探花直播 of Cambridge - Henrik Salje

System to auto-detect new variants will inform better response to future infectious disease outbreaks

jg533 — Wed, 01 Jan 2025 16:00:35 +0000

探花直播new approach uses samples from infected humans to allow real-time monitoring of pathogens circulating in human populations, and enable vaccine-evading bugs to be quickly and automatically identified. This could inform the development of vaccines that are more effective in preventing disease.

探花直播approach can also quickly detect emerging variants with resistance to antibiotics. This could inform the choice of treatment for people who become infected 鈥� and try to limit the spread of the disease.

It uses genetic sequencing data to provide information on the genetic changes underlying the emergence of new variants. This is important to help understand why different variants spread differently in human populations.

There are very few systems in place to keep watch for emerging variants of infectious diseases, apart from the established COVID and influenza surveillance programmes. 探花直播technique is a major advance on the existing approach to these diseases, which has relied on groups of experts to decide when a circulating bacteria or virus has changed enough to be designated a new variant.

By creating 鈥榝amily trees鈥�, the new approach identifies new variants automatically based on how much a pathogen has changed genetically, and how easily it spreads in the human population 鈥� removing the need to convene experts to do this.聽

It can be used for a broad range of viruses and bacteria and only a small number of samples, taken from infected people, are needed to reveal the variants circulating in a population. This makes it particularly valuable for resource-poor settings.

探花直播report was published in the journal Nature.

鈥淥ur new method provides a way to show, surprisingly quickly, whether there are new transmissible variants of pathogens circulating in populations 鈥� and it can be used for a huge range of bacteria and viruses,鈥� said Dr No茅mie Lefrancq, first author of the report, who carried out the work at the 探花直播 of Cambridge鈥檚 Department of Genetics.

Lefrancq, who is now based at ETH Zurich, added: 鈥淲e can even use it to start predicting how new variants are going to take over, which means decisions can quickly be made about how to respond.鈥澛�

鈥淥ur method provides a completely objective way of spotting new strains of disease-causing bugs, by analysing their genetics and how they鈥檙e spreading in the population. This means we can rapidly and effectively spot the emergence of new highly transmissible strains,鈥� said Professor Julian Parkhill, a researcher in the 探花直播 of Cambridge鈥檚 Department of Veterinary Medicine who was involved in the study.

Testing the technique

探花直播researchers used their new technique to analyse samples of Bordetella pertussis, the bacteria that causes whooping cough. Many countries are currently experiencing their worst whooping cough outbreaks of the last 25 years. It immediately identified 3 new variants circulating in the population that had been previously undetected.

鈥� 探花直播novel method proves very timely for the agent of whooping cough, which warrants reinforced surveillance given its current comeback in many countries and the worrying emergence of antimicrobial resistant lineages,鈥� said Professor Sylvain Brisse, Head of the National Reference Center for whooping cough at Institut Pasteur, who provided bioresources and expertise on Bordetella pertussis genomic analyses and epidemiology.

In a second test, they analysed samples of Mycobacterium tuberculosis, the bacteria that causes Tuberculosis. It showed that 2 variants with resistance to antibiotics are spreading.

鈥� 探花直播approach will quickly show which variants of a pathogen are most worrying in terms of the potential to make people ill. This means a vaccine can be specifically targeted against these variants, to make it as effective as possible,鈥� said Professor Henrik Salje in the 探花直播 of Cambridge鈥檚 Department of Genetics, senior author of the report.

He added: 鈥淚f we see a rapid expansion of an antibiotic-resistant variant, then we could change the antibiotic that鈥檚 being prescribed to people infected by it, to try and limit the spread of that variant.鈥�

探花直播researchers say this work is an important piece in the larger jigsaw of any public health response to infectious disease.

A constant threat

Bacteria and viruses that cause disease are constantly evolving to be better and faster at spreading between us. During the COVID pandemic, this led to the emergence of new strains: the original Wuhan strain spread rapidly but was later overtaken by other variants, including Omicron, which evolved from the original and were better at spreading. Underlying this evolution are changes in the genetic make-up of the pathogens.

Pathogens evolve through genetic changes that make them better at spreading. Scientists are particularly worried about genetic changes that allow pathogens to evade our immune system and cause disease despite us being vaccinated against them.

鈥淭his work has the potential to become an integral part of infectious disease surveillance systems around the world, and the insights it provides could completely change the way governments respond,鈥� said Salje.

探花直播research was primarily funded by the European Research Council.

Reference: Lefrancq, N et al: 鈥�Learning the fitness dynamics of pathogens from phylogenies.鈥� January 2025, DOI: 10.1038/s41586-024-08309-9
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Researchers have come up with a new way to identify more infectious variants of viruses or bacteria that start spreading in humans 鈥� including those causing flu, COVID, whooping cough and tuberculosis.

探花直播approach will quickly show which variants of a pathogen are most worrying in terms of the potential to make people ill. This means a vaccine can be specifically targeted against these variants, to make it as effective as possible.

Henrik Salje

Milan Krasula on Getty

探花直播text in this work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. Images, including our videos, are Copyright 漏探花直播 of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways 鈥� on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

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Birth by C-section more than doubles odds of measles vaccine failure

jg533 — Mon, 13 May 2024 09:01:04 +0000

A study by the 探花直播 of Cambridge, UK, and Fudan 探花直播, China, has found that a single dose of the measles jab is up to 2.6 times more likely to be completely ineffective in children born by C-section, compared to those born naturally.

Failure of the vaccine means that the child鈥檚 immune system does not produce antibodies to fight against measles infection, so they remain susceptible to the disease.

A second measles jab was found to induce a robust immunity against measles in C-section children.

Measles is a highly infectious disease, and even low vaccine failure rates can significantly increase the risk of an outbreak.

A potential reason for this effect is linked to the development of the infant鈥檚 gut microbiome 鈥� the vast collection of microbes that naturally live inside the gut. Other studies have shown that vaginal birth transfers a greater variety of microbes from mother to baby, which can boost the immune system.

鈥淲e鈥檝e discovered that the way we鈥檙e born - either by C-section or natural birth - has long-term consequences on our immunity to diseases as we grow up,鈥� said Professor Henrik Salje in the 探花直播 of Cambridge鈥嬧€檚 Department of Genetics, joint senior author of the report.

He added: 鈥淲e know that a lot of children don't end up having their second measles jab, which is dangerous for them as individuals and for the wider population.

鈥淚nfants born by C-section are the ones we really want to be following up to make sure they get their second measles jab, because their first jab is much more likely to fail.鈥�

探花直播results are published today in the journal Nature Microbiology.

At least 95% of the population needs to be fully vaccinated to keep measles under control but the UK is well below this, despite the Measles, Mumps and Rubella (MMR) vaccine being available through the NHS Routine Childhood Immunisation Programme.

An increasing number of women around the world are choosing to give birth by caesarean section: in the UK a third of all births are by C-section, in Brazil and Turkey over half of all children are born this way.

鈥淲ith a C-section birth, children aren鈥檛 exposed to the mother鈥檚 microbiome in the same way as with a vaginal birth. We think this means they take longer to catch up in developing their gut microbiome, and with it, the ability of the immune system to be primed by vaccines against diseases including measles,鈥� said Salje.

To get their results, the researchers used data from previous studies of over 1,500 children in Hunan, China, which included blood samples taken every few weeks from birth to the age of 12. This allowed them to see how levels of measles antibodies in the blood change over the first few years of life, including following vaccination.

They found that 12% of children born via caesarean section had no immune response to their first measles vaccination, as compared to 5% of children born by vaginal delivery. This means that many of the children born by C-section did still mount an immune response following their first vaccination.

Two doses of the measles jab are needed for the body to mount a long-lasting immune response and protect against measles. According to the World Health Organisation, in 2022 only 83% of the world's children had received one dose of measles vaccine by their first birthday 鈥� the lowest since 2008.

Salje said: 鈥淰accine hesitancy is really problematic, and measles is top of the list of diseases we鈥檙e worried about because it鈥檚 so infectious.鈥�

Measles is one of the world鈥檚 most contagious diseases, spread by coughs and sneezes. It starts with cold-like symptoms and a rash, and can lead to serious complications including blindness, seizures, and death.

Before the measles vaccine was introduced in 1963, there were major measles epidemics every few years causing an estimated 2.6 million deaths each year.

探花直播research was funded by the National Natural Science Foundation of China.

Reference

Wang, W et al: 鈥楧ynamics of measles immunity from birth and following vaccination.鈥� Nature Microbiology, 13 May 2024. DOI: 10.1038/s41564-024-01694-x

Researchers say it is vital that children born by caesarean section receive two doses of the measles vaccine for robust protection against the disease.

CHBD / E+ / Getty Images

Very sick 5 year old little boy fighting measles infection, boy is laying in bed under the blanket with an agonizing expression, boy is covered with rash caused by virus.

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Focus on COVID-19 deaths in under-65s for better insights into infection rates across populations, say researchers

jg533 — Mon, 02 Nov 2020 09:49:27 +0000

探花直播research, conducted by scientists at the 探花直播 of Cambridge and the Institut Pasteur, was published on 2 November聽in the leading journal Nature. It highlights how large COVID-19 outbreaks in European nursing homes, and the potential for missing deaths in some Asian and South American countries, have skewed COVID-19 death data for older age groups, rendering cross-country comparisons of the scale of the pandemic inaccurate.

探花直播researchers say that reporting of deaths from COVID-19 among those under the age of 65 is likely to be far more reliable, and can therefore give clearer insights into the underlying transmission of the virus and enable better comparisons between countries 鈥� crucial in guiding government strategies to try to get COVID-19 under control.聽

鈥淪imply comparing the total number of deaths across countries can be misleading as a representation of the underlying level of transmission of SARS-CoV-2. Most deaths are in older people, but they are the least comparable across countries,鈥� said Megan O鈥橠riscoll, a PhD researcher in the 探花直播 of Cambridge鈥檚 Department of Genetics and first author of the paper.

In countries including the UK, Canada and Sweden, the COVID-19 pandemic has disproportionately affected nursing home residents, who account for over 20% of all reported COVID-19 deaths. 探花直播level of SARS-CoV-2 transmission among the general population can be difficult to disentangle from these large outbreaks.聽

By contrast, some countries in Asia and South America have far fewer reported COVID-19 deaths in older people than expected. One potential explanation for these 鈥榤issing deaths鈥� is that causes of deaths in elderly populations may be less likely to be investigated and reported as countries struggle to contain the epidemic.

鈥淣ursing homes are enclosed communities of people, and once the virus gets in it can spread quickly resulting in higher levels of infection than in the general population. We鈥檙e seeing an excessively large number of deaths from COVID-19 in this older age group, particularly in countries that have many nursing homes,鈥� said Dr Henrik Salje in the 探花直播 of Cambridge鈥檚 Department of Genetics, the senior author of the report.

He added: 鈥淚t鈥檚 not just that residents are older than the general population, they are also generally more frail, so a 70-year old living in a nursing home is often more likely to die of COVID-19 than a 70-year old in the general population. To reduce the overall number of COVID-19 deaths it is vital to protect vulnerable elderly communities.鈥澛�

In their new model, the researchers integrated age-specific COVID-19 death data from 45 countries with 22 national-level seroprevalence surveys. Governments of many countries are using seroprevalence surveys to estimate the number of people in a population with antibodies against the coronavirus. Antibodies indicate if a person has been infected with SARS-CoV-2 at some point, so are a good indicator of population-wide infection rates.聽

鈥淥ur model shows that the number of COVID-19 deaths by age, in people under 65 years old, is highly consistent across countries and likely to be a reliable indicator of the number of infections in the population. This is of critical use in a context where most infections are unobserved,鈥� said O鈥橠riscoll.

探花直播model can be used at a country-wide level to predict a person鈥檚 likelihood of dying from COVID-19 following infection, depending on their age. It also works in reverse, to estimate a country鈥檚 total number of infections given its number of COVID-19 deaths in an age group, which is particularly useful in places where seroprevalence studies have not been conducted.

Using death data from under-65 age groups only, which is most representative of transmission in the whole population, it shows that by the 1 September this year an average of 5% of the population of a country had been infected with SARS-CoV-2. However, in some places it was much higher, especially South America.聽

For example, using Peru鈥檚 COVID-19 death figures, which equate to 0.01% of the country鈥檚 population, the model suggests that over half of the population of Peru has now been infected with SARS-CoV-2 鈥� a figure far higher than expected. This indicates particularly high rates of transmission of the virus in Peru.

But even after excluding data from the over 65鈥檚, the model shows that COVID-19 death rates cannot be compared between some countries, because the relationship between infections and deaths is not consistent when other widespread 鈥榗o-morbidity鈥� factors are involved.

鈥淚t seems that people living in places such as Slovenia and Denmark have a low probability of death following infection with SARS-CoV-2, even after accounting for the ages of their populations, which is very different to what we鈥檝e seen in New York, for example. There are likely to be fundamental differences in the populations across countries, which might include their underlying health,鈥� said Salje.

探花直播model also revealed a strong pattern across countries in the 5-9 year age group, which consistently has the lowest probability of death following SARS-CoV-2 infection.

探花直播work demonstrates how age-specific death data alone can be used to reconstruct the underlying level of SARS-CoV-2 infection in a country and how it has changed over time. 探花直播researchers say this approach could be applied at sub-national scale, and may be of particular use in settings where large seroprevalence studies might not be feasible.

This research was funded by the 探花直播 of Cambridge COVID-19 Rapid Response Grant.

Reference
O鈥橠riscoll, M. et al: 鈥�Age-specific mortality and immunity patterns of SARS-CoV-2.鈥� Nature, Nov 2020. DOI:聽10.1038/s41586-020-2918-0

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How you can support Cambridge鈥檚 COVID-19 research

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Simply comparing the total number of deaths across countries may provide a misleading representation of the underlying level of transmission of SARS-CoV-2, the virus that causes COVID-19, because of large differences in reported COVID-19 death rates in elderly populations in different countries.

Most deaths are in older people, but they are the least comparable across countries.

Megan O鈥橠riscoll

Gerd Altmann from Pixabay

Coronavirus

探花直播text in this work is licensed under a Creative Commons Attribution 4.0 International License. Images, including our videos, are Copyright 漏探花直播 of Cambridge and licensors/contributors as identified.聽 All rights reserved. We make our image and video content available in a number of ways 鈥� as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

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