H5N1

Cholera: Fifty deaths and more than 1,500 people hospitalized in Haiti

Via Le Nouvelliste, which has temporarily ceased to publish on paper owing to the conditions in Haiti: Cholera: fifty deaths and more than 1,500 people hospitalized in Haiti. Excerpt from the Google translation:

After three years without any case of cholera in Haiti despite active research, the Ministry of Public Health and Population detected a first case a month ago, which signals the resurgence of this disease in Haiti. Known for its great contagiousness, helped by the humanitarian crisis that has plagued the country for more than two months, cholera is responsible for more than 1,500 hospitalizations and around fifty deaths, including 14 in the civil prison of Port-au-Prince.

Relegated to the background in the face of the multiple crises that dominate the news in Haiti, cholera continues its path, leaving in its wake more than a thousand patients and fifty people who died in less than a month.  

"Anyone presenting with acute watery, profuse diarrhea, with or without vomiting, with or without dehydration, is considered a suspected case", according to the Department of Epidemiology, Laboratories and Research of the MSPP.  

As of October 1, 2022, 2,274 people fit this case definition. Of these, 253 were confirmed by a positive culture for Vibrio cholerae or by epidemiological link, 1,642 were hospitalized, for a total of 52 deaths.  

Still according to the latest MSPP bulletin published on October 26, 2022, 271 suspected cases and 14 deaths were counted in the civil prison of Port au Prince.  

Two facts draw attention in the bulletin: "the distribution of cumulative suspected cases by age group and the distribution of cases by department."  

More than 1,000 suspected cases have been listed among children under 15. A situation that continues to worry epidemiologists and infectious disease specialists.  

A week ago, Dr. Jean William Pape illustrated the seriousness of the situation by informing that out of 79 patients seen in a ward at the Gheskio centers cholera treatment center, 54 were children.  

“Among the children, we have 39 between 0-5 years old, in this age group we have 3 children with severe acute malnutrition and septic shock,” he revealed.  

Pointing to insecurity and fuel shortages, Dr. Jean William Pape had advocated strengthening awareness campaigns and taking oral serum even before going to a cholera treatment center for suspected cases. 

 Another highlight of the epidemiological bulletin of the MSPP is the spread of cholera in 8 departments of the country. The North and South-East are the only departments absent in the distribution of suspected cases, tested and confirmed by the MSPP.

Fungal disease spiked during Covid pandemic and pathogens spreading due to climate crisis, WHO says

Via The Guardian: Fungal disease spiked during Covid pandemic and pathogens spreading due to climate crisis, WHO says. Excerpt:

Health-threatening fungi are spreading in geographic range due to climate change, while some fungal diseases spiked during the Covid-19 pandemic, according to authors of a newly released World Health Organization report. 

On Tuesday the WHO published its first ever list of fungal priority pathogens, cataloguing 19 organisms that experts identified as being of the greatest threat to public health.  

“Currently, fungal infections receive less than 1.5% of all infectious disease research funding,” the report found, suggesting the true health burden of fungi is unknown, while “most treatment guidelines are informed by limited evidence and expert opinion”.

The WHO’s assistant director general of antimicrobial resistance, Dr Hanan Balkhy, said in a statement: “Emerging from the shadows of the bacterial antimicrobial resistance pandemic, invasive fungal diseases are growing ever more resistant to treatments, becoming an ever more pressing public health concern worldwide.”  

Dr Justin Beardsley, of the University of Sydney Infectious Diseases Institute, who led a group commissioned by the WHO, said historical research underspending was out of step with the “huge burden of disease” of fungal infections.  

“They’re causing as many deaths as tuberculosis, and more than malaria,” he said.  

The report, which involved more than 400 mycology experts and a review of more than 6,000 research papers, ranked fungal pathogens based on public health impact and risk of resistance to antifungal drugs.  

Of the 19 fungi included, four were identified as being of “critical” priority. These included Aspergillus fumigatus and Candida albicans – the two most common fungal pathogens globally – as well as Cryptococcus neoformans, which is a leading cause of death in people with HIV.  

Aspergillus fumigatus mainly affects the lungs, while Candida albicans is the most common cause of thrush – and invasive infections in vulnerable patients have high mortality rates.  

Infection rates of both pathogens rose in many countries during the Covid-19 pandemic. “We suddenly had a bunch of patients who were getting really sick, coming in with lung damage, being in intensive care and having immune-suppressing medications, and so we saw a spike in the rates of these infections,” Beardsley said.  

“Aspergillus fumigatus has got its own disease state called Covid-associated pulmonary aspergillosis.”  

The fourth critical priority pathogen, Candida auris, grows as a yeast and was first discovered in humans in 2009.  

“It just didn’t exist before then,” Beardsley said.  

“It literally appeared all over the world at the same time, and we’re still trying to work out why and how.”

Vietnam: Strengthen prevention and control of avian flu

Via Bao Phu Tho: Strengthen prevention and control of avian flu. This is a news outlet in the province where the current H5 case has been identified. The full report, in the Google translation:

Baophutho.vn - After more than eight years, a case of influenza A/H5 appeared in humans across the country. The case of a child infected with influenza A/H5 has an address in Dong Thanh commune, Thanh Ba district. After receiving the information, the specialized agencies of the Department of Agriculture and Rural Development, the Department of Health and Thanh Ba district actively coordinated, so the investigation and handling of the outbreak was carried out expeditiously, drastically.  

In order to actively prevent avian influenza, the health sector has also organized an investigation, review, and list of close contacts and neighbors with the patient to guide follow-up; organized sampling to send to the Central Institute of Hygiene and Epidemiology for testing, the results were negative for influenza A/H5 virus. Thanh Ba District People's Committee has directed specialized agencies and local authorities to organize zoning.  

Provincial Sub-Department of Animal Husbandry and Veterinary Medicine took samples and sent them to Sub-Department of Animal Health Region I for testing, all results were negative for avian influenza virus; recommending livestock producers to closely monitor the health of poultry flocks; mobilize breeders not to trade or transport poultry out of the locality and not to buy and sell poultry from other localities at the same time. 

According to experts, the human influenza A/H5 outbreak in Dong Thanh commune, Thanh Ba district has been detected in time, is basically being strictly controlled, the risk of spreading to the community is very low. .To date, no human-to-human transmission of influenza A/H5 has been recorded.

However, now is the time of autumn and winter, the weather is favorable for the virus strains causing respiratory infections to spread and develop. This is also the time when the resistance of livestock is reduced, the risk of infectious diseases is high. In order to protect the health of livestock and reduce the risk of disease outbreaks, including avian influenza strains, localities should promote propaganda so that people can fully vaccinate their flocks. livestock phase II in 2022.  

Mr. Nguyen Tat Thanh - Director of the Sub-Department of Livestock and Veterinary Medicine advised: In the current season change, the risk of livestock diseases, especially infectious diseases, is very high. Therefore, along with the implementation of full vaccination with vaccines, farmers also need to closely monitor the health of their livestock, immediately report to local authorities and veterinary agencies when detecting sick or dead pets. 

Strictly implement not to hide the epidemic, not to trade in livestock and poultry in the epidemic area; do not slaughter or eat sick or dead livestock or poultry. In the coming time, the Sub-department will continue to increase the collection of swabs samples in order to early detect disease outbreaks in livestock herds for timely prevention and control measures.

Vietnam: Child H5 bird flu patient no longer in critical condition

Via Dan Tri, a little good news: Child bird flu patient escapes critical condition. The Google translation:

A five-year-old child in the northern province of Phu Tho infected with A/H5 avian flu has escaped critical condition.  

The patient, Vietnam's first human case of A/H5 avian flu since 2014, was taken to the Vietnam National Hospital of Paediatrics on October 8 with severe symptoms, including respiratory failure, liver and acute kidney failure and multi-organ failure.  

Doctor Do Anh Tuan, head of the hospital’s Intensive Care Ward, said that endotracheal intubation has been removed, and she was now quite conscious. Doctors are keeping a close eye on her condition, particularly how her kidneys were functioning.  

The patient’s relatives said that she ate chicken and duck which must have been infected.  

Medical authorities in Thanh Ba District have provided A/H5 avian flu tests for 65 people who came into close contact with her. But, luckily, all of them tested negative for the disease.  

Vietnam has recorded 128 human cases of A/H5 since 2003, including 64 people who died. In 2014 alone, the country saw two cases of H5N1 in the southern provinces of Binh Phuoc and Dong Thap, and both of them died. They had contact with sick poultry.

Vietnam: MoH proposes to strengthen the prevention and control of avian influenza in Phu Tho province

Via the Ministry of Health: The Ministry of Health proposes to strengthen the prevention and control of avian influenza in Phu Tho province - Information on management direction. The Google translation:

Through the infectious disease surveillance system, on October 17, 2022, the Central Institute of Hygiene and Epidemiology - Ministry of Health recorded 1 patient who tested positive for influenza A(H5), currently living. in Thanh Ba district, Phu Tho province. This is the latest human case of influenza A(H5) in Vietnam since February 2014.  

According to information from the Department of Animal Health - Ministry of Agriculture and Rural Development, avian influenza is still recorded in poultry flocks in many localities across the country. Next time is the Lunar New Year and festival season, so the total poultry flock and poultry transport and trade may increase. Besides, the weather is currently in the period of changing seasons and abnormal changes favorable for avian influenza virus to develop. Therefore, there is always a potential risk of transmission of avian influenza to humans.  

In order to proactively prevent avian influenza from infecting humans, on October 20, 2022, the Department of Preventive Medicine - Ministry of Health sent Official Letter 1164/DP-DT requesting Comrade Director of Phu Tho Department of Health to only Directing to strengthen the prevention and control of avian influenza in the province with a number of key contents as follows:  

1. Organize the investigation and thoroughly handle the outbreak; strengthen surveillance to detect new outbreaks in humans; hospitals are ready to collect, isolate and treat according to regulations of the Ministry of Health and promptly notify the provincial Center for Disease Control for timely epidemic prevention and control measures.  

2. Work closely with veterinary authorities and local authorities in monitoring and detecting influenza outbreaks in poultry, promptly sharing information and thoroughly handling outbreaks.  

3. Strengthen communication of measures to prevent avian influenza from spreading to humans in areas with sick and dead poultry and high-risk areas.  

4. Prepare drugs, supplies, chemicals and means of timely support for the locality to implement measures to handle the outbreak.  

5. To coordinate in the prevention and control of diseases transmitted from animals to humans in accordance with the provisions of the Joint Circular No. 16/2013/TTLT-BYT-BNN&PTNT dated May 27, 2013 of the Ministry of Health and Ministry of Agriculture and Rural Development; Report on infectious diseases according to the Circular No. 54/2015/TT-BYT dated December 28, 2015 of the Minister of Health on the Department of Preventive Medicine.

Vietnam: A likely case of human H5N1

Thanks to @bactiman63 for alerting me to this story. Via TuoTre.vn: A girl infected with influenza A (H5): The family used to slaughter sick poultry to eat. This is almost certainly H5N1, and the first Vietnamese case in a human since 2014. The Google translation: 

TTO - According to a family member of a 5-year-old girl (in Phu Tho) infected with influenza A (H5), about a week before the child was admitted to the hospital, the family had geese and chickens showing signs of illness to eat. After that, the patient appeared tired, yellow skin, yellow eyes, vomiting a lot.  

The baby is currently in a state of respiratory failure, diagnosed with acute liver failure, acute kidney failure, septic shock, multi-organ failure,  influenza A  (H5), being treated at the National Children's Hospital.  

According to a report on the morning of October 21 by the Phu Tho Center for Disease Control, the case of influenza A (H5) infection is a girl in Thanh Ba district, Phu Tho province. On 5-10 days, the baby coughs, has a fever, the family buys medicine to take it, but it doesn't help.  

On 7-10 days, the baby was tired, yellow skin, yellow eyes, vomiting a lot, the family took the patient to Thanh Ba District Health Center for examination and was diagnosed with acute liver failure, acute kidney failure of unknown cause, referred to hospital. Phu Tho Obstetrics and Children Hospital.  

Here the baby was also diagnosed with acute liver failure, acute renal failure of unknown cause. On 8-10 days, the patient was transferred to the National Children's Hospital. Two days later the baby was tested for influenza type A (H5). On October 17, the National Institute of Hygiene and Epidemiology confirmed that the baby was positive for influenza A virus (H5).  

Currently, the patient is in a state of respiratory failure, intubated with a diagnosis of acute liver failure, acute kidney failure, septic shock, multi-organ failure, influenza A (H5).

Next pandemic may come from melting glaciers, new data shows

Via The Guardian: Next pandemic may come from melting glaciers, new data shows. Excerpt:

The next pandemic may come not from bats or birds but from matter in melting ice, according to new data.  

Genetic analysis of soil and lake sediments from Lake Hazen, the largest high Arctic freshwater lake in the world, suggests the risk of viral spillover – where a virus infects a new host for the first time – may be higher close to melting glaciers.  

The findings imply that as global temperatures rise owing to climate change, it becomes more likely that viruses and bacteria locked up in glaciers and permafrost could reawaken and infect local wildlife, particularly as their range also shifts closer to the poles.  

For instance, in 2016 an outbreak of anthrax in northern Siberia that killed a child and infected at least seven other people was attributed to a heatwave that melted permafrost and exposed an infected reindeer carcass. Before this, the last outbreak in the region had been in 1941.  

To better understand the risk posed by frozen viruses, Stéphane Aris-Brosou and her colleagues at the University of Ottawa in Canada collected soil and sediment samples from Lake Hazen, close to where small, medium and large amounts of meltwater from local glaciers flowed in.  

Next, they sequenced RNA and DNA in these samples to identify signatures closely matching those of known viruses, as well as potential animal, plant or fungal hosts, and ran an algorithm that assessed the chance of these viruses infecting unrelated groups of organisms.  

The research, published in Proceedings of the Royal Society B, suggested that the risk of viruses spilling over to new hosts was higher at locations close to where large amounts of glacial meltwater flowed in – a situation that becomes more likely as the climate warms.  

The team did not quantify how many of the viruses they identified were previously unknown – something they plan to do in the coming months – nor did they assess whether these viruses were capable of triggering an infection.  

However, other recent research has suggested that unknown viruses can, and do, loiter in glacier ice. For instance, last year, researchers at Ohio State University in the US announced they had found genetic material from 33 viruses – 28 of them novel – in ice samples taken from the Tibetan plateau in China. Based on their location, the viruses were estimated to be approximately 15,000 years old.  

In 2014, scientists at France’s National Centre for Scientific Research in Aix-Marseille managed to revive a giant virus they isolated from Siberian permafrost, making it infectious again for the first time in 30,000 years. The study’s author, Jean-Michel Claverie, told the BBC at the time that exposing such ice layers could be “a recipe for disaster”. 

Even so, Aris-Brosou’s team cautioned that predicting a high risk of spillover was not the same as predicting actual spillovers or pandemics. “As long as viruses and their ‘bridge vectors’ are not simultaneously present in the environment, the likelihood of dramatic events probably remains low,” they wrote.  

On the other hand, climate change is predicted to alter the range of existing species, potentially bringing new hosts into contact with ancient viruses or bacteria.  

“The only take-home that we can confidently put forward is that as temperatures are rising, the risk of spillover in this particular environment is increasing,” said Aris-Brosou. “Will this lead to pandemics? We absolutely don’t know.”

H5N1 bird flu kills close to a record number of poultry in the US

In the old days, we worried about H5N1 reaching the Americas. Now, without much fanfare, it's very much here. Via Reuters: Bird flu kills close to a record number of poultry in the U.S. Excerpt:

A near-record number of U.S. chickens and turkeys have died in this year's outbreak of avian flu, as a different form of the virus than farmers battled before has infected more wild birds that then transmit the disease, officials said.  

More than 47 million birds have died due to infections and cullings. This has spurred export bans, lowered egg and turkey production, and contributed to record prices of the staples ahead of the U.S. holiday season. The outbreak exacerbates economic pain for consumers grappling with soaring inflation.

In 2015, 50.5 million birds died in the deadliest U.S. outbreak, the nation's worst animal-health event to date.  

Farmers are fighting a subtype of the H5N1 strain of the virus that survived over the summer, when rising temperatures typically reduce avian flu, said Rosemary Sifford, chief veterinary officer for the U.S. Department of Agriculture (USDA).  

The same subtype, known as the goose/Guangdong lineage, is spreading in Europe, she said in an interview. Europe is already suffering its worst avian flu crisis, with nearly 50 million poultry culled.  

Officials are finding the subtype in a broader range of wild birds, such as ducks, than in the past and it seems to live in the birds longer, Sifford said. An elevated threat for infections may persist until summer 2023 as they migrate, she said.  

The United States is monitoring wild birds for avian flu in four migration paths known as flyways, up from two previously, and plans to do the same next year.

"This virus could be present in wild birds for the foreseeable future," Sifford said. "This one is certainly different."  

The outbreak has infected flocks in 42 states since February, twice as many as in 2015, USDA records show. Infections slowed over the summer this year but did not stop as they did in 2015.  

The tenacity of the virus surprised some producers, who have boosted cleaning and security in barns since the 2015 outbreak.  

"Unfortunately what we've done probably hasn't been enough to protect us from this high load of virus in the wild bird population," Sifford said.

Post-acute health care burden after SARS-CoV-2 infection: A retrospective cohort study

This helps to explain why our healthcare system is under such pressure. Via CMAJ: Post-acute health care burden after SARS-CoV-2 infection: a retrospective cohort study.

Background: The post-acute burden of health care use after SARS-CoV-2 infection is unknown. We sought to quantify the post-acute burden of health care use after SARS-CoV-2 infection among community-dwelling adults in Ontario by comparing those with positive and negative polymerase chain reaction (PCR) test results for SARS-CoV-2 infection.  

Methods: We conducted a retrospective cohort study involving community-dwelling adults in Ontario who had a PCR test between Jan. 1, 2020, and Mar. 31, 2021. Follow-up began 56 days after PCR testing. We matched people 1:1 on a comprehensive propensity score. We compared per-person-year rates for health care encounters at the mean and 99th percentiles, and compared counts using negative binomial models, stratified by sex.  

Results: Among 531 702 matched people, mean age was 44 (standard deviation [SD] 17) years and 51% were female. Females who tested positive for SARS-CoV-2 had a mean of 1.98 (95% CI 1.63 to 2.29) more health care encounters overall per-person-year than those who had a negative test result, with 0.31 (95% CI 0.05 to 0.56) more home care encounters to 0.81 (95% CI 0.69 to 0.93) more long-term care days. At the 99th percentile per-person-year, females who tested positive had 6.48 more days of hospital admission and 28.37 more home care encounters.  

Males who tested positive for SARS-CoV-2 had 0.66 (95% CI 0.34 to 0.99) more overall health care encounters per-person-year than those who tested negative, with 0.14 (95% CI 0.06 to 0.21) more outpatient encounters and 0.48 (95% CI 0.36 to 0.60) long-term care days, and 0.43 (95% CI −0.67 to −0.21) fewer home care encounters. At the 99th percentile, they had 8.69 more days in hospital per-person-year, with fewer home care (−27.31) and outpatient (−0.87) encounters.   

Interpretation: We found significantly higher rates of health care use after a positive SARS-CoV-2 PCR test in an analysis that matched test-positive with test-negative people. Stakeholders can use these findings to prepare for health care demand associated with post-COVID-19 condition (long COVID).

Estimated global proportions of individuals with persistent fatigue, cognitive, and respiratory symptom clusters following symptomatic COVID-19 in 2020 and 2021

Via JAMA Network: Estimated Global Proportions of Individuals With Persistent Fatigue, Cognitive, and Respiratory Symptom Clusters Following Symptomatic COVID-19 in 2020 and 2021. The abstravt:

Importance  Some individuals experience persistent symptoms after initial symptomatic SARS-CoV-2 infection (often referred to as Long COVID).  

Objective  To estimate the proportion of males and females with COVID-19, younger or older than 20 years of age, who had Long COVID symptoms in 2020 and 2021 and their Long COVID symptom duration.  

Design, Setting, and Participants  Bayesian meta-regression and pooling of 54 studies and 2 medical record databases with data for 1.2 million individuals (from 22 countries) who had symptomatic SARS-CoV-2 infection. Of the 54 studies, 44 were published and 10 were collaborating cohorts (conducted in Austria, the Faroe Islands, Germany, Iran, Italy, the Netherlands, Russia, Sweden, Switzerland, and the US). The participant data were derived from the 44 published studies (10 501 hospitalized individuals and 42 891 nonhospitalized individuals), the 10 collaborating cohort studies (10 526 and 1906), and the 2 US electronic medical record databases (250 928 and 846 046). Data collection spanned March 2020 to January 2022.  

Exposures  Symptomatic SARS-CoV-2 infection.  

Main Outcomes and Measures  Proportion of individuals with at least 1 of the 3 self-reported Long COVID symptom clusters (persistent fatigue with bodily pain or mood swings; cognitive problems; or ongoing respiratory problems) 3 months after SARS-CoV-2 infection in 2020 and 2021, estimated separately for hospitalized and nonhospitalized individuals aged 20 years or older by sex and for both sexes of nonhospitalized individuals younger than 20 years of age.  

Results  A total of 1.2 million individuals who had symptomatic SARS-CoV-2 infection were included (mean age, 4-66 years; males, 26%-88%). In the modeled estimates, 6.2% (95% uncertainty interval [UI], 2.4%-13.3%) of individuals who had symptomatic SARS-CoV-2 infection experienced at least 1 of the 3 Long COVID symptom clusters in 2020 and 2021, including 3.2% (95% UI, 0.6%-10.0%) for persistent fatigue with bodily pain or mood swings, 3.7% (95% UI, 0.9%-9.6%) for ongoing respiratory problems, and 2.2% (95% UI, 0.3%-7.6%) for cognitive problems after adjusting for health status before COVID-19, comprising an estimated 51.0% (95% UI, 16.9%-92.4%), 60.4% (95% UI, 18.9%-89.1%), and 35.4% (95% UI, 9.4%-75.1%), respectively, of Long COVID cases.  

The Long COVID symptom clusters were more common in women aged 20 years or older (10.6% [95% UI, 4.3%-22.2%]) 3 months after symptomatic SARS-CoV-2 infection than in men aged 20 years or older (5.4% [95% UI, 2.2%-11.7%]). Both sexes younger than 20 years of age were estimated to be affected in 2.8% (95% UI, 0.9%-7.0%) of symptomatic SARS-CoV-2 infections.  

The estimated mean Long COVID symptom cluster duration was 9.0 months (95% UI, 7.0-12.0 months) among hospitalized individuals and 4.0 months (95% UI, 3.6-4.6 months) among nonhospitalized individuals. Among individuals with Long COVID symptoms 3 months after symptomatic SARS-CoV-2 infection, an estimated 15.1% (95% UI, 10.3%-21.1%) continued to experience symptoms at 12 months.  

Conclusions and Relevance  This study presents modeled estimates of the proportion of individuals with at least 1 of 3 self-reported Long COVID symptom clusters (persistent fatigue with bodily pain or mood swings; cognitive problems; or ongoing respiratory problems) 3 months after symptomatic SARS-CoV-2 infection.