The California Department of Public Health is urging Californians to get immunized against a triple threat of viruses that are expected to surge in the coming months.
Rates of COVID-19, influenza, and respiratory syncytial virus, or RSV, are expected to spike in the late fall and winter months as more people gather indoors, and as fewer people are getting vaccinated against COVID-19.
But a shortage of RSV antibody doses this season has federal and state health officials shifting their guidance to include more vaccinations for pregnant women during certain periods of their pregnancies.
Vaccination rates for COVID-19 are much lower compared to the past two years. The vaccines were previously free for patients, with the cost paid by the federal government, but are now on the commercial market. Those without health insurance can still access free vaccines through a state program called My Turn, which can be accessed at myturn.ca.gov.
Dr. Tomas Aragon, the state's public health officer, said during a virtual press conference Thursday that vaccination rates have been lower among Californians with lower incomes, and among certain racial and ethnic groups.
About 4.6 percent of the state's population is up to date on the COVID-19 vaccine, compared to 75 percent of the state that was fully vaccinated at the height of the pandemic. White Californians are currently vaccinated at a rate of 6.7 percent, while Black Californians have a rate of 2.7 percent and Latinos have a 1.5 percent rate.
COVID-19 infections have come down in the state after a brief summer surge. Statewide, there were 610,381 people newly hospitalized with coronavirus between Aug. 20 and Oct. 14, an average of 248 per day. The state recorded over 104,000 deaths from COVID-19 from Aug. 1 to Sept. 25, an average of 19 per day, according to the state's COVID-19 tracker.
Aragon recommended anyone older than 6 months to get a COVID and a flu shot.
The current COVID-19 vaccinations only require one dose, rather than needing a booster, with the exception of the Novavax vaccine, which received emergency-use authorization from the U.S. Food and Drug Administration this month.
There is revised guidance for the flu vaccine for people with egg allergies who were previously cautioned against the shot. Now, people with egg allergies are encouraged to get the shot like everyone else, unless they have had an adverse reaction in the past, Aragon said.
More than 4,600 Californians died from the flu in 2021, the last full year the federal Centers for Disease Control and Prevention has published data for.
"October is a perfect time to get vaccinated against influenza so you have enough time to build up immunity, so as influenza picks up, you'll be protected," Aragon said.
Protection against RSV can come in the form of a vaccine for older adults and pregnant women, and immunization through antibodies for infants and children. There is currently a shortage of a newly developed antibody treatment from Sanofi and AstraZeneca, Beyfortus (nirsevimab-alip), across the country, prompting the CDC to issue a health advisory Monday recommending rationing the supply.
The state's public health department is encouraging women who are between 32-36 weeks pregnant to get the vaccine as a way to transmit immunity to the fetus that lasts about six months after birth.
Newborns and toddlers between birth and 19 months old are at the highest risk of severe RSV, along with adults older than 65.
Aragon recommended wearing masks, washing your hands, and staying home when sick as prevention methods.
More information on the differences and availability of vaccines can be found at vaccines.org.
SARS-CoV-2 Omicron infections were more common and linked to more severe outcomes than influenza and respiratory syncytial virus (RSV) in emergency department (ED) patients in Sweden, especially among those unvaccinated against COVID-19.
The findings were published yesterday in Clinical Infectious Diseases.
Karolinska Institutet researchers assessed rates of 30-day all-cause death, hospitalization, and intensive care unit (ICU) admission of adults seen in six EDs in Stockholm County for Omicron, flu, or RSV infection in 2021-2022 and 2015-2019. Of 6,385 patients in 2021-2022, 76% were infected with Omicron, 17% had flu, and 7% had RSV.
In total, 22.1% of Omicron patients were unvaccinated against COVID-19 before their ED visit, while 75% had received at least two doses.
Thirty-day death rates were 7.9% in the Omicron group, 2.5% in flu patients, and 6.0% in the RSV group. Omicron patients' adjusted death odds ratio (OR) was 2.36 compared with flu and 1.42 compared with RSV. Stronger links were seen in unvaccinated Omicron patients relative to flu (OR, 5.51) and RSV (OR, 3.29).
Death rates at 30 days were 15% among Omicron patients aged 75 years or older, compared with 8% in the 2021-2022 flu group, 12% in the 2021-2022 RSV cohort, 7% among 5,709 prepandemic flu patients, and 9% among 955 prepandemic RSV patients. Among Omicron patients who received at least two COVID-19 vaccine doses, the OR for death was 2.00 compared with flu and 1.20 compared with RSV.
This underscores the need for public health strategies for managing and mitigating the impact of Omicron and other viral respiratory infections, with continued assessments of their comparative severity.
Ninety-day mortality was 11% among Omicron patients, 3.7% in 2021-2022 flu patients, 8.7% in 2021-2022 RSV patients, 5.1% in the prepandemic flu group, and 9.6% in prepandemic RSV patients.
In 2021-2022, 30-day mortality was 2.6% for influenza A patients; none of the 17 influenza B patients died. From 2015 to 2019, 30-day mortality was 3.2% in influenza A patients and 3.8% in influenza B patients.
"This underscores the need for public health strategies for managing and mitigating the impact of Omicron and other viral respiratory infections, with continued assessments of their comparative severity," the authors wrote.
The Tennessee Department of Health is encouraging all Tennesseans not to wait to get their annual flu vaccinations as the best prevention against getting or spreading the flu virus.
The elderly, people with chronic medical conditions, pregnant women, and young children are all at risk of severe complications if they get the flu, Bradley County Health Department Director Brittany Hopkins said. Flu activity is expected to grow from this point forward, in Tennessee and nationally. So, dont delay getting a flu vaccine.
All Tennesseans, 6 months and older, are eligible to get the flu vaccine. Nationally, 7.5 million illnesses, 105,000 hospitalizations, and 6,300 deaths could be prevented annually if more people choose to get a flu vaccine. The flu vaccine is safe and effective and can protect against the most common types of circulating flu viruses, and the flus worst symptoms.
Bradley County Health Department will provide free flu vaccines to the public, from 4-7 p.m. on Wednesday, Nov. 1, at the Cleveland Family YMCA (220 Urbane Road NE, Cleveland) at its annual Fight Flu 23 event.
The local health department will join more than 100 Tennessee Department of Health locations across Tennessee where the flu vaccine will be free, beginning Nov. 1.
No appointment is needed to get the vaccine. Visit TDHs Fight Flu webpage, to find other locations where the vaccine is available and to get more information.
Fight Flu 23 is TDHs annual, large-scale preparedness exercise where medical staff and teams at county health departments statewide practice their emergency response plans using free flu vaccine for the public.
Avoid close contact with those who are sick with the flu. If you become sick, limit contact with others as much as possible and stay at home. Wash your hands often with soap and water, and cover your nose and mouth with a tissue, or with your arm at the elbow, when you cough or sneeze.
If you do get the flu, your doctor may prescribe antiviral drugs as treatment. Antivirals can make flu symptoms milder and shorten the time someone is sick with the flu. Antivirals are not available as an over-the-counter flu treatment and should be taken only as prescribed by a physician or health care provider.
Flu symptoms can range from mild to severe and include muscle aches, fever, fatigue, sore throat, cough, headaches, and stuffy or runny noses.
The mission of the Tennessee Department of Health is to protect, promote and improve the health and prosperity of people in Tennessee. Learn more about TDH services and programs at www.tn.gov/health.
Iowa health officials announce first flu death of the season
by IOWA'S NEWS NOW
FLU SHOT FILE IMAGE
The Iowa Department of Health and Human Services says the flu and other respiratory viruses are going around the state.
HHS announced the first influenza-related death of the season on Friday as an older adult, (61 to 80 years), from southern Iowa.
Iowas most recent Respiratory Virus Surveillance Report shows the virus at a low level of activity, and hospitals are currently reporting low patient admission rates.
But even though it's low right now, there's a few things you can do to keep you and your family healthy this fall and winter.
HHS says vaccination is important, because it protects from serious illness and death from respiratory diseases like flu, COVID-19, and respiratory syncytial virus (RSV).
They're encouraging Iowans to talk to their doctor or other trusted health care provider about vaccines, especially if you have a chronic health condition that could put you at higher risk for serious illness.
Additional Tips to Stay Healthy:
Iowans with questions about vaccines should speak to their health care provider. You can find healthcare providers with vaccines at https://www.vaccines.gov/.
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Francisco R. Velzquez, M.D., S.M., FCAP
By Francisco R. Velzquez, M.D., S.M., FCAP
The autumnal equinox came and went, and now fall colors adorn the Pacific Northwest landscape. The busy summer season is over, students are back in school, and believe it or not there are already signs of the upcoming seasonal holidays and festivities. These holiday previews seem to start earlier every passing year.
In addition to signaling changing weather patterns, fall also means that an increase in respiratory viral infections is coming. The seasonality and cyclical nature of respiratory viral diseases has been recognized for thousands of years. One of the earliest documented accounts of the seasonality of some viruses can be found in the Book of Epidemics written by Hippocrates around 400 BC. The causal relationship of temperature, humidity and human activities have been examined and debated for years.
With colder temperatures and more inclement weather, indoor activities increase, as well as the time that we all spend around each other in close proximity. Although warm, cozy and festive, these activities contribute to the transmission of viruses with familiar names like influenza, and respiratory syncytial virus. Others like adenovirus and rhinovirus, which cause the common cold, can be seen throughout the year. SARS-CoV-2, which causes COVID-19, has not demonstrated an identifiable seasonal pattern, but the same cold-weather behaviors can cause an increase in COVID-19 transmission too.
As we saw last year, we anticipate seeing flu, RSV and COVID-19 infections coincide. Lets review what we know, and how to best protect our community.
Lets start with the flu, whose expectant seasonality helps us to predict what transmission will look like. The flu season in the Southern Hemisphere is usually between April and September, giving us an early look at which flu types are circulating, the severity of illness, and the season longevity. What happens in the other half of the world does not mean we will see the exact same pattern, but it does inform the strategy for the upcoming flu season, including the composition of the current flu shot and the potential for severe disease. Flu season in the Northern Hemisphere can start as early as October and extend into April and May. Based on preliminary data from five countries in the Southern Hemisphere, the flu vaccines may have prevented up to 50% of potential hospitalizations. The quadrivalent vaccine for our flu season is available and being actively administered.
RSV season usually starts in September and runs through January. We have already seen an increase in positive tests and cases in the southeast portion of the country. Historically, such regional increases are typical with increased activity moving north and west over the following two or three months. This year we have two therapeutic options which were not available before. Two vaccines have been released this year for people 60 and older. Recommendations will be made individually using shared clinical decision making, which means age, comorbidities, and other variables will be taken into consideration. One of the vaccines has also been approved for pregnant women between 32 and 36 weeks of pregnancy during September through January. This provides up to six months of protection once the baby is born.
In addition, a monoclonal antibody compound can be given to babies under 8 months of age who are entering their first RSV season. Children who are 8 to 19 months old, who are at increased risk for severe disease, and who are entering their second RSV season can also receive this treatment.
Lastly, COVID-19 continues to be present in the environment. Members of the Omicron family, which have been with us for a long time, continue to mutate and become more effective at transmission. Cases around the country have increased over the past few weeks, including here in Spokane County. This fall, a reformulated vaccine was made available, which takes into consideration the newer sublineages. This type of reformulation isnt new. It happens every year with the flu vaccine as we determine which strains have the highest probability to cause disease.
Given the person-to-person transmission that each of these viruses is known for, it is important to follow a few very simple precautions:
Know your personal risk for severe disease and the risk for those around you, including family, friends, and co-workers.
Know the transmission risk in your community so you can plan your activities accordingly check transmission rates at covid.srhd.org and the Respiratory Illness Dashboard at doh.wa.gov.
Wash your hands thoroughly and often.
Properly cover your sneezes and coughs.
If you feel sick, get tested, stay home, and monitor your symptoms.
Dont forget to test and mask as recommended.
And, very importantly, talk to you provider about what vaccines are important for you, and when to get them.
Generally, I recommend you start thinking about getting your vaccinations after Labor Day and be completed with the process before Halloween. That makes it easy to remember. The best way to prevent these respiratory viruses is by getting the vaccines each year.
Stay safe, stay well and lets do our best to have great fall and winter seasons.
Francisco R. Velzquez, M.D., S.M., FCAP, is health officer for the Spokane Regional Health District.
Calgary
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Posted: October 27, 2023
Two weeks into the roll out of Alberta's fall immunization campaign, there are concerns uptake may not be keeping pace with the spread of COVID-19 and influenza.
The province's respiratory virus dashboard began reporting immunization statistics for this season on Thursday evening.
It shows 358,741 Albertans (7.9 per cent) had the rolled up their sleeves for the flu shot as of Oct. 21. By the end of last year's flu season, immunization coveragetopped out at 28 per cent.
COVID-19 vaccine uptake is lower, with a total of 236,649(5.2 per cent) having received those shots.
"What we've seen is a pretty steep uptake since these clinics opened," said Craig Jenne, professor in the department of microbiology, immunology and infectious diseases at the University of Calgary.
"[But] they're still nowhere near the level we need for a degree of community protection."
In both cases, the vast majority of doses were distributed last week (Oct. 16 - 21), when the general public first had access to the shots. Care homes had an earlier roll out.
The Calgary and Edmonton zones had the highest vaccination rates for both illnesses and pharmacies gave out the lion's share of doses.
Jenne is particularly concerned about the uptake of the COVID-19 vaccine.
"We know COVID isin the community. We know those cases have been escalating quite rapidly at hospitals. ... So it's probably more pressing to get that number up to at least the level we are seeing with the flushots."
He points to provincial datashowing 113 Albertans have died due to COVID-19 since the end of August, including seven people under the age of 60. Seven of the 57 ICU admissions have been people under the age of 20.
"This is not simply that the older people in Alberta need to get vaccinated. This is a vaccine that's protective across multiple age groups," Jenne said. "We really need to see those numbers start ticking up if we want to avoid significant illness over the holidays."
Jenne warned the number of COVID deaths reported since the end of August alone rivals the number of influenza deaths the province sees in some entire flu seasons.
Alberta's latest COVID vaccine roll out has been bumpy. The provincial government increased a limit on the number of doses pharmacies could order per week, after concerns were raised about cancelled appointments.
But some pharmacists continued to report supply issues during the second week of the immunization campaign.
Alberta's COVID positivity rate remains high at 17.8 per cent. A total of 1,214 people have been hospitalized since the end of August.
When it comes to influenza, 51 people have been hospitalized so far this season and one person hasdied.
Jennifer Lee is a CBC News reporter based in Calgary. She worked at CBC Toronto, Saskatoon and Regina before landing in Calgary in 2002. If you have a health or human interest story to share, let her know. Jennifer.Lee@cbc.ca
Probe-based capture drives viral enrichment
We developed a comprehensive viral capture approach using a diverse probe set across ten different sites on a weekly basis for nearly 1year. The probes (TWIST Comprehensive Viral Capture Panel) are directed against a panel of 3153 different human and animal virus genomes. As part of an initiative from the Texas Epidemic Public Health Institute23, composite 24-h wastewater influent was collected from six treatment plants in Houston, Texas, USA and four plants El Paso, Texas, USA from May 2022 through February 2023 (Fig.1A). Wastewater treatment plant catchment areas varied between 10,000 and 400,000 people (estimated 618,148 people served in Houston and 751,982 in El Paso County). These sites were chosen because they allowed us to examine the breadth and robustness of our approach across two large cities with different characteristics. Houston and El Paso also differ in size and diversity, have contrasting climate and rainfall (El Paso dry and Houston humid), are geographically distant (almost 1200 kilometers), and have different patterns of human travel (El Paso a border city with thousands of daily cross-border commuters, Houston a coastal city with one of the largest ports in the world).
A Map of wastewater catchment areas in Houston and El Paso, TX. The colored areas refer to the sites in each city (EP=4, Houston=6). B The treelike object was drawn with hierarchical taxonomical labels (kingdom, phylum, class, order, family, genus, species) rather than multiple sequence alignments due to independent origins of different virus phyla. Tip point size corresponds to number of wastewater samples with the virus detected, and color corresponds to the skew of the species to Houston (red) or El Paso (blue). C Number of distinct virus strains detected per sample from each wastewater treatment plant. D Rarefaction curves measuring distinct virus strains detected as more samples were analyzed. Lines represent average strains detected while shaded bands represent minimum and maximum values from 50 permutations. E Genome coverage of detected virus genome/segments for each sample. F Percentage of reads aligned to virus pathogen genome database in paired control (no-probe) and treatment (capture with the TWIST Comprehensive Virus Research Panel) groups. n=18 biologically independent samples. Boxplots are defined as: center line=median, lower and upper box-bounds=25th and 75th data percentiles, and whiskers extend to the minimum and maximum values.
The efficacy of probe-based enrichment methods was tested on 18 pilot samples. Following clearance of solids and nucleic acid extraction using methods designed for SARS-CoV-2 detection24, we first sequenced and examined viral read numbers from unenriched samples. Low proportions of viral reads were derived from these unenriched samples (4 78 aligned reads out of 9.8 18.0 million total reads), with 0 to 1 total mammalian viruses detected. In contrast, utilizing the TWIST Comprehensive Viral Research Panel probes on the same extractions, a 3,374-fold enrichment in the proportion of virus reads was observed (Fig.1F) (14.9 thousand 407.0 thousand aligned reads out of 11.6 24.2 million total reads), with 42 to 128 total mammalian viruses detected).
Read mapping-based virus detection and abundance measurement was conducted using EsViritu, a bioinformatics tool we developed for this purpose (Fig.S1). EsViritu leverages sequence information to sensitively detect mammalian viruses and filter out false positives (see materials and methods) (https://github.com/cmmr/EsViritu).
Applying these methods to 363 longitudinal wastewater samples, we detected 28 viral families, 77 genera, 191 species, and 465 distinct virus strains in total (Fig.1B), with a median of 54 to 98 strains detected per sample, depending on the wastewater treatment plant (Fig.1C). Furthermore, rarefaction analysis of virus strains showed that the unique detections were not saturated, and additional virus strains are likely to be detected in future samples (Fig.1D). A median of 28.5 reference genomes or segments had sequencing reads aligning to over 90% of their length with an additional 41 (median) genomes or segments with over 50% alignment (Fig.1E). From a methodological standpoint, this emphasizes the potential for in-depth analysis of circulating viruses beyond abundance measurements.
To infer the quantitative dynamic range for pathogen detection of this assay, we added in lab-grown respiratory syncytial virus A (RSV) virions to real wastewater samples (samples were previously determined to have no detectable RSV). Based on a stepwise dilution series, we could accurately detect and quantify RSV from a spike-in of 51 genome copies to 4 million genome copies with a Pearson correlation of at least R=0.975 (Fig.S2).
Having established a capture-based approach that offers the prospect of a comprehensive virome analysis of complex wastewater samples, we next asked whether signals generated from sequencing data mirror trends observed from publicly available clinical datasets. Case data from select viral pathogens, namely SARS-CoV-2, influenza virus, and monkeypox virus, were obtained for Houston and, when available El Paso, from local or state government sources. We started first with SARS-CoV-2, as wastewater levels have previously been correlated with case data25. Using the reads per kilobase of transcript per million filtered reads (RPKMF) as a proxy for relative virus levels in a given sample, there was a positive correlation between case data and positivity rate for SARS-CoV-2 summer and winter waves and the wastewater signal in Houston (Fig.2A, S3A, B, R=0.50.78) and case data from El Paso (Fig.2B, R=0.59 - 0.73). This finding is strengthened by the fact that a second orthogonal technique to measure SARS-CoV-2 levels in wastewater (i.e., qPCR which is the current standard) was also closely correlated with the RPKMF (Fig.S3C, D) for both Houston (R=0.64) and El Paso (R=0.84).
A SARS-CoV-2 wastewater sequencing abundance compared to reported cases (top) and scatter plot with Pearson correlation coefficients and p-value for two-sided test between wastewater sequencing abundance compared to reported cases of SARS-CoV-2 (bottom) in Houston, TX. B SARS-CoV-2 wastewater sequencing abundance compared to reported cases (top) and scatter plot with Pearson correlation coefficients and p-value for two-sided test between wastewater sequencing abundance compared to reported cases of SARS-CoV-2 (bottom) in El Paso, TX. C Influenza wastewater sequencing abundance compared to reported Weekly Percentage of Visits with Discharge Diagnosed Influenza (top) and scatter plot with Pearson correlation coefficients and p-value for two-sided test between wastewater sequencing abundance compared to Weekly Percentage of Visits with Discharge Diagnosed of Influenza (bottom) in Houston, TX. D Monkeypox virus wastewater sequencing abundance compared to reported Mpox cases (top) and scatter plot with Pearson correlation coefficients and p-value for two-sided test between wastewater sequencing abundance. E Heatmap for all ten wastewater sites for presence/absence and abundance for 11 pathogens of major concern (y-axis) across the entire study period (x-axis).
Similarly, Influenza A Virus abundance in the virome sequencing data was highly concordant with reporting of Weekly Percentage of Visits with Discharge Diagnosed Influenza in the Houston area (Fig.2C, R=0.9). Influenza variants H3N2 and H1N1 were also resolved in our data, concordant with clinical subtyping of this flu season in Texas (see Data and Materials Availability). Once more, the virome sequencing data was highly correlated with qPCR measurements from the same samples (Fig.S3E, F, R=0.57 0.73). Finally, a Monkeypox (Mpox) outbreak occurred in the summer of 2022 in several U.S. cities. Rather strikingly, monkeypox virus was detected numerous times at low abundance in Houston wastewater samples (Fig.2D, R=0.46) in our virome dataset, even though only 1,050 cases were reported in the entire Houston area between July and November 2022. Meanwhile, no detection events of monkeypox virus were recorded from El Paso wastewater samples, consistent with only 10 total reported clinical cases in this metro area.
Encouraging from a detection and possibly public health standpoint, 11 categories of major viral pathogens were routinely detected and could be tracked over the sampling period (Fig.2E), including noroviruses, rotavirus A, hepatitis A virus, RSV, parainfluenza viruses, and enterovirus D68. Interestingly, at times, there were different trends in virus levels observed in both cities and at different periods of the year (Fig.S4).
We wished to understand how the human wastewater virome changed over space and time. Important variables in the structure of virome communities were realized by generating t-distributed stochastic neighbor embedding (t-SNE) plots from the virus abundance data of each sample. There was a stark separation of the samples by the city of collection and date of collection (Fig.3AB). Virus species from several families showed an uneven distribution between Houston and El Paso (Fig.S5A). For example, while we expect most viruses to have a prevalence bias towards El Paso due to higher median levels of strain detection per site (Fig.1C), El Paso had especially strong signals from many Parvoviridae and Sedoreoviridae whereas Houston samples had higher prevalence of many Calicivirdae and Astroviridae, the reasons for which are currently unknown (Fig.S5A).
A t-SNE of wastewater samples using virome abundance data, showing different cities/sites. B t-SNE of wastewater samples using virome abundance data, showing samples over time. C Temporal analysis of intra-site community changes. Each dot is a comparison between two samples. The x-axis measures days in between sampling. The y-axis measures Bray-Curtis dissimilarity between the samples. D Bray-Curtis dissimilarity between samples taken +/- 7days apart, comparing samples from the same site, different site but same city, and different city. ****Represents t-test p-value<1e-04. Different City vs Same Site, p=6.2e164. Different City vs Same City, p=2.1e214. Same City vs Same Site, p=2.9e30.
To assess community dynamics over time, all samples from each site were compared to each other using the Bray-Curtis dissimilarity statistic (Fig.3C). In general, as time went on, the composition of the virome in samples diverged such that samples taken closer in time were quite similar, whereas those separated by many months were very different. Interestingly, a possible exception to the temporal divergence rule can be seen in samples taken from the wastewater treatment plant serving Houstons large intercontinental airport, which likely reflects a transient population of world travelers (Fig.3C, HOU R5). Here, the compositional dissimilarity was poorly correlated with the passing of time, possibly due to flux of the virome from incoming people. On the other hand, as the data collection approaches 1year and the seasons repeat, samples from 3 of 4 El Paso sites seem to be re-converging on their community structures from the previous year. In general, dissimilarity follows a pattern where sites from different cities are more different than sites within the same city, and samples from the same site are more similar than everything else (Fig.3D, Fig.S5B). Finally, we assessed the impact of human population size on virome diversity. The alpha diversity (Shannons statistic) was measured for each sample (Fig.S5C), and the average diversity and population of the service area for each site were plotted (Fig.S5D). Average diversity increases from catchment populations of 10,000 to 100,000 inhabitants, but the diversity values level off with greater numbers of people. Collectively, this data confirms that the structure of wastewater virome communities are substantially determined by temporal and geospatial factors.
A handful of viruses had high or complete genome coverage across many wastewater samples and were therefore suitable for variant analysis. Although a single lineage seemed to dominate the sample read abundance for some virus strains, many samples had a mix of two or more lineages. Therefore, allelic variants were measured by the frequency of non-synonymous mutations compared to the reference genome. We focused on three examples.
Astrovirus MLB1, which has a seroprevalence in Americans close to 100%26, was the virus contained at high genome coverage in the most samples in our dataset. The variant landscape of Astrovirus MLB1 was largely dictated by the city-of-origin of the sample (Fig.4E), with gene-specific mutations in the capsid, ORF1a, and ORF1b showing strong regional localization in time (Fig.4B, Fig.S6B). Human Adenovirus 41 is an enteric virus associated with diarrhea and, possibly, hepatitis27 in children and was also quite common in wastewater. This virus splits into two major lineages (Fig.4A, D, Fig.S6A), with the hypervariable capsid (hexon) gene having a lot of diversity28. Although both lineages dominated in samples from either city, each city had one lineage that was more common. JC Polyomavirus, which is secreted in the urine, commonly establishes long, asymptomatic infections in a high proportion of the population29. Consistent with non-acute, rarely transmitted infections, the variant landscape of this virus seems to lack meaningful spatiotemporal structure and most samples appear to have a diversity of lineages (Fig.4C, F, Fig.S6C).
A Genome map of Human Adenovirus 41 (middle) with non-synonymous variants displayed above (Houston, TX) and below (El Paso, TX) according to genome position (X-axis) and date (Y-axis). B Like (A) but with Astrovirus MLB1. C Like (A) but with JC Polyomavirus. D t-SNE of non-synonymous variant frequency of astrovirus MLB1. E Like (D) but with JC Polyomavirus. F Like (D) but with JC Polyomavirus.
Treatment for HIV could become like receiving a flu jab and require only one injection a year to keep the condition under control, according to a leading pharmaceutical boss.
Deborah Waterhouse, chief executive of ViiV Healthcare, which specialises in the treatment of HIV/AIDS, told The Mail on Sunday that the company wants to release an annual jab within the next decade.
ViiV owned by British pharma giant GlaxoSmithKline (GSK) currently offers an injection that people with HIV need to take every two months to keep their virus levels suppressed.
Sold under the brand name Cabenuva, it has been available on theNHS since April last year as an alternative to the more common daily tablets.
But ViiV is working to develop a new version that will extend the gap between injections to four months and Ms Waterhouse said there was also 'a path towards' an injection that needs to be administered only twice a year.
She added that once-a-year treatments to suppress the virus were also becoming close at hand and could potentially be available in the early 2030s.
'You can get to a point where you only have to treat somebody once a year, almost like taking a flu vaccine,' she said
Meanwhile, ViiV is planning to offer the four-monthly injection by 2027 and the six-monthly dose by the end of the decade.
If left untreated, Human immunodeficiency virus (HIV) can lead to acquired immune deficiency syndrome (AIDS), which reduces the body's ability to defend itself against illness and infection.
The condition has been responsible for tens of millions of deaths since it was first identified in the early 1980s.
However, advances in medical treatment since then mean that these days someone with HIV can have a normal life expectancy provided they continue to take the medication.
Most current treatments still require patients to take the daily tablets, but ViiV says that reducing the number of doses will not just keep virus levels low, but also reduce the anxiety around the condition.
HIV is estimated to affect around 100,000 people in the UK.
By Connor Boyd Health And Science Editor For Dailymail.Com and Cassidy Morrison Senior Health Reporter For Dailymail.Com 12:47 26 Oct 2023, updated 17:24 26 Oct 2023
The Covid vaccine may be linked to a small increase in stroke risk when given alongside a high-dose flu shot, health officials say.
A new analysis by the Food and Drug Administration found the link was clearest in adults over 85 and only applied to thePfizer and Modernabivalent Covid booster vaccines.
The FDAsaid the risk might stem from the flu vaccine alone and be completely unrelated to the Covid shots. Regardless, the report said the risk is still very small.
There were roughly three strokes or stroke-like events called transient ischemic attacks for every 100,000 doses given.
For comparison, in 2022 the death rate from Covid in over-85s was 1,224 per 100,000, with US health experts saying vaccination still outweighs the small risk.
It is the second analysis by health officials to flag a possible association with strokes and seniors after getting the combination of seasonal vaccines.
Meanwhile, a separate analysis by the FDA flagged up a small increase in the incidence of seizures after Covid vaccinations in children ages two to five.
The papers were posted online last week, and have not yet been vetted for publication in a scientific journal. Experts in vaccine safety said the studies were well done.
Both studies were observational, meaning they cannot show a causal link, just an association.
Still,many scientists have credited the body's inflammatory response to vaccines with creating a domino effect of physiological changes leading to stroke and possibly seizures.
In the first analysis, FDA officials analyzed medical claims of nearly 5.4 million Americans aged 65 and older who were enrolled in the government-run health insurance program Medicare.
Researchers looked at the high-dose Fluzone seasonal flu shot, designated specifically for seniors because it contains quadruple the amount of flu protection compared to a normal shot.
They wanted to examine the effect of receiving the Fluzone shot and the Moderna or Pfizer bivalent Covid booster on the same day, looking specifically at rates ofnon-hemorrhagic stroke (NHS) and transient ischemic attack (TIA), also referred to as a 'mini stroke'.
Researchers at the Kaiser Family Foundation in California, found 52 percent of adults said they 'definitely' or 'probably' weren't getting the updated Covid booster this year.
Both types of stroke are caused by a blood clot that blocks blood flow to the brain.
Scientists do not know for sure what exactly causes a vaccine to increase the risk of stroke, and still say it is a rare occurrence.
Studies have shown that soon after receiving a Covid jab, people's blood pressure increased, meaning the heart was working harder than it normally would.
Over time, stress causes damage to the inner lining of blood vessels and narrowing of arteries, creating the perfect condition for a dangerous clot.
But the rise in blood pressure following vaccination is typically temporary, whereas the degree of stress on the arteries leading to a stroke accumulates more gradually.
There is also a risk that the vaccine will cause a strong, abnormal immune response that turns on itself and causes severe inflammation, affecting normal blood flow to the brain.
The group that received a high-dose flu shot and the Moderna bivalent booster had an increased risk of a transient or 'mini' stroke of 35 percent.
The group that got a flu shot and the bivalent Pfizer booster had a 20 percent increased risk.
Further analysis into the link between stroke and flu vaccines alone among more than 6.9 million seniors found that shot increased their risk of stroke by about nine percent, a small yet significant rise.
Because researchers could not find a statistically significant link between stroke and Covid boosters alone, this finding suggested to researchers that it was perhaps the flu vaccine alone that was driving stroke risk.
Still, the risk of suffering a stroke after receiving both a high-dose flu shotas well as a Pfizer or Moderna bivalent booster was low for both.
In absolute terms, there were an additional 3.1 strokes per 100,000 doses following the Pfizer and flu shots and 3.3 strokes per 100,000 doses of the flu and Moderna shots.
The risk of suffering a stroke following a Covid infection is far higher than that after getting a booster shot.
A 2022 study in the journal Nature Medicinereported that military veterans who survived the first 30 days of Covid infection had a 52 percent increased risk of suffering a stroke as well as a 49 percent increased risk of a 'mini stroke'.
A straightforward way to mitigate risk would be to space out vaccines by a couple of weeks, and getting the jabs in different arms rather than receiving both in the upper arm.
The researchers did not dispute the fact that the benefits of getting vaccinated far outweigh the risk of getting severely ill and possibly dying. As President Joe Biden said last fall: 'I really believe this is why God gave us two arms one for the flu shot and the other one for the COVID shot.'
In the second analysisconducted by the FDA, researchers found a very tenuous link between seizures in children ages two to five and older iterations of the Pfizer and Moderna vaccines.
They looked at health data of more than 4.1 million American children ranging in age from six months to 17 years old who had received the vaccines through April 2023. At that point, these types of monovalent vaccines were removed from the FDA's list of approved shots and replaced by the updated bivalent varieties.
There were eight seizures in children six months to five years old reported to the Centers for Disease Control and Prevention's voluntary vaccine side effect reporting database.
Children ages two to five had a slightly higher seizure risk after receiving a Covid vaccination compared to the background seizure rates in the general population in 2020, when overall rates of infectious disease were lower thanks to social distancing.
A signal that the shots prompted seizures disappeared, however, when the researchers compared it to 2022 rates when infections among children came roaring back.
According to the study's authors, the association between convulsions and shots should be taken with a grain of salt.
They said: 'Since febrile seizures can be common in young children for a variety of reasons; the analysis may have identified febrile seizures unrelated to the vaccination later in the risk window.'
Most of those seizures were linked to fevers, not unexpected because many vaccines induce fevers in children, an indication that they have jumpstarted the immune system.
Seizures triggered by fever are relatively common among infants and young children. A rapid temperature increase in the body interferes with normal electrical patterns in the brain, which experts believe leads to seizures.
And infections from flu, Covid, and respiratory syncitial virus are known to cause fever in children, and all of these staged a powerful comeback in 2022.
The benefits of vaccinating outweighed the known and potential risks of Covid infection, they said. Yet millions of parents have declined to get their children vaccinated because the youngest Americans typically fare far better than older adults and seniors.
With Halloween just days away, and the wider autumn and winter holiday season fast approaching, now is the time for most everyone to get their updated COVID-19 vaccine, officials say especially since initial supply shortages have eased.
There are some indications the winter respiratory virus season is just beginning, exacerbating the threat not only of another potential coronavirus wave, but a resurgence of flu and respiratory syncytial virus, or RSV. Last year, all three viruses surged roughly simultaneously, leaving hospitals straining under the weight of a so-called tripledemic.
We have a good supply of COVID-19 and flu vaccines in Los Angeles County and there are options for everyone 6 months and older, county Public Health Director Barbara Ferrer said in a statement. I hope that if many people take advantage of the updated vaccines, L.A. County can avoid a big surge in respiratory virus cases this winter that strains our healthcare system and leads to more deaths.
So far, though, uptake of the updated shots has not been up to snuff for public health officials.
Only 5% of Californians, or 1.8 million people, have received the updated COVID-19 vaccine since it became available last month. Among seniors, the rate is 14%.
Thats not good enough. We should really be seeing much higher rates, especially amongst the old, Dr. Toms Aragn, director of the California Department of Public Health, said at a briefing Thursday. Winter is coming.
Getting the updated shot now, health officials say, will help protect people against the expected wave of COVID-19 thats historically arrived in November and December.
Federal survey data suggest that 7% of U.S. adults got the new COVID-19 vaccine in the first month of the rollout. In a survey in August, 43% of U.S. adults said they planned to get the latest COVID-19 vaccine, according to findings shared by the U.S. Centers for Disease Control and Prevention.
Such uptake would be more in line with that of the annual flu shot. Survey results suggest 47% of U.S. adults got vaccinated during the 202223 flu season. By contrast, only 21% of adults nationwide received the previously updated COVID-19 shot after it was introduced a year ago.
Separately, a survey of more than 1,000 L.A. County adults by the USC Pandemic Research Center suggested that 64% planned on getting the updated COVID-19 vaccine. That would be significantly higher than the 20% of county residents 5 and older and 41% of seniors countywide who received last years reformulated COVID-19 vaccine.
While state officials are pushing for more residents to get vaccinated, the L.A. City Council on Wednesday introduced a motion to sunset that requirement for city employees. If enacted, it would align with similar outside policies, including in L.A. County and the federal government. The state of California ended coronavirus test requirements for unvaccinated state employees in 2022.
There remain demographic disparities among those who are getting vaccinated. Nearly 9% of those living in Californias wealthiest communities have received the new COVID vaccine, compared with fewer than 2% of those living in the lowest-income areas.
Roughly 7% of white Californians have gotten the vaccine, as have 6% of Asian Americans, 4% of Native Hawaiian/Pacific Islanders, 3% of Black, Native American and multiracial Californians and 1.5% of Latino residents.
If youre 6 months or older, you should be getting vaccinated against COVID-19, regardless of previous immunizations, Aragn said. Its no longer a booster. This is now just one shot. And if its been at least two months since the last time you may have received the old bivalent ... booster, or at least three months since youve recovered from an infection, all you need is one shot.
There are a couple of exceptions. The youngest children and those who are immunocompromised may need more than one dose. That is also the case for previously unvaccinated people choosing to get the Novavax vaccine for their first COVID inoculation.
Vaccine supply shortages have eased in recent weeks. But Kaiser Permanente members in Southern California in particular have reported major problems, including being unable for weeks to find appointments close to their homes.
In a statement Thursday, Kaiser said it has a stable supply of the Pfizer-BioNTech vaccine for all age groups.
All healthcare providers nationwide have experienced supply and shipment challenges during the initial launch of the updated COVID-19 vaccine. The majority of those issues have been resolved, the statement said.
Kaiser said some of its locations do not require appointments and that appointments are being added as needed.
The L.A. County Department of Public Health has said anyone including Kaiser members can get the COVID-19 vaccine at no cost at their vaccine sites, including Ted Watkins Memorial Park in Florence-Firestone and Eugene A. Obregon Park in East L.A., which are open from 11 a.m. to 6 p.m. Wednesday through Sunday.
The county also offers vaccinations at eight public health centers in downtown L.A., Hollywood, Willowbrook, Monrovia, Pacoima, Pomona, Whittier and Lancaster.
The county Department of Public Health is considered in-network for all insurers, and can bill Kaiser for the vaccinations.
Uninsured children can get COVID vaccines for free through the Vaccines for Children program. Uninsured adults can get access to free vaccines through Bridge Access Program sites, which include federally qualified health centers and CVS and Walgreens.
No-cost COVID-19 vaccines are also available at the Orange County Health Care AgencysFamily Health Clinic in Santa Ana.
For now, coronavirus levels in wastewater continue to trend downward in Los Angeles County. For the week that ended Oct. 14, the most recent available, the coronavirus level in sewage was 12% of last winters peak, down from 14% the previous week.
This late-year respiratory virus season is the first since the official end of the COVID-19 emergency. And as many return to pre-pandemic norms such as large indoor family gatherings, Aragn urged residents to get vaccinated not only against COVID-19, but the flu and, for those who are recommended, RSV.
As with COVID, officials recommend everyone 6 months and older get vaccinated against the flu via either a shot or a nasal spray. October is an ideal time to get the flu vaccine, but getting it later in the season can still be helpful. Older people also are eligible for a high-potency version of the flu vaccine.
One new development for the flu vaccine this year is that people with a history of allergy to eggs no longer need to take additional safety precautions, according to the CDC.
Most flu vaccines contain a small amount of egg proteins, such as ovalbumin. However, studies that have examined the use of both the nasal spray vaccine and flu shots in egg-allergic and non-egg-allergic patients indicate that severe allergic reactions in people with egg allergies are unlikely, the CDC said.
People who have allergies to other ingredients in the flu vaccine should still avoid getting vaccinated, the CDC said.
Though flu and COVID-19 are not yet spreading widely, circulation of RSV is starting to pick up, Aragn said. RSV can be dangerous, especially for infants and older adults. Immunizations are available at least for certain people.
Those who are at least 60 should talk with their doctor about getting an RSV vaccine, officials say. There are two brands of RSV vaccines available for this age group, one made by GSK, known as Arexvy;and Abrysvo, made by Pfizer.
Those that have chronic medical conditions are the ones that are at highest risk, Aragn said. However, if youre otherwise a very, very healthy 60-year-old, 65-year-old, in consultation with your doctor, you may decide that youre not going to get the vaccine for RSV.
Those who are pregnant can also get a RSV vaccine. They should get it during September through January, only when they are weeks 32 and 36 of their term, to reduce the risk of severe disease in their infants, as the baby will receive protection that will last for months after birth.
Another option to protect newborns is to give them, after birth, an immunization that has preventive antibodies that helps fight RSV infections and protects them from getting very sick.
The immunization is suggested for infants 8 months and younger, as well as those age 8 to 19 months who are at higher risk of severe illness. These antibodies known by the generic name nirsevimab and the trademarked name Beyfortus, which was developed by AstraZeneca and Sanofi are recommended between September and January to help protect babies during RSV season.
There is a shortage of the nirsevimab immunization, the CDC said this week, particularly for prefilled syringe doses intended for babies weighing 11 or more pounds. The CDC recommended that for babies in that weight range, only those at highest risk for severe RSV disease get the immunization.
Masking up continues to be an important tool to help prevent the transmission of infectious diseases, Aragn added, as well as opening the windows, choosing to eat outdoors, being in spaces that are well ventilated, making sure that you wash your hands, and of course, staying home when youre sick, and making sure that you get tested.
Free coronavirus tests remain available at libraries run by the city and the county of Los Angeles, vaccination sites run by the county Department of Public Health, and many food banks and senior centers. Households are also eligible to order four free at-home tests through covid.gov/tests.
In California, most private insurance plans regulated by the state must reimburse their members for eight at-home COVID test kits a month through Nov. 11. After that date, free COVID tests must still be provided through most insurance plans, but covered people must go through an in-network provider to get them at no cost.
For a number of Medicare patients in California, free COVID-19 at-home tests ended on May 11, but COVID-19 testing remains free if ordered by a doctor. For people with a Medicare Advantage plan, the cost of at-home test kits varies and might remain free in some plans, according to the California Department of Public Health.
The L.A. County Department of Public Health suggested that people test for the coronavirus ahead of indoor Halloween and other holiday activities if the guest list includes people at higher risk, such as grandparents, infants and those who are pregnant.
People who get COVID-19 or flu should ask their healthcare provider about treatment options, such as Paxlovid for COVID or a number of anti-flu drugs.
