WHO COVID Epidemiological Update #46

 

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The latest epidemiological update on the COVID-19 pandemic from the World Health Organization finds that the number of new cases reported over the past week has increased slightly (2%), and that the two WHO regions that reported increases in their last report (Eastern European & African) are now joined by Europe (up 10%) in this report. 

The most dramatic increases continue to come out of Africa, which is up another 34% this week. 

Deaths, however, continue to decline globally - with 57,000 reported in the last 7 days - the lowest weekly toll since November 2020.   How much of this is due to the global uptake of vaccines, better medical care - possibly diminished virulence in some variants - or simply under-reporting of COVID related deaths by some countries is unknown. 

The WHO summary reads:

Global overview

Data as of 27 June 2021

The global number of new cases over the past week (21-27 June 2021) was over 2.6 million, a similar number compared to the previous week (Figure 1). The number of weekly deaths continued to decrease, with more than 57 000 deaths reported in the past week, a 10% decrease as compared to the previous week. This is the lowest weekly mortality figure since those recorded in early November 2020. Globally, COVID-19 incidence remains very high with an average of over 370 000 cases reported each day over the past week. The cumulative number of cases reported globally now exceeds 180 million and the number of deaths is almost 4 million.

This week, the African region recorded a sharp increase in incidence (33%) and mortality (42%) when compared to the previous week (Table 1). The Eastern Mediterranean and European Regions also reported increases in the number of weekly cases. All Regions, with the exception of the African Region, reported a decline in the number of deaths in the past week.

The highest numbers of new cases were reported from Brazil (521 298 new cases; 3% increase), India (351 218 new cases; 12% increase), Colombia (204 132 new cases; 5% increase), the Russian Federation (134 465 new cases; 24% increase), and Argentina (131 824 new cases; 11% decrease). Over the past week, the highest numbers of new cases per 100 000 population were reported from Seychelles (708 new cases per 100 000 pop), Namibia (509 new cases per 100 000 pop) and Mongolia (491 new cases per 100 000 pop).

Globally, cases of the Alpha variant have been reported in 172 countries, territories or areas (hereafter countries; two new countries in the past week), of Beta in 120 countries (one new country), Gamma in 72 countries (one new country) and Delta in 96 countries (11 new countries).

Once again, this report's special focus is on the rise, and global spread (see map below), of the 4 VOCs (Variants Of Concern); Alpha, Beta, Gamma, and most notably, Delta. 

Although Delta was the more recent arrival, it has already surpassed Gamma in the number of countries reporting cases (n=96) (see The Delta Variant's World Tour).

While the easing of cases over the past few weeks - and the falling death toll - are both encouraging signs, everywhere we see the Delta variant take hold, we are seeing a significant increase in disease transmission. 

Over the next couple of months Delta is expected to become dominant across much of the world.  How much of an impact that will have will depend largely upon vaccine uptake, vaccine efficiency (VE) against VOCs, and how willing people are to continue to use and practice NPIs (nonpharmaceutical interventions), like face covers, hand hygiene, and social distancing. 

The WHO sums up the challenges still facing us with this pandemic:

Special Focus: Current challenges in the context of the COVID-19 pandemic

Well into the second year of the COVID-19 pandemic, the global situation remains highly fragile. While at the global level, trends in cases and deaths have been declining in recent weeks, there is significant variation by region, by country and within countries. In all WHO regions, there are countries reporting sharp increases in cases and hospitalizations. There are a number of factors contribute to this, as repeatedly outlined by WHO, 1 including the emergence and circulation of more transmissible variants of SARS-CoV-2, increased social mixing and mobility, uneven and inequitable vaccination; and considerable pressure to lift public health and social measures.

SARS-CoV-2 variants of concern

On 11 May 2021, WHO designated Delta (B.1.617.2) as a variant of concern due to evidence of increased transmissibility. 2 The increase in the effective reproduction number compared with the Alpha variant (B.1.1.7) is estimated to be 55% (95% CI: 43–68). 3 Given the increase in transmissibility, the Delta variant is expected to rapidly outcompete other variants and become the dominant variant over the coming months. 3 As of 29 June 2021, 96 countries have reported cases of the Delta variant, though this is likely an underestimate as sequencing capacities needed to identify variants are limited. A number of these countries are attributing surges in infections and hospitalizations to this variant.

Low vaccination coverage at the global level

While more than 2.65 billion doses of COVID-19 vaccines have been administered, 4 the majority of these have been in a small number of high-income countries. The gap in vaccine administration between high- and low-income countries is starting to shrink due to the delivery of vaccines through the COVAX facility, but the majority of the world’s population still remains susceptible to SARS-CoV-2 infection and at risk of developing COVID-19.

Increased social mixing and lifting of public health and social measures

Countries have moved in and out of restrictions of varying stringency over the past 18 months. Now, many face considerable pressure to lift any remaining public health and social measures. Social mixing and mobility are increasing, as are the number of gatherings – from small-scale gatherings of friends and family to large sporting and side events, and religious celebrations. Improper planning or assessment of risk of transmission provide opportunities for the virus to spread.

While the virus will have the final say on when this pandemic ends, we still have weapons to use to blunt its impact.  

Assuming we choose to use them. 

LA County Public Health Dept. Statement: `Strongly Recommends' Indoor Mask Wearing Due to Delta Variant

How to Wear Face Cover -CDC 

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Although a lot of people are going to be dismayed at the idea, the announcement overnight from Los Angeles County isn't entirely unexpected, as the Delta variant has already made serious inroads in the UK, India, and more recently Israel (see Israel to reinstate indoor mask mandate next week as COVID-19 cases keep rising).

Last week the ECDC issued a new Threat Assessment On Spread of COVID Variant B.1.617.2 (Delta) VOC which which bluntly warned against relaxation of nonpharmaceutical measures to reduce the spread of the Delta variant, and last the WHO urged fully vaccinated people to continue to wear face masks.

While not a mandate, the revised advice from the L A County Health department is clear.  Vaccinated or not, they strongly urge everyone to wear a mask in public spaces. 

June 28, 2021

 

As Delta Variant Circulates, Public Health Recommends Masking Indoors as a Precaution - 3 New Deaths and 259 New Confirmed Cases of COVID-19 in Los Angeles County

With increase circulation of the highly transmissible Delta variant, the Los Angeles County Department of Public Health (Public Health) strongly recommends everyone, regardless of vaccination status, wear masks indoors in public places as a precautionary measure. In the week ending June 12, Delta variants comprised of nearly half of all variants sequenced in Los Angeles County. The Centers for Disease Control and Prevention (CDC) noted that Delta variants are now responsible for about one in every five new infections across the country, up from approximately one in every 10 the week before.

Public Health strongly recommends people wear masks indoors in settings such as grocery or retail stores; theaters and family entertainment centers, and workplaces when you don't know everyone's vaccination status. Until we better understand how and to who the Delta variant is spreading, everyone should focus on maximum protection with minimum interruption to routine as all businesses operate without other restrictions, like physical distancing and capacity limits.

Fully vaccinated people appear to be well protected from infections with Delta variants, however people with only one vaccine dose of Pfizer or Moderna are not as well-protected. The smaller number of COVID-19 infections identified in people who are fully vaccinated have been mild illnesses.

For masks to work properly, they need to completely cover your nose and mouth and fit snugly against the sides of your face and around your nose. If you aren’t fully vaccinated, your mask is one of the most powerful tools you have to protect yourself and other unvaccinated people. This is especially true when you are in an indoor or crowded outdoor space. If you are not fully vaccinated and work in a setting where you have sustained close contact with others who are not fully vaccinated or whose vaccination status is unknown, consider wearing a respirator for additional protection.

Public Health has confirmed 3 new deaths and 259 new cases of COVID-19. The number of cases and deaths are likely to reflect reporting delays over the weekend. Of the three new deaths reported today, one person that passed away was between the ages of 65 and 79, one person who died was between the ages of 50 and 64, and one person who died was between the ages of 30 and 49.

To date, Public Health identified 1,249,560 positive cases of COVID-19 across all areas of L.A. County and a total of 24,480 deaths. There are 238 people with COVID-19 currently hospitalized. Testing results are available for more than 7,013,000 individuals with 17% of people testing positive. Today's daily test positivity rate is 0.9%.

"We send our deepest condolences to everyone who is mourning a loved one or friend who has passed away from COVID-19,” said Barbara Ferrer, PhD, MPH, MEd, Director of Public Health. “While COVID-19 vaccine provides very effective protection preventing hospitalizations and deaths against the Delta variant, the strain is proving to be more transmissible and is expected to become more prevalent. Mask wearing remains an effective tool for reducing transmission, especially indoors where the virus may be easily spread through inhalation of aerosols emitted by an infected person.”

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I expect we'll see other agencies and jurisdictions follow suit as Delta continues to increase its presence across the United States (see CDC: Alpha Variant Continues To Decline In US As Delta & P.1 Rise).

While I certainly don't enjoy wearing a mask - and I've been fully vaccinated since April - I've never stopped wearing one in public.  

For me, not wearing a mask because you are vaccinated is like not wearing a seatbelt because you have airbags in your car.  You don't know if they will deploy until you actually crash, and even if they do, they don't provide full protection.

And while I'm quite happy to have the protection from the vaccine, I recognize there are limits to its ability to prevent infection, particularly against the Delta variant.  Some recent blogs on that topic include:

Cell: Reduced Neutralization of SARS-CoV-2 B.1.617 by Vaccine and Convalescent serum

CDC Elevates Delta (B.1.617.2) Variant to VOC & Lancet Report On Hospitalizations & Vaccine Effectiveness

UK: Updated Risk Assessment On Delta Variant As Daily Cases Rise To Highest Since February

 

Cell: Reduced Neutralization of SARS-CoV-2 B.1.617 by Vaccine and Convalescent serum

 

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The Delta variant, first detected in India and now embarked on its world tour, has demonstrated its increased transmissibility every place it has landed, but its other attributes are less clear cut.  

There is some evidence that it may increase hospitalizations, that it may evade previously acquired immunity, and that it may render some vaccines less effective.  But how significant these traits are remain unknown. 

The CDC's SARS-CoV-2 Variant Classifications and Definitions page describes Delta as:

B.1.617.2 (Pango lineage)a

Spike Protein Substitutions: T19R, (G142D*), 156del, 157del, R158G, L452R, T478K, D614G, P681R, D950N

Name (Nextstrain)b: 20A/S:478K

WHO Label: Delta

First Identified: India

Attributes:

• Increased transmissibility 29
• Potential reduction in neutralization by some EUA monoclonal antibody treatments 7, 14
• Potential reduction in neutralization by post-vaccination sera 21

Other than increased transmissibility, the remaining attributes remain murky.  In an attempt to better understand the risks posed by the Delta variant, a multi-national collaboration of research scientists have published a new paper in the journal  CELL, which attempts to identify and quantify Delta's antibody escape abilities. 

We've a link and excerpt from the journal pre-proof, along with a media release from FIOCRUZ, which was one of the research organizations involved.  

The good news is, most vaccines appear to offer protection against the Delta variant - albeit not as robust as against older `wild-type' COVID - but comparable to the protection they offer against the Alpha and Gamma variants.  

While vaccines remain protective, it is likely the rate of `breakthrough' infections among the vaccinated will be higher with these three variants. 

The researchers did find that immunity among those previously infected with COVID to be less protective against the Delta variant. This lack of immunity was most apparent (11-fold reduction) in those previously infected with the Gamma (P.1) or Beta (B.1.351) variants. 

For those hoping that a previous bout and recovery from COVID will protect them against future infection, this isn't exactly reassuring news.  Vaccine recipients, while not 100% protected, appear far more resistant to infection. 

First stop, excerpts from the summary from FIOCRUZ. 

Research suggests increased risk of reinfection by the Delta variant

06/28/2021

Maíra Menezes (IOC/Fiocruz)

A recently published study with the participation of the Oswaldo Cruz Foundation (Fiocruz) suggests that the Delta variant of the new coronavirus, initially detected in India, may increase the risk of reinfections. Research shows that serum from people previously infected with other strains is less potent against this viral variant. The problem is markedly observed among individuals previously infected by the Gamma variant, originally identified in Manaus and currently dominant in Brazil, as well as by the Beta variant, first detected in South Africa. In these cases, the ability to neutralize the strain Delta is eleven times smaller.

Serum from vaccinated people also has reduced potency against the Indian-originated variant, but data show that the vaccines remain effective. The ability to neutralize the strain is 2.5 times lower for Pfizer's immunizing agent and 4.3 times lower for Astrazeneca's. The authors of the work emphasize that the indices are similar to those verified with the Gamma and Alpha variants – which emerged in Brazil and the United Kingdom, respectively. There is no evidence of widespread avoidance of neutralization, unlike that recorded with the Beta variant – originating in South Africa.

“It seems likely from these results that current RNA and viral vector vaccines will provide protection against the B.1.617 strain [which has three sublineages, including the Delta variant], although an increase in infections may occur as a result of the ability to reduced serum neutralization,” the researchers state in the article.

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This is a lengthy (74-page) and highly detailed PDF file, and so I've only hit the highlights.  Follow the link to read it in its entirety. 

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum

Chang Liu, Helen M. Ginn, Wanwisa Dejnirattisai, Piyada Supasa, Beibei Wang, Aekkachai Tuekprakhon, Rungtiwa Nutalai, Daming Zhou, Alexander J. Mentzer, Yuguang Zhao, Helen M.E. Duyvesteyn, César López-Camacho, Jose Slon-Campos, Thomas S. Walter, Donal Skelly, Sile Ann Johnson, Thomas G. Ritter, Chris Mason, Sue Ann Costa Clemens, Felipe Gomes Naveca, Valdinete Nascimento, Fernanda Nascimento, Cristiano Fernandes da Costa, Paola Cristina Resende, Alex PauvolidCorrea, Marilda M. Siqueira, Christina Dold, Nigel Temperton, Tao Dong, Andrew J. Pollard, Julian C. Knight, Derrick Crook, Teresa Lambe, Elizabeth Clutterbuck, Sagida Bibi, Amy Flaxman, Mustapha Bittaye, Sandra Belij-Rammerstorfer, Sarah C. Gilbert, Tariq Malik, Miles W. Carroll, Paul Klenerman, Eleanor Barnes, Susanna J. Dunachie, Vicky Baillie, Natali Serafin, Zanele Ditse, Kelly Da Silva, Neil G. Paterson, Mark A. Williams, David R. Hall, Shabir Madhi, Marta C. Nunes, Philip Goulder, Elizabeth E. Fry, Juthathip Mongkolsapaya, Jingshan Ren, David I. Stuart, Gavin R. Screaton

Received 25 May 2021, Revised 4 June 2021, Accepted 11 June 2021, Available online 17 June 2021.

Highlights

• Vaccine/convalescent sera show reduced neutralization of B.1.617.1 and B.1.617.2

 

• Sera from B.1.351 and P.1 show markedly reduced neutralization of B.1.617.2

• B.1.351, P.1 and B.1.617.2 are antigenically divergent

• Vaccines based on B.1.1.7 may broadly protect against current variants

Summary

SARS-CoV-2 has undergone progressive change with variants conferring advantage rapidly becoming dominant lineages e.g. B.1.617. With apparent increased transmissibility variant B.1.617.2 has contributed to the current wave of infection ravaging the Indian subcontinent and has been designated a variant of concern in the UK.

Here we study the ability of monoclonal antibodies, convalescent and vaccine sera to neutralize B.1.617.1 and B.1.617.2 and complement this with structural analyses of Fab/RBD complexes and map the antigenic space of current variants. Neutralization of both viruses is reduced when compared with ancestral Wuhan related strains but there is no evidence of widespread antibody escape as seen with B.1.351. 

However, B.1.351 and P.1 sera showed markedly more reduction in neutralization of B.1.617.2 suggesting that individuals previously infected by these variants may be more susceptible to reinfection by B.1.617.2. This observation provides important new insight for immunisation policy with future variant vaccines in non-immune populations.

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NHC Eyeing Disturbances Off Southeast US & Central Tropical Atlantic

 

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Although it is still June, the tropics are showing more signs of life as two areas of disturbed weather are being monitored by the National Hurricane Center.   The first, off the South Carolina coast, may require tropical storm warnings later today. 

The second may pose a threat to the Leeward islands by mid-week. 

This morning's 8am Tropical Outlook reads:

ZCZC MIATWOAT ALL

TTAA00 KNHC DDHHMM

Tropical Weather Outlook

NWS National Hurricane Center Miami FL

800 AM EDT Mon Jun 28 2021

For the North Atlantic...Caribbean Sea and the Gulf of Mexico:

1. A well-defined low pressure system located about 190 miles  east-southeast of Hilton Head Island, South Carolina, is producing a  large area of showers and thunderstorms mainly west of the center. However, any additional increase in organization of the thunderstorm  activity would result in the issuance of advisories for a tropical  depression or tropical storm later this morning or afternoon.  The low is forecast to move west-northwestward at 15 to 20 mph, and the  system should reach the coast of southern South Carolina or Georgia  by this evening. 

If advisories are initiated, then tropical storm warnings could be required for a portion of the Georgia and South Carolina coasts with short notice. Regardless of development, a few  inches of rain are possible along the immediate coasts of Georgia and southern South Carolina through Tuesday.  An Air Force Reserve  Unit reconnaissance aircraft is scheduled to investigate the system this afternoon.

* Formation chance through 48 hours...high...70 percent.

* Formation chance through 5 days...high...70 percent.

2. A broad area of low pressure associated with a tropical wave is producing a small cluster of showers and thunderstorms over the central tropical Atlantic Ocean.  Some slow development is possible through the end of the week while this system moves quickly westward to west-northwestward at about 20 mph, likely reaching the Lesser Antilles Wednesday night.

* Formation chance through 48 hours...low...20 percent.

* Formation chance through 5 days...medium...40 percent.

Forecaster Papin/Stewart

While it is uncertain whether either of these systems will reach tropical storm status, the next `named' storm will be `Danny'. 

This year's busy forecast, released in late May by NOAA (see NOAA predicts another active Atlantic hurricane season),  calls for between 13 and 20 named storms. How many of those might impact the United States, and of what severity, is unknown.

So if you haven't done so already, plan a visit to NOAA's National Hurricane Preparedness web page, and decide what you need to do now to keep you, your family, and your property safe during the coming tropical season.

You'll find a list of my 2021 Hurricane Preparedness blogs below.  

Hurricane Preparedness Week: Day 7 - Complete A Written Plan

Hurricane Preparedness Week: Day 6 - Help Your Neighbors 

Hurricane Preparedness Week: Day 5 - Strengthen Your Home

Hurricane Preparedness Week: Day 4 - Get An Insurance Check-up

Hurricane Preparedness Week: Day 3 - Assemble Disaster Supplies

Hurricane Preparedness Week: Day 2 - Develop An Evacuation Plan

National Hurricane Preparedness Week: Day 1 - Determine Your Risk

 

SSI Study: Denmark's Cluster-5 mink Variant Had Increased Antibody Resistance

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A full month before the B.1.1.7 (Alpha) variant was announced by the UK's Health Secretary in  December, and 5 months before the first detection of the B.1.617.2 (Delta) variant in India, Denmark was frantically trying to contain a SARS-CoV-2 variant that had arisen as the virus swept through millions of farmed mink. 

As early as May of 2020 (see COVID-19: Back To The Mink Farm) it was apparent that farmed mink were particularly susceptible to SARS-CoV-2 infection and there were even  hints of possible mink-to-human transmission.   

The susceptibility of mink to COVID wasn't that much of a surprise given they are closely related to ferrets - which are often used in influenza research - and have a long history of hosting both human and novel flu strains (see Nature: Semiaquatic Mammals As Intermediate Hosts For Avian Influenza). 

In early November of last year,  Denmark announced the discovery of a mutated SARS-CoV-2 virus in both Mink and in humans, prompting authorities to order the depopulation of 17 million mink (see Denmark Orders Culling Of All Mink Following Discovery Of Mutated Coronavirus).

 

In response, Denmark temporarily locked down North Jutland,  where most of the human cases had been identified, and the UK quickly banned travel to and from Denmark.

Actually, there were multiple `mink variant's' (B.1.1.298 lineage), but only one - dubbed `Cluster 5' - appeared to pose any enhanced threat over the `wild type' COVID  (see EID Journal: SARS-CoV-2 Transmission between Mink (Neovison vison) and Humans, Denmark). 

Although spreading widely in Denmark as late as October, `Cluster 5' proved to be not nearly as transmissible as many of its competitors, and it quickly gave way to more biologically `fit' COVID variants (including, eventually, Alpha).  

While this mink crisis was averted (or, at least traded for a different crisis), SARS-CoV-2 continues to spread through farmed mink - and presumably other animal populations - around the world (see March 2021 CDC: Investigating Possible Mink-To-Human Transmission Of SARS-CoV-2 In The United States), and additional `zoonotic variants' are likely to emerge. 

Just as we've seen humanized flu viruses enter the swine population - mutate over time - and then jump back into humans as a `novel' flu (see Canada: Manitoba Public Health Announces 3rd Swine Variant Case (H3N2v), the the potential for new SARS-CoV-2 variants to emerge from non-human reservoirs is an ongoing concern. 

`Cluster 5' is no longer circulating in humans, but understanding how it evolved - and any increased threat to humans - will be critical in detecting, and containing, any future zoonotic evolution of COVID-19.  

To that end Denmark's SSI (Statens Serum Institut) has published - in Frontiers of Microbiology - their analysis of the Cluster-5 mink Variant.   First, their press release, then a link to the full paper.  I'll have a brief postscript when you return.

The Cluster-5 mink virus variant has now been studied: Decreased sensitivity to antibodies has been confirmed

SSI has investigated the mink variant called cluster-5 (hCoV-19 / Denmark / DCGC-3024/2020, which belonged to the variants under the collective designation B1.1.298). The conclusion is that the worrying findings from the preliminary studies in the autumn of 2020 were correct.

Last edited June 28, 2021

Threat from new virus variants

The unhindered spread of the virus through millions of mink led to accumulations of mutations in i.a. the important nail protein, which is the primary target of protective antibodies. The potential threat from new atypical virus variants necessitated timely investigations of the newly emerged mink variants, such as the cluster-5 variant seen in infected patients.

The need for rapid clarity led to preliminary studies of cluster-5 in the fall of 2020, and the studies showed evidence of resistance to antibodies.

Cluster-5 had 11 amino acid changes, including 5 amino acid changes in spike (Y453F, I692V, M12291I and amino acid elimination 69 + 70) and spread to 19 farms and 14 individuals.

The conclusion is clear: Cluster 5 showed resistance

The new study concludes that the combination of the nail mutations in the cluster-5 virus led to a certain significantly increased degree of antibody resistance in some people after covid-19 infection.

The findings thus confirm the preliminary studies in November 2020.

Following the study of cluster-5 virus, some cluster-5 mink viruses continued to mutate into six amino acid changes in the nail protein. The additional mutated cluster-5 virus variant has not been studied, but shows that the mink variants continued to mutate through infected mink.

Covid among animals should be closely monitored

It is recommended in the article that timely monitoring of zoonotic SARS-CoV-2 infections in animals and especially herds of production animals should be controlled, limited, and closely monitored through sequencing to identify new virus variants of concern or under observation for increased morbidity, increased spread and infectivity as well as increased antibody resistance.

The results have been peer-reviewed and published in the scientific journal Frontiers in Microbiology, June 25, 2021.

Title: "In vitro characterization of fitness and convalescent antibody neutralization of SARS-CoV-2 Cluster-5 variant emerging in mink at Danish farms" .

In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms

Ria Lassaunière1, Jannik Fonager1, Morten Rasmussen1, Anders Frische1, Charlotta Polacek1, Thomas Bruun Rasmussen1, Louise Lohse1, Graham J. Belsham2, Alexander Underwood3,4, Anni Assing Winckelmann3,4, Signe Bollerup4, Jens Bukh3,4, Nina Weis4,5, Susanne Gjørup Sækmose6, Bitten Aagaard7, Alonzo Alfaro-Núñez1, Kåre Mølbak2,8, Anette Bøtner1,2 and Anders Fomsgaard1*

Mink aren't the only possible non-human reservoir for SARS-CoV-2, and while farmed animals pose the highest risk - due mostly to high livestock densities and greater opportunities for human contact - it is also possible that the virus could establish itself in the wild (see EID Journal: SARS-CoV-2 Exposure in Escaped Mink, Utah, USA).

It is worth noting that while MERS-CoV has never evolved to transmit well enough in humans to sustain a major epidemic, it remains a perennial threat because it is endemic in camels (where it  continues to evolve), and occasionally jumps to humans.   

Companion animals, primarily dogs and cats, are also also susceptible to infection.  The CDC maintains a website on what we currently know about SARS-CoV-2 in non-human hosts. 

 

COVID-19 and Animals 

updated June 4, 2021 

Risk of animals spreading SARS-CoV-2, the virus that causes COVID-19, to people

Risk of people spreading SARS-CoV-2 to animals

Animals with reported SARS-CoV-2 infection

Research on animals and COVID-19

What CDC is doing

Guidance and recommendations

More Information

Media Announcements

What you need to know

We do not know the exact source of the current outbreak of coronavirus disease 2019 (COVID-19), but we know that it originally came from an animal, likely a bat.

At this time, there is no evidence that animals play a significant role in spreading SARS-CoV-2, the virus that causes COVID-19, to people.

Based on the available information to date, the risk of animals spreading COVID-19 to people is considered to be low.

More studies are needed to understand if and how different animals could be affected by COVID-19. We are still learning about this virus, but we know that it can spread from people to animals in some situations, especially during close contact.

People with suspected or confirmed COVID-19 should avoid contact with animals, including pets, livestock, and wildlife.

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Denmark: Statens Serum Institut Announces 1st Detection of AY.1 Variant (Delta with K417N)

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A couple of days ago, in The Delta Variant's World Tour, we looked briefly at recent reports of a new COVID variant (AY.1) - which is essentially the Delta Variant with the K417N mutation, or B.1.617.2.1) - that first appeared in India in April, and has now been reported in a dozen countries around the globe. 

Despite alarming media reports (which immediately dubbed this variant `Delta Plus'), it isn't clear how much of an additional threat - if any - this variant poses over the Delta variant.  

Up until Friday, only 11 countries had reported detecting this variant, with the UK and Switzerland leading with 42 and 40 cases respectively.  India, where the variant was first discovered, has only reported 6 cases to GSAID (see Pango Lineages Update)

Surveillance, and genomic sequencing being limited, these numbers almost certainly under represent the global prevalence and spread of this variant, so we should not be surprised to see Denmark adding themselves to the list with the following announcement from their SSI.

The first case of the virus variant AY.1, also called Delta Plus, has now been found in Denmark

The case was found on June 21, 2021, and the follow-up variant PCR and subsequent whole genome sequencing found Delta Plus on June 25. This is a passenger on a plane from Portugal.Last edited June 26, 2021

The Delta Plus case is handled, like the other Delta variant B.1.617.2, according to the highest level in the infection detection by the Danish Agency for Patient Safety. Both the passengers in question and the rest of the aircraft's passengers are detected and must be kept in isolation.

No other Delta-AY.1 have been found yet. positive.

More contagious

Delta –AY.1. is characterized by a mutation in the spike protein called "K417N", which is also known from the Beta variant. Delta-AY.1. have been mentioned in association with increased infectivity and decreased efficacy of neutralizing antibodies, but very preliminary data with serum from vaccinated indicate that vaccines work.

Found in other countries

Delta-AY.1. has been present in England sigen 26/4, but there are still only 41 cases of this variant in total. The variant has not increased in England since its discovery.

Cases of Delta-AY.1 have now been found worldwide in several countries.

See the current figures for Delta-AY.1 here

Not even greater spread than Delta

"At present, there is no indication that Delta-AY.1 is spreading more than the Delta variant without mutation K417N," says Troels Lillebæk, head of department at SSI and professor in the Department of Global Health at the University of Copenhagen. "But we need more data to be able to assess the risk of the Delta-AY.1 variant accurately."

Experts monitor

The health authorities in Denmark have chosen to monitor all positive Corona samples, and a joint SARS-CoV-2 variant risk assessment group has been set up, which continuously assesses all new variants that can be potentially problematic. The variant risk assessment group includes i.a. several expert groups at the Statens Serum Institut, Aalborg University, the Danish Agency for Patient Safety, the Danish Health and Medicines Authority, the Danish Medicines Agency, representatives from clinical microbiological departments and the Danish Regions.

Sources https://www.gisaid.org/hcov19-variants/ https://www.ssi.dk/aktuelt/nyheder/2021/nyvariantpcrsporerb1617_07062021

Given the Delta variant's enhanced transmissibility, and ability to evade some antibodies, any possibility of  a `new and improved'  Delta variant is worthy of our attention.  Whether AY.1 has what it takes to be a contender, and can compete with its parental strain, remains to be seen. 

The K417N amino acid substitution seen in AY.1 has been seen in other variants - including B.1.351 (Beta) - and is thought might contribute to immune escape. But with the possible exception of the Beta variant, it doesn't seem to have propelled any of the other variants where it has appeared to greatness.

Regardless of where AY.1 ends up in the history of the COVID pandemic, the virus continues to mutate, and churn out new iterations of itself.  Most of these will be evolutionary failures - or at least unremarkable compared to what is already out there - and will end up in the dustbin of COVID history. 

But as we saw last December with Alpha, followed less than six months later by Delta - given enough throws of the evolutionary dice - a game changer can sometimes emerge.  

 Stay tuned.

Australian DOH: Declaration of Sydney as a COVID Hotspot

@NSWHealth  tweet https://twitter.com/NSWHealth/status/1408733366334025731

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It's a story that is being repeated around the world.  In places where COVID cases have either been declining or - in the case of Australia, remarkably well controlled -  the pandemic is showing signs of new life as the Delta (B.1.617.2) variant takes hold (see The Delta Variant's World Tour).

Nowhere is this trend more apparent than in the UK, where six weeks ago fewer than 2000 cases were being reported daily, but over the past 3 days more than 45,000 new cases have been confirmed; a 7-fold increase (see UK dashboard below).

Concurrent with this reversal of pandemic fortune has been the rise of the Delta variant, which now accounts for > 95% of all UK cases.  We are seeing similar scenarios occurring in a number of other countries, as this more transmissible COVID variant takes over. 

Australia, which has maintained remarkable control over the spread of the virus (see chart below) for the last 10 months (often reporting daily cases in the single digits), now finds itself dealing with the Delta variant in their most populous city; Sydney (pop. 5 million). 

While the case numbers remain low - having seen Delta's trajectory in the UK and elsewhere - public health officials are reacting quickly, and have ordered a 2-week lockdown for the city (see NSW DOH Additional restrictions for NSW).

Essentially, this order calls for:

Following updated health advice from the Chief Health Officer Dr Kerry Chant about the growing risk to the community, the stay-at-home orders will apply to all people in the Greater Sydney area including the Blue Mountains, Central Coast and Wollongong.

Everyone in Greater Sydney must stay at home unless it is for an essential reason. 

The reasons you may leave your home include:

• Shopping for food or other essential goods and services;
• Medical care or compassionate needs (people can leave home to have a COVID-19 vaccination unless you have been identified as a close contact);
• Exercise outdoors in groups of 10 or fewer;
• Essential work, or education, where you cannot work or study from home.
• Community sport will not be permitted during this period. Weddings will not be permitted from 11.59pm, Sunday 27 June. Funerals will be limited to one person per four square metres with a cap of 100 people, and masks must be worn indoors.

In all other parts of NSW the following restrictions will apply: 

• People who have been in the Greater Sydney region (including the Blue Mountains, Central Coast and Wollongong) on or after June 21 should follow the stay-at-home orders for a period of 14 days after they left Greater Sydney. 
• Visitors to households will be limited to 5 guests – including children;
• Masks will be compulsory in all indoor non-residential settings, including workplaces, and at organised outdoor events;
• Drinking while standing at indoor venues will not be allowed;
• Singing by audiences and choirs at indoor venues or by congregants at indoor places of worship will not be allowed;
• Dancing will not be allowed at indoor hospitality venues or nightclubs however, dancing is allowed at weddings for the wedding party only (no more than 20 people); 
• Dance and gym classes limited to 20 per class (masks must be worn);
• The one person per four square metre rule will be re-introduced for all indoor and outdoor settings, including weddings and funerals;
• Outdoor seated, ticketed events will be limited to 50 per cent seated capacity;
• We have always indicated we will not hesitate to go further with restrictions to protect the people of NSW. 

We understand this is a difficult time for everyone, however we need to take these steps now to get on top of this outbreak.

People across NSW should only enter Greater Sydney for essential purposes. 

Additionally the Australian CMO has declared Synded a hotspot for COVID transmission.

Declaration of Sydney as a hotspot for Commonwealth support extended

The Australian Government Chief Medical Officer, Professor Paul Kelly, has extended the City of Sydney, Waverley, Woollahra, Bayside, Canada Bay, Inner West and Randwick as a COVID-19 Hotspot for the purposes of Commonwealth support until 2 July 2021.
 
Date published:
25 June 2021
 
Media release
 
General public

The Australian Government Chief Medical Officer, Professor Paul Kelly, has extended the City of Sydney, Waverley, Woollahra, Bayside, Canada Bay, Inner West and Randwick as a COVID-19 Hotspot for the purposes of Commonwealth support until 2 July 2021.

On 23 June, the Australian Government Chief Medical Officer, Professor Paul Kelly, declared parts of Sydney a COVID-19 hotspot for the purposes of Commonwealth support from 23 June 2021 for an initial 7 days, and has now extended the hotspot to 2 July 2021.

There have been a further 26 cases across Sydney since the hotspot declaration. This takes the total number of cases associated with the outbreak to 65.

In line with further NSW Government restrictions announced today, Commonwealth support has been extended for another two days until 11:59pm on 2 July 2021, with further review on or before 1 July 2021.

Professor Kelly requests members of the public to continue to follow the directions of NSW Health and encourages all people to continue to seek out their COVID-19 vaccination. Getting vaccinated is considered a valid reason to leave home.

Declaring a hotspot for Commonwealth support triggers, if required:

• Provision of PPE from the National Medical Stockpile
• Actions for aged care facilities including PPE, single site workforce supplement and integration of an aged care response centre into the Public Health Emergency Operations Centre
• Assistance with contact tracing
• Asymptomatic testing via General Practice Respiratory Clinics
• Reprioritisation of vaccine supplies, if required
• Access to COVID-19 Disaster Payment, if eligibility criteria is met, including that state based public health orders run for greater than 7 days.

Read more about listing areas as COVID-19 hotspots.

Granted, Australia is pulling out all of the stops to keep COVID from doing there, what it has done across much of the rest of the world.  Countries and regions where COVID is already well entrenched may not be as motivated to act that aggressively. 

But, even as the world enjoys the lowest level of COVID cases in a year, the spectre of a new Delta-fuelled wave of infection looms large, and - for the time being at least - the prospects of going back to `normal' anytime soon seem to be dimming. 

Current evidence suggests that regions and communities that have a higher uptake of the vaccine will likely be less adversely affected by the Delta variant, even if the vaccines prove less effective in preventing breakthrough infections. 

But vaccines alone are probably not enough to combat these new variants. Earlier this week, the ECDC warned against dropping community NPIs (Non-pharmaceutical Interventions) in the face of rising COVID variants, and yesterday the WHO urged fully vaccinated people to continue to wear face masks. 

Despite being fully vaccinated since April, I'm still wearing face covers in public, and quite frankly I expect to be doing so throughout this fall and winter.  

Because as badly as we want to be done with this pandemic, this pandemic is obviously not ready to be done with us. 

The Delta Variant's World Tour

Credit WHO COVID Epidemiological Update #45

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Although the latest WHO report continues to show COVID in decline - or flat - nearly everywhere in the world except the African Continent (see table below), there are numerous red flags suggesting the pandemic's  tide may be about to turn once again.

We've been watching the erosion of progress against COVID in the UK over the past few weeks as the Delta variant has risen from obscurity, to become dominant, and for the past two days the UK has reported 16,000+ new cases.  Numbers they haven't seen since early February. 

Today, the UK's PHE reported:

Delta cases continue to rise across the UK

PHE’s weekly COVID-19 variant cases data show that numbers of the Delta (VOC-21APR-02) variant in the UK have risen by 35,204 since last week to a total of 111,157. This represents a 46% increase. Of these, 42 are the Delta AY.1 sub lineage. The Delta variant now accounts for approximately 95% of cases that are sequenced across the UK.

PHE has also published the new edition of the variant technical briefing which continues to show that the vaccines continue to have a crucial effect on hospitalisation and death.

An additional 514 people were admitted to hospital in England with a diagnosis of COVID-19 in the week up to 21 June. Of these, 304 were unvaccinated.

Yesterday, the WHO issued a warning about the surge in Africa, and while a combination of factors are at work, the spread of variants - in particular the Delta variant - is listed as a major concern. 

Africa faces steepest COVID-19 surge yet
24 June 2021

Brazzaville, 24 June 2021 – Africa is facing a fast-surging third wave of COVID-19 pandemic, with cases spreading more rapidly and projected to soon overtake the peak of the second wave the continent witnessed at the start of 2021.

COVID-19 cases have risen for five consecutive weeks since the onset of the third wave on 3 May 2021. As of 20 June—day 48 into the new wave—Africa had recorded around 474 000 new cases—a 21% increase compared with the first 48 days of the second wave. At the current rate of infections, the ongoing surge is set to surpass the previous one by early July.

The pandemic is resurging in 12 African countries. A combination of factors including weak observance of public health measures, increased social interaction and movement as well as the spread of variants are powering the new surge. In the Democratic Republic of the Congo and Uganda that are experiencing COVID-19 resurgence, the Delta variant has been detected in most samples sequenced in the past month. Across Africa, the variant—first identified in India—has been reported in 14 countries.

“The third wave is picking up speed, spreading faster, hitting harder. With rapidly rising case numbers and increasing reports of serious illness, the latest surge threatens to be Africa’s worst yet,” said Dr Matshidiso Moeti, World Health Organization (WHO) Regional Director for Africa. “Africa can still blunt the impact of these fast-rising infections, but the window of opportunity is closing. Everyone everywhere can do their bit by taking precautions to prevent transmission.”

WHO is deploying more experts to some of the worst-affected countries, including Uganda and Zambia as well as supporting South Africa-based regional laboratories to monitor variants of concern. WHO is also boosting innovative technological support to other laboratories in the region without sequencing capacities to better monitor the evolution of the virus. In the next six months, WHO is aiming for an eight- to ten-fold increase in the samples sequenced each month in Southern African countries.

The COVID-19 upsurge comes as the vaccine supply crunch persists. Eighteen African countries have used over 80% of their COVAX vaccine supplies, with eight having exhausted their stocks. Twenty-nine countries have administered over 50% of their supplies. Despite the progress, just over 1% of Africa’s population has been fully vaccinated. Globally, around 2.7 billion doses administered, of which just under 1.5% have been administered in the continent.

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Even in highly vaccinated Israel, which a couple of weeks ago was reporting daily cases in the single digits, announced over 200 new cases yesterday, and warned it may reinstitute the requirement of wearing face masks indoors next week. 

Once again, the spread of the Delta variant is getting much of the blame. 

Although it first emerged in India, we arguably have the best information on the Delta variant from the UK, where it is now comprises > 95% of all COVID cases, and their latest risk assessment (June 25th) reads:

And while the United States is currently enjoying a summer lull in COVID cases (13,000 yesterday), the most recent `Nowcast' from the CDC (see CDC: Alpha Variant Continues To Decline In US As Delta & P.1 Rise) estimates the Delta variant now makes up roughly 20% of US cases, and is growing at a rate that all but ensures its dominance a month from now. 

Ready or not, Delta has the potential to reverse many of the gains we've made over the past 6 months against the SARS-CoV-2 pandemic, and the UK is unfortunately at the forefront. What happens there over the weeks ahead could serve as a harbinger of what is to come here in the US and other nations later this summer and fall. 

While the effectiveness of some of the vaccines appears to be degraded against Delta, vaccination is still believed to substantially reduce your chances of being infected - or if infected, seriously sickened - by the virus. 

Earlier this week the ECDC issued a new Threat Assessment On Spread of COVID Variant B.1.617.2 (Delta) VOC  which which bluntly warned against  relaxation of nonpharmaceutical measures to reduce the spread of the Delta variant, in order to have time to fully vaccinate more people. 

Although Delta is seemingly unstoppable, the same could have been said about the Alpha variant just 3 months ago. Now, it is in decline, giving way to Delta. And it is not unreasonable to assume that another, potentially more biologically `fit' variant, could come along to usurp Delta. 

There is currently a lot of chatter about the `Delta Plus' variant (officially B.1.617.2.1 or AY.1) - essentially Delta with the K417N mutation - as being the next `big threat'.  While it carries some concerning changes, it is far from certain how much of a factor it will become (see Science Media Centre expert comment on the ‘Delta plus’ variant (B.1.617.2 with the addition of K417N mutation)).

The UK has detected 42 cases of the Delta AY.1 sub lineage, and is well positioned to monitor how well it fares against its parental strain.  If it is going to be competitive, we should know within a few weeks. 

Until then, I prefer to take this pandemic one Delta at a time. 

  

Two Preprints on `Long COVID' To Ponder

Slide From June 17th CDC COCA Call on `Post-COVID' Syndrome
 

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Viral epidemics and pandemics have a long history of leaving behind a legacy of under-recognized and  poorly understood `post-pandemic' illness, often leaving victims with life-long disabilities.  The most famous of these was the decade-long global epidemic of Encephalitis Lethargica of the 1920s following the 1918 pandemic (The Lancet: COVID-19: Can We Learn From Encephalitis Lethargica?).

 

Among those who survived, Parkinsonism and other neurological sequelae was common.

ME/CFS is another apparent post-viral syndrome, for years scoffed at by many doctors, that is now taken very seriously by the National Institute of Health. Even non-viral infections, like Lyme Disease, can leave lingering and debilitating sequelae. 

We've seen cases of non-polio paralysis - particularly in children and adolescents - following outbreaks of enteroviruses, including EV-71 and more recently, EV-D68 (see CDC MMWR/Vital Signs: Acute Flaccid Myelitis (2020 Edition)).

And over the past year we've seen increasing reports of recovered COVID patients enduring a wide spectrum of chronic, and often debilitating symptoms - such as fatigue, recurrent fevers, `brain fog', myalgias, etc. - that are highly reminiscent of ME/CFS.

Last week the CDC held a COCA call on Evaluating and Caring for Patients with Post-COVID Conditions which focused on a wide range of issues (see graphic below).

While there seems little doubt that Post-COVID or `Long-COVID' is very real, there is much we don't know, including its root cause, and how widespread it is. 

Yesterday two Pre-prints on `Long COVID' were released, which attempt to answer some of these questions. 

The first - from Imperial College London - examines self-reported symptom data from over half a million people included in three REACT-2 rounds, from 15 September to 8 February. The report finds a substantial number of people experiencing persistent symptoms for 12 weeks or more after COVID infection. 

Persistent symptoms following SARS-CoV-2 infection in a random community sample of 508,707 people

Authors: Whitaker, M    Elliott, J  Chadeau-Hyam, M   Riley, S   Darzi, A  Cooke, G  Ward, H  Elliott, P

Item Type: Working Paper

Abstract: Introduction Long COVID, describing the long-term sequelae after SARS-CoV-2 infection, remains a poorly defined syndrome. There is uncertainty about its predisposing factors and the extent of the resultant public health burden, with estimates of prevalence and duration varying widely. 

Methods Within rounds 3–5 of the REACT-2 study, 508,707 people in the community in England were asked about a prior history of COVID-19 and the presence and duration of 29 different symptoms. We used uni- and multivariable models to identify predictors of persistence of symptoms (12 weeks or more). We estimated the prevalence of symptom persistence at 12 weeks, and used unsupervised learning to cluster individuals by symptoms experienced. 

Results Among the 508,707 participants, the weighted prevalence of self-reported COVID-19 was 19.2% (95% CI: 19.1,19.3). 37.7% of 76,155 symptomatic people post COVID-19 experienced at least one symptom, while 14.8% experienced three or more symptoms, lasting 12 weeks or more. This gives a weighted population prevalence of persistent symptoms of 5.75% (5.68, 5.81) for one and 2.22% (2.1, 2.26) for three or more symptoms.

Almost a third of people 8,771/28,713 (30.5%) with at least one symptom lasting 12 weeks or more reported having had severe COVID-19 symptoms (“significant effect on my daily life”) at the time of their illness, giving a weighted prevalence overall for this group of 1.72% (1.69,1.76). The prevalence of persistent symptoms was higher in women than men (OR: 1.51 [1.46,1.55]) and, conditional on reporting symptoms, risk of persistent symptoms increased linearly with age by 3.5 percentage points per decade of life.

Obesity, smoking or vaping, hospitalisation , and deprivation were also associated with a higher probability of persistent symptoms, while Asian ethnicity was associated with a lower probability. Two stable clusters were identified based on symptoms that persisted for 12 weeks or more: in the largest cluster, tiredness predominated, while in the second there was a high prevalence of respiratory and related symptoms. 

Interpretation A substantial proportion of people with symptomatic COVID-19 go on to have persistent symptoms for 12 weeks or more, which is age-dependent. Clinicians need to be aware of the differing manifestations of Long COVID which may require tailored therapeutic approaches. Managing the long-term sequelae of SARS-CoV-2 infection in the population will remain a major challenge for health services in the next stage of the pandemic.

Issue Date: 24-Jun-2021

A second report, published in Nature Medicine, reports on a relatively small cohort (n=312) in a single geographic location (Bergen, Norway), but finds a high incidence of `Long COVID' symptoms, even among younger individuals who had mild illness. 

Long COVID in a prospective cohort of home-isolated patients

Bjørn Blomberg, Kristin Greve-Isdahl Mohn, Karl Albert Brokstad, Fan Zhou, Dagrun Waag Linchausen, Bent-Are Hansen, Sarah Lartey, Therese Bredholt Onyango, Kanika Kuwelker, Marianne Sævik, Hauke Bartsch, Camilla Tøndel, Bård Reiakvam Kittang,
Bergen COVID-19 Research Group, Rebecca Jane Cox & Nina Langeland

Nature Medicine (2021)Cite this article

Abstract

Long-term complications after coronavirus disease 2019 (COVID-19) are common in hospitalized patients, but the spectrum of symptoms in milder cases needs further investigation. We conducted a long-term follow-up in a prospective cohort study of 312 patients—247 home-isolated and 65 hospitalized—comprising 82% of total cases in Bergen during the first pandemic wave in Norway.

At 6 months, 61% (189/312) of all patients had persistent symptoms, which were independently associated with severity of initial illness, increased convalescent antibody titers and pre-existing chronic lung disease. We found that 52% (32/61) of home-isolated young adults, aged 16–30 years, had symptoms at 6 months, including loss of taste and/or smell (28%, 17/61), fatigue (21%, 13/61), dyspnea (13%, 8/61), impaired concentration (13%, 8/61) and memory problems (11%, 7/61). 

Our findings that young, home-isolated adults with mild COVID-19 are at risk of long-lasting dyspnea and cognitive symptoms highlight the importance of infection control measures, such as vaccination.

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Both of these papers have some weaknesses, such as self-reporting of symptoms, a lack of a  control group - and in the case of the Bergen study - a relatively small data sample.  But we continue to see compelling, and remarkably consistent reporting on the lingering sequelae of COVID infection, suggesting these are legitimate illnesses. 

A bigger unknown is what slower, and more insidious, manifestations of Post-COVID might still arise.  It has been suggested by Cardiologists and Neurologists that we may see a wave of serious post-COVID sequelae 5 or even 10 years down the road. 

Are we facing a crashing wave of neuropsychiatric sequelae of COVID-19? Neuropsychiatric symptoms and potential immunologic mechanisms 

Emily A. Troyer, Jordan N. Kohn, and Suzi Hong

Similarly, what appears to be minor heart damage today may, over time, progress into something more problematic. 

Coronavirus Disease 2019 (COVID-19) and the Heart—Is Heart Failure the Next Chapter?

Clyde W. Yancy, MD, MSc1,2; Gregg C. Fonarow, MD3,4

 

JAMA Cardiol. Published online July 27, 2020. doi:10.1001/jamacardio.2020.3575

And, similar to what was seen in the 1920's with Encephalitis Lethargica, there are concerns over a rise in Parkinson's disease in aftermath of COVID (see  Review Article: Parkinsonism as a Third Wave of the COVID-19 Pandemic?).

Many people dismiss COVID infection as mostly mild, and point to the high survival rate - even among those hospitalized - as if that tells the whole story. 

But there are millions of people who have survived their initial COVID infection, and have found that what doesn't kill you, doesn't always make you stronger.