COVID evolution

The emergence of JN.1 is an evolutionary ‘step change’ in the COVID pandemic. Why is this significant?

Lightspring/Shutterstock

Suman Majumdar, Burnet Institute; Brendan Crabb, Burnet Institute; Emma Pakula, Burnet Institute, and Stuart Turville, UNSW Sydney

Since it was detected in August 2023, the JN.1 variant of COVID has spread widely. It has become dominant in Australia and around the world, driving the biggest COVID wave seen in many jurisdictions for at least the past year.

The World Health Organization (WHO) classified JN.1 as a “variant of interest” in December 2023 and in January strongly stated COVID was a continuing global health threat causing “far too much” preventable disease with worrying potential for long-term health consequences.

JN.1 is significant. First as a pathogen – it’s a surprisingly new-look version of SARS-CoV-2 (the virus that causes COVID) and is rapidly displacing other circulating strains (omicron XBB).

It’s also significant because of what it says about COVID’s evolution. Normally, SARS-CoV-2 variants look quite similar to what was there before, accumulating just a few mutations at a time that give the virus a meaningful advantage over its parent.

However, occasionally, as was the case when omicron (B.1.1.529) arose two years ago, variants emerge seemingly out of the blue that have markedly different characteristics to what was there before. This has significant implications for disease and transmission.

Until now, it wasn’t clear this “step-change” evolution would happen again, especially given the ongoing success of the steadily evolving omicron variants.

JN.1 is so distinct and causing such a wave of new infections that many are wondering whether the WHO will recognise JN.1 as the next variant of concern with its own Greek letter. In any case, with JN.1 we’ve entered a new phase of the pandemic.

Where did JN.1 come from?

The JN.1 (or BA.2.86.1.1) story begins with the emergence of its parent lineage BA.2.86 around mid 2023, which originated from a much earlier (2022) omicron sub-variant BA.2.

Chronic infections that may linger unresolved for months (if not years, in some people) likely play a role in the emergence of these step-change variants.

In chronically infected people, the virus silently tests and eventually retains many mutations that help it avoid immunity and survive in that person. For BA.2.86, this resulted in more than 30 mutations of the spike protein (a protein on the surface of SARS-CoV-2 that allows it to attach to our cells).

The sheer volume of infections occurring globally sets the scene for major viral evolution. SARS-CoV-2 continues to have a very high rate of mutation. Accordingly, JN.1 itself is already mutating and evolving quickly.

How is JN.1 different to other variants?

BA.2.86 and now JN.1 are behaving in a manner that looks unique in laboratory studies in two ways.

The first relates to how the virus evades immunity. JN.1 has inherited more than 30 mutations in its spike protein. It also acquired a new mutation, L455S, which further decreases the ability of antibodies (one part of the immune system’s protective response) to bind to the virus and prevent infection.

The second involves changes to the way JN.1 enters and replicates in our cells. Without delving in to the molecular details, recent high-profile lab-based research from the United States and Europe observed BA.2.86 to enter cells from the lung in a similar way to pre-omicron variants like delta. However, in contrast, preliminary work by Australia’s Kirby Institute using different techniques finds replication characteristics that are aligned better with omicron lineages.

Further research to resolve these different cell entry findings is important because it has implications for where the virus may prefer to replicate in the body, which could affect disease severity and transmission.

Whatever the case, these findings show JN.1 (and SARS-CoV-2 in general) can not only navigate its way around our immune system, but is finding new ways to infect cells and transmit effectively. We need to further study how this plays out in people and how it affects clinical outcomes.

Is JN.1 more severe?

JN.1 has some characteristics which distinguish it from other variants. Elizaveta Galitckaia/Shutterstock

The step-change evolution of BA.2.86, combined with the immune-evading features in JN.1, has given the virus a global growth advantage well beyond the XBB.1-based lineages we faced in 2023.

Despite these features, evidence suggests our adaptive immune system could still recognise and respond to BA.286 and JN.1 effectively. Updated monovalent vaccines, tests and treatments remain effective against JN.1.

There are two elements to “severity”: first if it is more “intrinsically” severe (worse illness with an infection in the absence of any immunity) and second if the virus has greater transmission, causing greater illness and deaths, simply because it infects more people. The latter is certainly the case with JN.1.

What next?

We simply don’t know if this virus is on an evolutionary track to becoming the “next common cold” or not, nor have any idea of what that timeframe might be. While examining the trajectories of four historic coronaviruses could give us a glimpse of where we may be heading, this should be considered as just one possible path. The emergence of JN.1 underlines that we are experiencing a continuing epidemic with COVID and that looks like the way forward for the foreseeable future.

We are now in a new pandemic phase: post-emergency. Yet COVID remains the major infectious disease causing harm globally, from both acute infections and long COVID. At a societal and an individual level we need to re-think the risks of accepting wave after wave of infection.

Altogether, this underscores the importance of comprehensive strategies to reduce COVID transmission and impacts, with the least imposition (such as clean indoor air interventions).

People are advised to continue to take active steps to protect themselves and those around them.

For better pandemic preparedness for emerging threats and an improved response to the current one it is crucial we continue global surveillance. The low representation of low- and middle- income countries is a concerning blind-spot. Intensified research is also crucial.

Suman Majumdar, Associate Professor and Chief Health Officer - COVID and Health Emergencies, Burnet Institute; Brendan Crabb, Director and CEO, Burnet Institute; Emma Pakula, Senior Research and Policy Officer, Burnet Institute, and Stuart Turville, Associate Professor, Immunovirology and Pathogenesis Program, Kirby Institute, UNSW Sydney

This article is republished from The Conversation under a Creative Commons license. Read the original article.

SARS-CoV-2: Pandemic or endemic ?

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As the world is preoccupied with the war in Europe, other geopolitical tensions and economic recovery, the pandemic has taken more of a backseat than its current risk would suggest is prudent. COVID-19 is far from gone and continues to circulate in communities world-wide. While the impact has been lessened through an extraordinary vaccination program, the virus still has capacity to develop variants as it has done with Delta and the more infectious Omicron. With an uneven supply and distribution of vaccines many communities particularly in developing nations or conflict zones remain potentially exposed to the virus and hence possible hosts for variants to develop. The detection of a merged Delticron variant (Delta and Omicron) being a point in case.

Various statements from Governments around the world, rather than health professionals, have canvassed that living with COVID-19 is the new normal as the virus is now more endemic than pandemic. This is not the case. As the World Health Organisation (WHO) has warned, classifying COVID-19 as endemic assumes there is stable circulation of the virus at predictable levels with predictable waves of transmission.

Bringing the virus to manageable levels depends on four key factors: global vaccination rates, the evolution of the virus itself; medical advances in both limiting infection and the treatment of those infected; and preventative measures such as improved ventilation and social distancing. At this time the race between vaccine development and deployment versus evolution of COVID-19 variants is head to head.

Terminology and meaning is important in this context. An epidemic is a disease that is surging in cases, and a pandemic is an epidemic that has spread over several continents. For a disease to be endemic the number of cases is more or less stable with possible seasonal fluctations similar, for example, to colds and flu. As COVID -19 is going through surges in different countries at present, it cannot be termed as endemic at this time.

Ventilation is a key control for limiting transmission of COVID-19

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Since March 2021 when the World Health Organisation (WHO)  finally accepted that COVID-19 is an airborne transmitted virus, a stronger focus on ventilation has led to a greater emphasis on air quality, circulation and replacement. While the virus is transported across room spaces in small particles, it can build-up in density in poorly ventilated spaces. But what is the best protection against virus laden aerosols ? How frequently should air in a room space be replaced ?

The basic measure for what constitutes good air is the number of replacements made in an hour and the level of carbon dioxide present (that represents the concentration of exhaled air in a room that comes from other people - and commensurately, the risk of COVID-19).

  

New Scientist (August 2021) published some relevant data from various selected environments around London with surprising results as the chosen locations have an wider application than only that large city in the UK. While the key measure for air quality is the amount of CO2  present representing the air breathed out by other people, it is also dependent on there being no other source such as a natural gas cooker or heater. Outdoor air has a concentration of around 410 parts per million (ppm) and below 800 ppm is generally regarded as well ventilated and above 1500 ppm is regarded as critical to exit.

Space, details and highest reading

• Outdoors:  413 ppm

• Private car, two people, windows closed: 1,740 ppm
• Private car, two people, windows open:  413 ppm
• Private car, two people, non recirculating ventilation on: 413 ppm  
• Private car, two people recirculating air con on: 1,589 ppm 

• Bus, lower deck, full doors opening at stops: 724 ppm
• London train tube: platform between trains: 783 ppm
• London train tube full carriage standing room only: 1,076 ppm

• Supermarket, large, empty: 413 ppm
• Supermarket, small, busy: 1,100 ppm

• Restaurant, busy by open door: 739 ppm
• Pub, main bar, full, doors and windows open: 420 ppm

Indoor air quality standards essentially fail to protect from airborne pathogens such as viruses and bacteria leading to a urgent needs for new building and ventilation designs to mitigate airborne risks.  

SARS-CoV-2 two years on

It's now two years since SARS-CoV-2 started its move across the world. From 2020, the Johns Hopkins Tracker has charted the data in terms of cases, mortality, jurisdiction and vaccinations. There has always been a level of under-reporting and poor data capture in many countries, nonetheless the staggering number of infections (over 300 million and still counting) and deaths (over 5 million and continuing) is sobering.

The link to the tracker: Johns Hopkins COVID tracker

The World Health Organisation has warned that the current variant, Omicron should not be considered a 'mild' disease simply due to being less lethal than the Delta variant. It can still be a serious infection as with COVID-19 generally.

2022 - the COVID-19 period continues

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A new year has commenced and brings the continuing pandemic with it. The new variant of COVID-19 (SARS-CoV-2), Omicron, is considered by health professionals to be two to three times more infectious than its predecessors. This is thought to be due to changes in the spike protein and its immune evasion properties in comparison to previous COVID infections. 

Of note, no longer will the basic surgical mask or the cloth masks provide any protection (if these ever did) but rather it must be the P2/N95 level of mask which must be correctly fitted so that air is drawn through the mask rather than from any gaps around the face. The benefit of using face masks to prevent transmission of the virus has been demonstrated across the world and will need to remain a basic part of the community's attire for the immediate future. 

The Pfizer BioNTech vaccine for SARS-CoV-2

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 As the vaccine roll-out increases world-wide, one of the strongest candidates is the Pfizer BioNTech vaccine. A few facts assist with understanding the strength and value of this vaccine - 

• The Pfizer vaccine is designated as BNT162b2. 
• It is a lipid nanoparticle-formulated, nucleoside-modified RNA vaccine encoding a prefusion stabilized, membrane-anchored SARS-CoV-2 full-length spike protein.
• Pfizer's method has been not to follow a traditional vaccine method that uses inactive, dead or portions of the actual virus to create an immune response but rather utilise mRNA to instruct human cells to develop their own spike protein similar to one found on the surface of coronavirus particles. The result is that a generation of antibodies are generated specifically targetted to the SAR-CoV-2 spike protein.
• The clinical trial had 43,548 participants in a multinational, placebo-controlled, observer-blinded, pivotal efficacy trial.
• The vaccine was trialed with each participant receiving two doses, 21 days apart.
• BNT162b2 was 95% effective in preventing COVID-19 and the efficacy was the same across all subgroups: age, sex, race, ethnicity, baseline body-mass index and co-existing conditions.
• Side effects were short-term including mild-to-moderate pain at the injection site, fatigue and headache.
• Of note, the Pfizer BioNTech vaccine can be stored up to 5 days at standard refrigerator temperatures when ready for use. It is essential however for very cold temperatures for initial shipping and longer storage.

The clinical trial results, peer reviewed are published in the New England Journal of Medicine (NEJM) which can be located at this link: Pfizer COVID vaccine results

Pfizer have a simple description of the vaccine on their website: Pfizer: the facts about Pfizer and BioNTechs COVID 19 vaccine

The terminology of viruses

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The coronavirus SARS-CoV-2 which causes COVID-19 will change over time and often terminology is inadvertantly misquoted in non-authoritative sources.  SARS-CoV-2 replicates itself by invading a new cell and fusing its genetic material termed RNA (or ribonucleic acid) into the new host. As the RNA is then duplicated, the new copy may not be an exact replica of the original virus.

In understanding the development of the virus changing into different forms, its worth distinguishing between the terms used to describe new versions of viruses generally -

• when an error occurs in duplicating viral RNA these changes are called mutations
• the viruses containing these mutations are termed variants (variants can have a single or many such mutations)
• when a variant virus shows distinct physical difference from the original parent virus, this is termed a strain. All strains are variants but not all variants are strains. 

COVID-19 and the challenges of mass population vaccination programs

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Pfizer-BioNTech, Oxford-AstraZeneca, Moderna, Johnson & Johnson - the vaccines that have been approved through 'Emergency Use Authorisation' in many jurisdictions across the world are rolling out. It's a mammoth effort involving a staggering number of individuals and inherent risks, some of which have already become apparent.

Global management consulting firm, McKinsey & Company, has assessed the process for vaccine roll-outs and identified six critical emerging risks, a number of which already exist in some form -

1. raw material constraints in production scaling: while there are early indications of sufficient global capacity for syringes and fill-finish materials, niche chemical and biological vaccine components are scattered. This creates the risk of competition between countries becoming reality and the challenges of supply which is created.
2. quality-assurance challenges in manufacturing: A new class of vaccines (such as those based on mRNA or viral vectors) at an unprecedented scale of 1.8 billion to 2.3 billion does by mid 2021 requires " massive volumes of inputs, a larger technical workforce, and much expanded ecosystem of production facilities".
3. cold-chain logistics and storage-management challenges: maintaining cold chain control for distribution and storage of mRNA-based vaccines will place strain on the production of dry-ice manufacturing. Fast distribution and usage of vaccines due to demand may alleviate some of this potential risk.
4. increased labour requirements: estimates show that the need for a trained workforce remains acute given the vaccination protocols which are complex in the handling and preparation of vaccines and the added care requirements for patients. Estimates suggest that COVID-19 vaccination is 3.5 times slower than the annual flu vaccination programs even with streamlined site management.
5. wastage at points of care: storing, preparing, scheduling administration of doses at points of care all have error risks. Perhaps the most significant is if there is product wastage when doses are not allocated sufficiently. Vaccine doses come in multidose vials and must be used in a short space of time.
6. IT challenges: Vaccine tracking system systems (VTrckS) or immunization information systems (IIS) designed to manage double doses in populations present software challenges. Given there has already been cyber attacks against COVID-19 vaccine developers and regulators, security has a whole new meaning.

The level of vaccination required is also vast with "..twice as many doses of COVID-19 vaccines being administered in one month than were administered for the whole of the 2009 H1N1 flu vaccine'' (McKinsey and Company 2021).  

McKinsey's propose a range of responses to the six critical emerging risks -

• scale manufacturing in new and existing facilities
• establishment of predictable supplier plans
• built-in redundancy into distribution
• leverage feedback loops
• use of several types of point-of-care facilities
• track and monitor spoilage at points of care
• pace first-dose allocation 
• balance IT upgrades and resilience 

A  link to the research article is below:

McKinsey & Company - the risks and challenges COVID 19 vaccine rollout 

SARS-CoV-2 - explaining the UK variant of the virus

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The emergence of three new variants of SARS-CoV-2 with what appears to be greater transmission amongst human populations again points to the manner in which viruses evolve and adapt in relatively short timespans. The new variants are from the UK (B.1.1.7), South Africa (B.1.351) and Brazil (P.1).  

The engine of SARS-CoV-2 is its ribonucleic acid (or RNA) that is similar to human DNA but more primitive. SARS-CoV-2 spreads by binding to human cells through the spike proteins on its surface that allow it to penetrate cells and fuse its RNA into the target thus enabling it to replicate itself.

As the virus moves from population to population, this process of replication can and does lead to mutations occuring in the RNA which is then passed on to new hosts.

The UK strain of SARS-CoV-2 contains eight mutations to its spike protein of which three are of concern. These three mutations have been designated as -

• N501Y: which enables increased binding to human and murine ACE2 receptors (or the angiotensin-converting enzyme 2 which is found on the surface of human cells)
• 69-70del: which is traced to evolving from the outbreak in farmed minks
• P681H: which is associated with the furin cleavage site (FCS) in the spike protein and enhances what is known as "fusogenicity' or the ability to bind with other cells. The FCS in SARS-CoV-2 appears unique compared to other coronaviruses and more potent.

The efficacy of vaccines currently being deployed in respect of the new strains remains under investigation. The early data from vaccines produced by Johnson & Johnson, Oxford/AstraZeneca and Novavax is not as promising for the UK variant as the original virus although Pfizer appears to be effective. 

COVID-19 impact as at 31 January 2021

Johns Hopkins COVID-19 Dashboard

As COVID-19 continues its march across the globe with new strains emerging from the United Kingdom, South Africa and now Brazil, the continuing health burden remains critical. With 102.5 million confirmed cases worldwide, 2.2M deaths (of which the United States accounts for 439,000 followed by Brazil with 224,000) the vaccination program combined with public health measures (use of face masks, social distancing, use of hand sanitisers and on-site deep cleaning) remains the best course of action to bring the pandemic under control and ultimately end it.

SARS-CoV-2: effectiveness of the Oxford AstraZeneca vaccine

 

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Of the 58 vaccines under development to combat COVID-19, three vaccines so far have proceeded satisfactorily through the clinical trials process - one of these from the Oxford University - AstraZeneca partnership is scheduled for widespread inoculation of the Australian population during 2021 and onwards. This vaccine has been developed as a non-profit intervention aimed at "global supply, equity, and commitment to low-income and middle -income countries" (www.gavi.org/news) and has an agreement under the COVAX facility. Currently the vaccine is shown to have 70.4% efficacy.

Designated as ChAdOx1 nCoV-19, it utilises a chimpanzee adenovirus to enable a vectored vaccine. 

The four randomised controlled clinical trials of this vaccine took place in the UK, South Africa and Brazil with the UK and Brazil components being the first to report with interim efficacy results. Of note from these studies:

• 11, 636 participants were in the clinical trials
• 87.8% were aged 18-55 years
• 82.7% were white
• 60.5% were female

The phase 1 stage of the trial had supported a two dose regimen administered 28 days apart. There were no hospital admissions for those who received the vaccine whereas ten admissions occured in the control groups. An interesting development for the Oxford-AstraZeneca trial was the accidental provision of a low dose of the vaccine for some participants in the UK which was then boosted by a standard dose 28 days later that appears to have not reduced the level of effectiveness.

The clinical trials for this vaccine had substantial strengths including -

• a large sample size
• randomisation to vaccine groups
• inclusion of diverse sites with different races and ethnicities
• standardisation of key elements between trials
• balance of participant characteristics between the vaccine groups 
• similar results in Brazil and the UK for those receiving the standard dose regime providing credibility.

There have been limitations for the clinical trial studies as well such as -

• less than 4% of participants were older than 70 years of age
• no participants older than 55 years received the mixed dose regime
• unavailable results as yet on those participants with comorbidities and any impact.

The two dose regime poses its own challenges for health systems to coordinate and manage. A substantial practical advantage of the the Oxford AstraZeneca vaccine is that it can be transported and stored through the routine refrigerated cold chain whereas in contrast the Pfizer vaccine requires ultra-low temperature freezers.

[Information for this post has been drawn from The Lancet December 8, 2020]

A link is provided below.

Oxford- AstraZeneca vaccine - The Lancet

Clinical trials - the four phase process

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Much of the focus on managing and ultimately containing COVID-19 has naturally centred on the successful development of vaccines to protect people from the onset of infection. 2020 has seen an extraordinary race in the biomedical and pharmaceutical industries to find suitable candidates which can be deployed for public health programmes. Central to this process is the time taken to test drug for efficacy and safety - for the COVID vaccines, a process which normally proceeds over  years has taken only months.

Prior to proceeding to a clinical trial, compounds which constitute the drug are screened at a laboratory setting using computer modelling, tissue samples and pathology to assess which are likely to function with humans. The compounds are tested in at least two species of animals to establish performance, how they are metabolised and any side effects. After this preliminary stage, a candidate drug typically proceeds through a four stage process -

Phase 1: After approval from a human clinical trial ethics committee, and the appropriate health authority (Food and Drug Administration or FDA in the US, and the Therapeutic Goods Administration or TGA in Australia), the drug candidates which are the most promising are tested in small groups of healthy volunteers, usually young to lower middle age, non-smoking and normal body weight. For Phase 1 trials targetting life threatening diseases such as cancer, terminally ill patients as test drug recipients are included. Only one in five Phase-1 tested drugs are successful and proceed to being available for use.

Phase 2: The candidate drug is tested on a larger group of people with an illness to evaluate whether it works and to confirm safety, tolerance for patients and dosage requirements.

Phase 3: The trial is expanded for testing with hundreds or thousands of patients often in multi-institutions in various countries in what is termed a 'randomised controlled trial'. Some patients receive placebos (such as harmless sugar pill) while others receive the test drug itself. Neither doctors nor patients know whether they are using the placebo or the drug which enables an unbiased analysis of the response to the treatment and any side effects. This stage also enables measurement of how effectively the drug works in comparison to existing therapies, the economics of treatment and in quality-of-life terms.

Phase 4: Drug receives regulatory approval and is included in routine clinical practice. Ongoing surveillance studies may reveal any rare side effects or extra benefits.

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COVID-19 World-wide as at the end of October 2020 - 45.5 Million

As the world continues to grapple with COVID-19, Australia now ranks 89th for the virus transmission. The staggering figure of 45.5M infected people almost certainly under-estimates the true figure due to various factors such under-reporting, different measurement of data and low testing rates in some countries. Vaccines, even with considerable advances in virology, still take time to develop and coronaviruses in general are difficult to treat.

COVID-19 incidence and mortality as at 2 May 2020

As the novel coronavirus COVID-19 continues its movement across the world, the overall mortality rate is around 7 % of total infections based on 3.4M persons infected. This however does not accurately represent the number of deaths nor the actual burden of disease due to under-reporting in several jurisdictions, factors of co-morbidity from other conditions and poorer outcomes in several countries compared to others. The timing differential between earlier outbreaks in Europe and South East Asia and later outbreaks in Africa, the Middle East and Africa means the impact of this disease still has some way to progress.

At this point higher mortality rates are shown in the UK (15%), Italy (13%) and Spain (11%) whereas Germany has a low level of death (4%). The United States is currently tracking at 5.8%. These figures sadly can be expected to alter in varying measures with slow or fast upward swings depending on the success of control measures being adopted.

Back in March 2020, Australia was ranked around 19th in the top twenty countries with confirmed numbers of people infected with COVID-19. Using a suite of methods to reduce transmission including closure of borders, social distancing, banning of mass gatherings, shutting down non-essential services, rigorous testing and contact tracing, Australia is now ranked 47th in the world. This is a significant achievement but one which is bittersweet. It comes with significant costs for the country whether  psychological, social welfare and economic - impacts that are being reflected world-wide.

Johns Hopkins University and Medicine remains the main global surveillance site:
Coronavirus Johns Hopkins Map

COVID-19 mapping in NSW by the University of Sydney

The University of Sydney has produced a simple heat map of incidence of COVID-19 for NSW, Australia similar to the Johns Hopkins University format for Global and US incidence of the virus.

As various control measures continue to bring transmission of the virus to much lower levels, the location of much of the disease can be tracked along the coastal regions of the State where the largest population centres are located. Of note the sources of infection remain as -

• Overseas 59 %
• Known contact or cluster 26 %
• No contact or source identified 12 %
• Interstate 2 % 

It is the 12 % which continues to be of the most concern given the unknown source of the original infection which is occurring mainly at the level of community transmission.

The University of Sydney map can be accessed at this location:
COVID 19 data - NSW - University of Sydney

COVID-19 and the United States - updated prevalence and mortality map from Johns Hopkins

As COVID-19 continues to move through the United States, Johns Hopkins University has updated their highly regarded COVID-19 prevalence global heat map with a separate US one tracking the progression of the disease across the States. This graphic presentation enables easier visualisation of the prevalence, recovery and mortality in the currently, worst affected country.

The new feature on the Johns Hopkins University and Medicine map can be accessed at the link:
Johns Hopkins University COVID-19 US Map

COVID-19 as at 11 April 2020

Australia was ranked at number 19 for COVID 19 incidence a week ago but has now dropped to 26 as other countries record increasing rates of disease and mortality.

The Johns Hopkins University & Medicine map can be accessed at this link (below)
Johns Hopkins COVID-19 Map

Monitoring and mapping COVID-19 across the world

Johns Hopkins University and Medicine has developed a real time global case tracker tool for monitoring the movement of COVID-19 across the world.

The map can be access at this link -
World-wide coronavirus map