How Long-COVID Risk Varies By Variant

(J. Harris: good quick read.)

”…The Omicron variant is less likely to give you long COVID than a previous strain of the virus, British researchers say…..But because the Omicron variant is far more contagious than Delta, more people get infected with Omicron and, therefore, more experience long COVID, they added…For the study, Steves and her colleagues used the U.K.-based ZOE COVID Symptom study app to collect data on 56,000 people infected with the Omicron strain. They were compared with more than 41,000 people infected with the Delta strain…The upshot: Odds of getting long COVID were 20% to 50% lower with Omicron than Delta. The odds were dependent on a patient’s age and time since vaccination.

Paxlovid rebound symptoms rare, Mayo study finds

”…Last month, an FDA official cautioned that the antiviral treatment couldn’t block recurring symptoms. Pfizer CEO Dr. Albert Bourla disagreed, arguing a symptom relapse was rare…

The CDC issued an alert May 24 warning that some Paxlovid patients were symptomatic two to eight days after testing negative.

With an 89 percent efficacy rate in diminishing symptoms, Paxlovid is currently the nation’s most popular COVID-19 treatment.

Moderna’s vaccine had fewer side effects than Pfizer’s in study

”…An observational study of nearly half a million inoculated people found the Pfizer and Moderna COVID-19 vaccines had similar side effects, but the risk was lower in Moderna’s…

Of the 433,762 veterans studied over a 38-week period, receivers of the Pfizer shot had a higher risk of ischemic stroke, kidney injury, myocardial infarction and other thromboembolic events compared to those jabbed with Moderna’s vaccine, according to the research published June 13 in JAMA…

Side effect risk of both mRNA-based vaccines was relatively low overall. The median age in the study was 69, and men made up 93 percent of participants.

AND LASTLY:

NORWEGIAN FATHERS DAY JOKES: (TRANSLATIONS AVAILABLE)

1. If you see a crime at an Apple store, are you an iWitness?

2 The wedding was so beautiful, even the cake was in tiers.

3. I used to be able to play the piano by ear, but now I have to use my hands.

4. To whoever stole my copy of Microsoft Office, I will find you. You have my Word!

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CORONAVIRUS INFO PROVIDED BY DR. JIM HARRIS – 6/17/2022

I WISH YOU A NICE WEEKEND, BUT DON’T TAKE UNNECESSARY CHANCES.

REPEAT COMMENTS FROM JUNE 8 NYT REGARDING BA .4 AND .5

”…Globally, the most recent data suggest that BA.4 and BA.5 still represent a relatively small share of cases, but that could change in the weeks ahead. In a recent report, the U.K. Health Security Agency noted that in many countries, the two subvariants were replacing BA.2 about as quickly as BA.2 replaced the original version of Omicron….The subvariants have become especially common in parts of the southern United States. In the region comprising Arkansas, Louisiana, New Mexico, Oklahoma and Texas, BA.4 and BA.5 account for more than one in five infections, according to the new figures….”

”…Latest trends IN LA FROM NYT

An average of 1,421 cases per day were reported in Louisiana in the last week. Cases have increased by 38 percent from the average two weeks ago. Deaths have increased by 38 percent..”

(J. Harris: Bossier and Caddo Parishes are right next door. They may test more there, but we 

will be increasingly plagued by the new BA.4 and BA.5 variants. I have just been told that “BA” stands for Bad Ass in Norwegian.)

IF YOU HAVE HAD COVID BUT ARE STILL TEST POSITIVE, ARE YOU CONTAGIOUS?

1. Some Test Positive for COVID for 10 Days or Longer

2. Early data suggests many individuals still COVID+ after 5 days of isolation, challenging return-to-work recommendations

3. From Positive to Negative to Positive Again—The Mystery of Why COVID-19 Rebounds in Some Patients Who Take Paxlovid

FROM NEJM:

Effects of Previous Infection and Vaccination on Symptomatic Omicron Infections

RESULTS:

1. The effectiveness of previous infection alone against symptomatic BA.2 infection was 46.1%

2. The effectiveness of vaccination with two doses of BNT162b2 and no previous infection was negligible , but nearly all persons had received their second dose more than 6 months earlier.

3. The effectiveness of three doses of BNT162b2 and no previous infection was 52.2%

4. The effectiveness of previous infection and two doses of BNT162b2 was 55.1%

5. The effectiveness of previous infection and three doses of BNT162b2 was 77.3%.

CONCLUSIONS:”No discernable differences in protection against symptomatic BA.1 and BA.2 infection were seen with previous infection, vaccination, and hybrid immunity. Vaccination enhanced protection among persons who had had a previous infection. Hybrid immunity resulting from previous infection and recent booster vaccination conferred the strongest protection.

(Most of the people with whom I confer, have had a total of 4 jabs of vaccine — and are waiting now for a recommendation for a new vaccine or a “mix and match” with existing vaccines.

ALSO FROM NEJM LETTER TO THE EDITOR:

In this study, we characterized infection-induced immunity and vaccine-induced immunity against newly emerged omicron subvariants. Booster vaccination provided sufficient neutralizing-antibody titers against the BA.4/5 and BA.2.12.1 subvariants, albeit to a lower extent than against BA.1 and BA.2.4,5 These findings underscore the importance of booster vaccination for protection against emerging variants.

FROM HOPKINS:

1. ACUTE HEPATITIS & LONG COVID Researchers from Israel published findings from their study on instances of long-term COVID-19 liver manifestation among children. The study, published in the Journal of Pediatric Gastroenterology and Nutrition, involved a retrospective investigation of 5 patients hospitalized in an Israeli children’s hospital. Each of the patients had a confirmed SARS-CoV-2 infection and presented with long-term liver injury stemming from their infection. Two of the patients in the study, both under 6 months of age, presented with acute liver failure, the other 3 patients, ranging between ages 8 and 13 years, presented with acute hepatitis and cholestasis.

This review adds to the growing list of evidence tying post-acute sequelae of COVID-19 (PASC/Long COVID) to cases of acute hepatitis of unknown origin. Last month, multiple technical and news media publications documented an international cohort of children with severe hepatitis. Many experts have suggested that COVID-19 could be a potential source for this unexplained manifestation, considering the lack of apparent epidemiological explanations. The US CDC is examining a series of US cases of acute hepatitis as well, and a recent update indicates that adenovirus type 41 could be a possible causative agent as well. While much has been written about Long COVID, many questions remain, and advocates continue to call for expanded research efforts into explanations and treatments.

2. BA.4 & BA.5 SUBVARIANTS IN EUROPE The European CDC published an epidemiological update on the emergence and prevalence of the BA.4 and BA.5 sublineages of the SARS-CoV-2 Omicron variant of concern (VOC). The subvariants were first detected in Europe in March, and in May, Portugal was the first European country to report a COVID-19 surge associated with one of the subvariants (BA.5). Notably, Portugal’s daily incidence appeared to peak in late May/early June. While most European countries have reported relatively low prevalence of these subvariants, they represent an increasing proportion of new sequenced specimens in multiple countries over the past several weeks, including Austria, Belgium, Denmark, France, Germany, Ireland, Italy, Netherlands, Spain and Sweden. In particular, the BA.4 and BA.5 subvariants represent more than 25% of sequenced specimens in Belgium over the second half of May, and more than 10% in some communities in Spain. The increasing prevalence of BA.4/BA.5 corresponds to increasing COVID-19 daily incidence in most of those countries as well. 

The ECDC projects that BA.4 and BA.5 will become the dominant variants across Europe “in the coming weeks” and that the continent can expect an associated COVID-19 surge like those in the countries noted above. The daily incidence in Europe has increased nearly 30% since June 6, with even larger increases in the UK. While there is “no evidence” these subvariants pose higher risk of severe disease, the ECDC notes that an overall increase in transmission can be associated with subsequent increases in hospitalizations and mortality.

J. Harris: So why is the USA reducing vigilance in travelers from Europe? 


3. WASTEWATER SURVEILLANCE Researchers from the University of Illinois and University of Florida published (preprint) findings from a study on the implementation of neighborhood-scale SARS-CoV-2 wastewater surveillance systems. The COVID-19 pandemic has popularized wastewater surveillance as a tool to provide early warning of impending outbreaks; however, most of these efforts have focused on large-scale sewer systems. Neighborhood-scale systems can provide more targeted early warning capacity, but as the catchment population decreases, the volume of fecal matter is less consistent, which can make it more difficult to analyze the concentration of SARS-CoV-2 and accurately detect emerging outbreaks. This study covered 7 neighborhood-scale wastewater surveillance systems in Champaign County, Illinois, from January-November 2021, with catchment populations ranging from 853 to 2,402 individuals. In an effort to improve the system’s accuracy, the researchers developed a methodology to normalize the concentration of SARS-CoV-2 N gene fragments by the concentration of pepper mild mottle virus (PMMOV) detected in the system. The presence and concentration of PMMOV served as an analogue for the presence of fecal matter in the sample, which enabled the researchers to establish more accurate baseline metrics and better analyze the relative concentration of SARS-CoV-2. Based on the concentration of SARS-CoV-2 N gene fragments to PMMOV, the system output a binary risk assessment (ie, Low or High). Over the 11 months of the study, the 7 neighborhoods experienced 26 total local COVID-19 outbreaks, and the surveillance system identified High COVID-19 risk corresponding to 19 of those time periods (73% sensitivity). The system identified 17 total High-risk time periods, and 12 of those corresponded to local COVID-19 outbreaks (71% specificity). The researchers also indicated that the surveillance system was capable of providing sufficiently accurate risk assessment for specific variants of SARS-CoV-2, which could provide early warning of the geographic spread of variants of concern. This study provides evidence that smaller-scale wastewater surveillance systems can provide indication of increased transmission risk among specific communities, particularly during periods of relatively low local incidence 



 



 

4. Newest Omicron Covid-19 Lineages Gaining Ground in United States (STAT News) The Omicron lineage BA.2 and its spinoff, BA.2.12.1, drove cases this spring, building into waves of infections in places like the Northeast and parts of California. Now, two other forms of Omicron, BA.4 and BA.5, are eating into the BA.2 group’s dominance. More than 1 in 5 Covid-19 infections last week were caused by BA.4 and BA.5, according to updated estimates posted  by the Centers for Disease Control and Prevention. That’s up from 13% the week prior. The rest of the cases are from the BA.2 lineages. BA.4 and BA.5 are picking up speed because they’re able to evade the body’s antibody response even more so than other variants, meaning they’re very good at establishing infections in people who have some level of protection.

5. Pfizer Reports Additional Data on PAXLOVID (Pfizer) Today, we shared data from the Phase 2/3 EPIC-SR study evaluating the use of PAXLOVID™ tablets and ritonavir tablets in patients who are at standard risk for developing severe COVID-19. In previously reported interim analyses, the company disclosed that the novel primary endpoint of self-reported, sustained alleviation of all symptoms for four consecutive days was not met, and a non-significant 70% relative risk reduction was observed in the key secondary endpoint of hospitalization or death (treatment arm: 3/428; placebo: 10/426). An updated analysis from 1,153 patients enrolled through December 2021 showed a non-significant 51% relative risk reduction (treatment arm: 5/576; placebo: 10/569). A sub-group analysis of 721 vaccinated adults with at least one risk factor for progression to severe COVID-19 showed a non-significant 57% relative risk reduction in hospitalization or death (treatment arm: 3/361; placebo: 7/360).

6. How Months-long COVID Infections Could Seed Dangerous New Variants (Nature) Virologist Sissy Sonnleitner tracks nearly every COVID-19 case in Austria’s rugged eastern Tyrol region. So, when one woman there kept testing positive for months on end, Sonnleitner was determined to work out what was going on. Sonnleitner and her colleagues collected more than two dozen viral samples from the woman over time and found through genetic sequencing that it had picked up about 22 mutations. Roughly half of them would be seen again in the heavily mutated Omicron variants of SARS-CoV-2 that surged around the globe months later. “When Omicron was found, we had a great moment of surprise,” Sonnleitner says. “We already had those mutations in our variant.”  

(J. Harris: Here’s the article from Nature: )

How months-long COVID infections could seed dangerous new variants

FROM JAMA:

1. Effect of Text Messaging and Behavioral Interventions on COVID-19 Vaccination Uptake

”There was no detectable increase in vaccination uptake among patients receiving text messaging compared with telephone calls only or behaviorally informed message content.”

FROM BERCKER SELECTIONS”

Former Houston Methodist employees lose appeal in vaccination mandate case

FROM THE NYT:

Here’s how long some popular at-home virus test kits actually last, according to the F.D.A.

AND LAST BUT NOT LEASED:

EARLY PHOTO OF NORWEGIAN INVASION OF TEXAS:

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Harold Nixon Porter Botanical Gardens – 5 June 2021 – Betty’s Bay, South Africa

Editor note:

Another Tom Allin travel story  

By Tom Allin

After watching the penguins for an hour or more we drove five minutes to the Harold Nixon Porter Botanical Gardens.  As noted before our timing was off.  It is the middle of winter not the spring flower blooming season.  However, this botanical garden was still a great visit.

We then decided to walk or at least for us it was more of a hike up into the higher reaches of the gardens.  We spent about three hours hiking up and then back down to the formal gardens.  We slept well and long that night and the next morning.

Use the links below to read Tom’s complete story

CLICK HERE TO READ THE COMPLETE STORY

ANDROID USERS CHICK HERE TO READ THE COMPLETE STORY

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