H5N1

August 2022 Ebola case in DRC linked to 2018-2020 Nord Kivu EVD outbreak

Thanks to Helen Branswell for tweeting the link to this excellent report at Virological.org: August 2022 EVD case in DRC linked to 2018-2020 Nord Kivu EVD outbreak. Excerpt:

The new case of Ebola Virus Disease in Beni is genetically linked to the 2018-2020 Nord Kivu/Ituri EVD outbreak and does not represent a new spillover event.**  

Context  

On Monday, August 15, 2022, the Institut National de Recherche Biomédicale (INRB) Beni mobile laboratory received an oropharyngeal secretion sample taken from a deceased patient who was being treated at the Beni General Reference Hospital (HGR-Beni). The sample tested positive for Ebola virus (EBOV) using the Cepheid Xpert Ebola assay with ct- values of 32.5 for viral glycoprotein (GP), and 28.2 for viral nucleoprotein (NP). For quality control and confirmation, samples were sent to the Rodolphe Mérieux INRB-Goma Laboratory on Tuesday August 16, 2022, where the analysis confirmed the EVD case.  

The patient was admitted on July 23, 2022 to the Internal Medicine department of the HGR-Beni for cough, headache, polyarthralgia, intense physical asthenia dating back several days and for which she had self-medicated with non-specified drugs. She was HIV-positive on antiretroviral treatment, and she had also presented with tuberculosis for which she was receiving anti-tuberculosis treatment.  

On August 13, 2022, her health condition deteriorated with the onset of bronchial congestion and kidney failure, which prompted her transfer to the intensive care unit for better care. She died on August 15, 2022. In total her hospitalization lasted 23 days. The body was collected by the family the same day for burial.  

On August 17, 2022, 131 contacts were listed, including 60 front-line healthcare workers and 71 co-patients. Of the 131 pre-listed contacts, 59 of the 60 HCWs are vaccinated. The vaccination status of the index case and 71 co-patients is not yet known.

Tomato flu outbreak in India

Via The Lancet Respiratory Medicine, another new threat to children and perhaps adults: Tomato flu outbreak in India. Excerpt:

Just as we are dealing with the probable emergence of fourth wave of COVID-19, a new virus known as tomato flu, or tomato fever, has emerged in India in the state of Kerala in children younger than 5 years. The rare viral infection is in an endemic state and is considered non-life-threatening; however, because of the dreadful experience of the COVID-19 pandemic, vigilant management is desirable to prevent further outbreaks.

Although the tomato flu virus shows symptoms similar to those of COVID-19 (both are associated with fever, fatigue, and bodyaches initially, and some patients with COVID-19 also report rashes on the skin), the virus is not related to SARS-CoV-2. Tomato flu could be an after-effect of chikungunya or dengue fever in children rather than a viral infection. The virus could also be a new variant of the viral hand, foot, and mouth disease, a common infectious disease targeting mostly children aged 1–5 years and immunocompromised adults, and some case studies have even shown hand, foot, and mouth disease in immunocompetent adults. Tomato flu is a self-limiting illness and no specific drug exists to treat it.  

The tomato flu was first identified in the Kollam district of Kerala on May 6, 2022, and as of July 26, 2022, more than 82 children younger than 5 years with the infection have been reported by the local government hospitals. The other affected areas of Kerala are Anchal, Aryankavu, and Neduvathur. This endemic viral illness triggered an alert to the neighbouring states of Tamil Nadu and Karnataka. Additionally, 26 children (aged 1–9 years) have been reported as having the disease in Odisha by the Regional Medical Research Centre in Bhubaneswar. To date, apart from Kerala, Tamilnadu, and Odisha, no other regions in India have been affected by the virus. However, precautionary measures are being taken by the Kerala Health Department to monitor the spread of the viral infection and prevent its spread in other parts of India.

The primary symptoms observed in children with tomato flu are similar to those of chikungunya, which include high fever, rashes, and intense pain in joints. Tomato flu gained its name on the basis of the eruption of red and painful blisters throughout the body that gradually enlarge to the size of a tomato. These blisters resemble those seen with the monkeypox virus in young individuals. Rashes also appear on the skin with tomato flu that lead to skin irritation. As with other viral infections, further symptoms include, fatigue, nausea, vomiting, diarrhoea, fever, dehydration, swelling of joints, body aches, and common influenza-like symptoms, which are similar to those manifested in dengue. 

In children with these symptoms, molecular and serological tests are done for the diagnosis of dengue, chikungunya, zika virus, varicella-zoster virus, and herpes; once these viral infections are ruled out, contraction of tomato virus is confirmed. Because tomato flu is similar to chikungunya and dengue as well as hand, foot, and mouth disease, treatment is also similar—ie, isolation, rest, plenty of fluids, and hot water sponge for the relief of irritation and rashes. Supportive therapy of paracetamol for fever and bodyache and other symptomatic treatments is required.

The forgotten virus: Zika families and researchers struggle for support

Via The New York Times, Stephanie Nolen writes: The Forgotten Virus: Zika Families and Researchers Struggle for Support.

RECIFE, Brazil — A procession of mothers pushed children in bulky wheelchairs down a long corridor at a health center in this northeastern Brazilian city, passing patients who glanced at the children, looked away, then looked back, quickly and uneasily.  

The children were smartly turned out in Disney T-shirts, striped socks, plastic sandals. Girls had ponytails tied with big bows; many wore brightly colored glasses. And all were profoundly disabled, their limbs rigid, their mouths slack, many with foreheads that sloped sharply back above their dark eyes.  

Most Brazilians know as soon as they see them: These are Zika babies, whose mothers were infected with the virus while pregnant during a virulent outbreak of the mosquito-borne illness in 2015 and 2016. The chief signifier at birth was microcephaly, unusually small heads that hinted at the devastating brain damage the virus caused while they were still in utero.

Seven years later, they are now children, many of them nearly as big as their mothers. The sight of them visibly startles people who have not thought about them for years. After the Zika epidemic did not turn into a pandemic that swept the globe, Brazil and the rest of the world moved on.  

That has left families in this scrappy corner of Brazil, where the epidemic originated, struggling, mostly alone, to get help for their children, whose mysterious condition presents new challenges constantly. Many rely on charity, such as free physical therapy at the private foundation where they come each week in the procession of wheelchairs. Many of the women pushing the chairs wear T-shirts that say “Fight like a Mother” in Portuguese.  

It has also left scientists unable to answer basic questions about the virus and the danger it could pose.  

The virus is still circulating at a low level in Brazil and elsewhere in Latin America, as well as in South and Southeast Asia. But attention and funding dried up after the global concerns faded, said Dr. Diana Rojas Alvarez, who leads the Zika work by the World Health Organization. 

“This is what happens when you have a public health emergency that affects tropical countries and that doesn’t have the global impact Covid had,” she said. “Initially, there was a lot of interest in developing good treatments and diagnostic tests — I remember being in a meeting where there were 40 vaccine candidates in development. But since 2017, everything went quiet.”

Even low levels of air pollution can damage health, study finds

Via The Guardian: Even low levels of air pollution can damage health, study finds. Excerpt:

A study in one of the cleanest countries in the world could help governments think about future ways to manage air pollution.  

Abundant data from London’s infamous 1952 smog onwards tells us that breathing high concentrations of air pollution harms our health. This feeds into the 20th-century idea of targets for the quality of our air. However, the new study looked at the health harm from air pollution from another angle.  

Census records for more than 7 million Canadians from between 1981 and 2016 were combined with air pollution data to find out if small amounts of particle pollution were still harmful.  

Despite the relatively clean air, the study found that nearly 8,000 Canadians were dying early each year from outdoor air pollution. Notably, even people in the cleanest areas were experiencing an impact on their health.  

Air pollution harm was seen at concentrations that were at about one half of the latest World Health Organization guideline and at just quarter of the 2040 target proposed for England.  

The Canadian study was one of three funded by the US Health Effects Institute. The other two looked at more than 60 million people in the US and 27 million people in Europe. They reached similar conclusions: there is no lower limit that can be used to define safe air quality. This means governments should not constrain their ambition around setting targets for the worst air that people should breathe.  

Prof Michael Brauer from the University of British Columbia, who led the Canadian study, said: “These findings suggest important health benefits could be gained from continued reductions in air pollution and more stringent regulatory standards, including in countries such as Canada and the UK.  

“Considering that we don’t identify a ‘safe’ level of air pollution, we should rethink our approach and focus on continued reductions year by year, rather than just setting fixed concentration standards that are only reviewed every five to 10 years. The health impacts are far too large.”

Japan's daily COVID-19 tally hits record 250,000 cases

Via The Mainichi Shimbun: Japan's daily COVID-19 tally hits record 250,000 cases.

TOKYO (Kyodo) -- Japan's daily coronavirus tally soared to a record 250,403 cases on Wednesday, as Prime Minister Fumio Kishida's new Cabinet faces the challenge of tackling the seventh wave of the COVID-19 pandemic amid renewed concerns over a strain on the medical system.  

"We will move into a new phase toward" a life with COVID-19 without delay, Kishida said at a press conference after the new lineup for his Cabinet was announced the same day.  

Fueled by the highly transmissible Omicron BA.5 subvariant, Japan's new COVID-19 cases topped 250,000 for the first time, exceeding the previous record of around 249,800 on Aug. 3.  

New coronavirus cases had been increasing since June and in mid-July, the figure more than doubled from a week before. The number of deaths and of people suffering from severe conditions has also been quickly rising.  

Out of Japan's 47 prefectures, 20 reported a record number of cases on Wednesday, while Tokyo reported 34,243 cases and Osaka and Aichi prefectures saw 23,730 and 18,862 cases, respectively.

ECDC: Monkeypox multi-country outbreak

Via ECDC, an August 8 situation update: Monkeypox multi-country outbreak. Excerpt:

Since the start of the monkeypox outbreak and as of 8 August 2022, 13 912 confirmed cases of monkeypox (MPX) have been reported from 29 EU/EEA countries: Spain (4 942), Germany (2 887), France (2 423), Netherlands (959), Portugal (710), Italy (545), Belgium (482), Austria (173), Denmark (123), Sweden (114), Ireland (97), Poland (76), Norway (65), Hungary (48), Greece (39), Slovenia (38), Luxembourg (34), Malta (30), Czechia (28), Romania (28), Finland (20), Croatia (12), Iceland (11), Estonia (9), Slovakia (8), Bulgaria (4), Latvia (3), Lithuania (3) and Cyprus (1).  

Two deaths have been reported from Spain.  

Since the start of the monkeypox outbreak and as of 8 August 2022, the following Western Balkan countries have reported confirmed cases of monkeypox: Serbia (23), Bosnia and Herzegovina (1) and Montenegro (1). In addition, five cases have been reported from Turkey.  

Since the start of the outbreak, ECDC provides updates for EU/EEA countries, the Western Balkans and Turkey twice a week (Tuesdays and Fridays), with the number of MPX cases reported to The European Surveillance System (TESSy) or collected through ECDC’s epidemic intelligence from official public sources.

A zoonotic henipavirus in febrile patients in China

Via NEJM, a letter to the editor: A Zoonotic Henipavirus in Febrile Patients in China. Excerpt:

The Hendra virus and the Nipah virus, which belong to the genus henipavirus in the family Paramyxoviridae, are known to infect humans and cause fatal disease; however, other related henipaviruses have been detected in bats, rodents, and shrews. During sentinel surveillance of febrile patients with a recent history of animal exposure in eastern China, a phylogenetically distinct henipavirus, named Langya henipavirus (LayV), was identified in a throat swab sample from one patient by means of metagenomic analysis and subsequent virus isolation. 

The genome of LayV is composed of 18,402 nucleotides with a genome organization that is identical to that of other henipaviruses (Figure 1A). LayV is most phylogenetically related to Mojiang henipavirus, which was discovered in southern China (Figure 1B). 

Subsequent investigation identified 35 patients with acute LayV infection in the Shandong and Henan provinces of China, among whom 26 were infected with LayV only (no other pathogens were present). These 26 patients presented with fever (100% of the patients), fatigue (54%), cough (50%), anorexia (50%), myalgia (46%), nausea (38%), headache (35%), and vomiting (35%), accompanied by abnormalities of thrombocytopenia (35%), leukopenia (54%), and impaired liver (35%) and kidney (8%) function. 

A serosurvey of domestic animals detected seropositivity in goats (3 of 168 [2%]) and dogs (4 of 79 [5%]). Among 25 species of wild small animals surveyed, LayV RNA was predominantly detected in shrews (71 of 262 [27%]), a finding that suggests that the shrew may be a natural reservoir of LayV. (Additional details of the study are provided in the Supplementary Methods section in the Supplementary Appendix, available with the full text of this letter at NEJM.org.) 

Although the current study does not fulfill Koch’s postulates, the following findings from the patients with acute LayV infection suggest that LayV was the cause of febrile illness: LayV was the only potential pathogen detected in 26 of the 35 patients (74%) with acute LayV infection; in paired serum samples that were obtained from 14 patients during the acute and convalescent phases of infection, the IgG titers in 86% of the convalescent-phase samples were 4 times as high as those in the acute-phase samples; viremia was associated with acute LayV infection; and the patients with pneumonia had higher viral loads than those without pneumonia (mean [±SD] log10-transformed copies per milliliter, 7.64±0.98 vs. 4.52±1.13). 

Although human-to-human transmission has been reported for the Nipah virus, we found no obvious spatial or temporal aggregation of human cases or the assigned haplotypes on the basis of three common single-nucleotide polymorphisms (Figure 1C). There was no close contact or common exposure history among the patients, which suggests that the infection in the human population may be sporadic. Contact tracing of 9 patients with 15 close-contact family members revealed no close-contact LayV transmission, but our sample size was too small to determine the status of human-to-human transmission for LayV. 

The potential cross-reaction with Mojiang virus should be assessed to improve serologic testing. In our study, a newly identified henipavirus of probable animal origin was associated with febrile illness, a finding that warrants further investigation to better understand associated human illness.

Over half of known human pathogenic diseases can be aggravated by climate change

Via Nature Climate Change: Over half of known human pathogenic diseases can be aggravated by climate change. The abstract:

It is relatively well accepted that climate change can affect human pathogenic diseases; however, the full extent of this risk remains poorly quantified. Here we carried out a systematic search for empirical examples about the impacts of ten climatic hazards sensitive to greenhouse gas (GHG) emissions on each known human pathogenic disease. 

We found that 58% (that is, 218 out of 375) of infectious diseases confronted by humanity worldwide have been at some point aggravated by climatic hazards; 16% were at times diminished. Empirical cases revealed 1,006 unique pathways in which climatic hazards, via different transmission types, led to pathogenic diseases. 

The human pathogenic diseases and transmission pathways aggravated by climatic hazards are too numerous for comprehensive societal adaptations, highlighting the urgent need to work at the source of the problem: reducing GHG emissions.

Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada

Via eLife: Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada. The abstract:

Tracking the emergence and spread of SARS-CoV-2 lineages using phylogenetics has proven critical to inform the timing and stringency of COVID-19 public health interventions. We investigated the effectiveness of international travel restrictions at reducing SARS-CoV-2 importations and transmission in Canada in the first two waves of 2020 and early 2021. 

Maximum likelihood phylogenetic trees were used to infer viruses’ geographic origins, enabling identification of 2263 (95% confidence interval: 2159–2366) introductions, including 680 (658–703) Canadian sublineages, which are international introductions resulting in sampled Canadian descendants, and 1582 (1501–1663) singletons, introductions with no sampled descendants. 

Of the sublineages seeded during the first wave, 49% (46–52%) originated from the USA and were primarily introduced into Quebec (39%) and Ontario (36%), while in the second wave, the USA was still the predominant source (43%), alongside a larger contribution from India (16%) and the UK (7%). 

Following implementation of restrictions on the entry of foreign nationals on 21 March 2020, importations declined from 58.5 (50.4–66.5) sublineages per week to 10.3-fold (8.3–15.0) lower within 4 weeks. Despite the drastic reduction in viral importations following travel restrictions, newly seeded sublineages in summer and fall 2020 contributed to the persistence of COVID-19 cases in the second wave, highlighting the importance of sustained interventions to reduce transmission. Importations rebounded further in November, bringing newly emergent variants of concern (VOCs). 

By the end of February 2021, there had been an estimated 30 (19–41) B.1.1.7 sublineages imported into Canada, which increasingly displaced previously circulating sublineages by the end of the second wave. Although viral importations are nearly inevitable when global prevalence is high, with fewer importations there are fewer opportunities for novel variants to spark outbreaks or outcompete previously circulating lineages.

See also this CTV report on the study.

Joint ECDC-WHO Regional Office for Europe Monkeypox Surveillance Bulletin

Via ECDC: Joint ECDC-WHO Regional Office for Europe Monkeypox Surveillance Bulletin. The summary:

A total of 15926 cases of monkeypox have been identified through IHR mechanisms and official public resources up to 2 August 2022, 14:00, from 38 countries and areas throughout the European region. Case-based data were reported for 15624 cases from 32 countries and areas to ECDC and the WHO Regional Office for Europe through The European Surveillance System (TESSy), up to 2 August 2022, 10:00. 

Of the 15624 cases reported in TESSy, 15524 were laboratory confirmed. Furthermore, where sequencing was available, 203 were confirmed to be of the West African clade. 

The earliest date of symptom onset was reported as 11 March 2022. The majority of cases were between 31 and 40 years-old (6349/15595 - 41%) and male (15439/15572 - 99.1%). Among cases with known HIV status, 36% (2690/7487) were HIV-positive. The majority of cases presented with a rash (9126/9626 - 94.8%) and systemic symptoms such as fever, fatigue, muscle pain, chills, or headache (6300/9626 - 65%). 

399 cases were hospitalised (5.6%), of which 150 cases required clinical care. Three cases were admitted to ICU, among whom one was admitted to ICU for reasons unrelated to monkeypox infection. The two other cases admitted to ICU were reported to have died of monkeypox. 

Some (41) cases were reported to be health workers, however no occupational exposure has been reported.