H5N1

Tanzania confirms first-ever outbreak of Marburg Virus Disease

Via WHO AFRO: Tanzania confirms first-ever outbreak of Marburg Virus Disease.

Brazzaville/Dar es Salaam – Tanzania today confirmed its first-ever cases of Marburg Virus Disease after laboratory tests were carried out following reports of cases and deaths in the country’s north-west Kagera region.  

Tanzania’s National Public Health Laboratory analysed samples to determine the cause of illness after eight people developed symptoms including fever, vomiting, bleeding and renal failure. Five of the eight cases, including a health worker, have died and the remaining three are receiving treatment. A total of 161 contacts have been identified and are being monitored.  

“The efforts by Tanzania’s health authorities to establish the cause of the disease is a clear indication of the determination to effectively respond to the outbreak. We are working with the government to rapidly scale up control measures to halt the spread of the virus and end the outbreak as soon as possible,” said Dr Matshidiso Moeti, World Health Organization (WHO) Regional Director for Africa.  

WHO is supporting the Ministry of Health to deploy an emergency team to Kagera to carry out further epidemiological investigations. The emergency team will focus on active case finding in the community and local health care facilities to identify more contacts and provide them with appropriate care.  

While Tanzania has never previously recorded a Marburg case, it has had to respond to other health emergencies including COVID-19, cholera and dengue within the past three years. A strategic risk assessment conducted by WHO in September 2022 showed that the country is at high to very high risk for infectious diseases outbreaks.   

“The lessons learnt, and progress made during other recent outbreaks should stand the country in good stead as it confronts this latest challenge,” said Dr Moeti. “We will continue to work closely with the national health authorities to save lives.”  

Marburg virus disease is highly virulent and causes haemorrhagic fever, with a fatality ratio of up to 88%. It is in the same family as the virus that causes Ebola virus disease. Illness caused by Marburg virus begins abruptly, with high fever, severe headache and severe malaise. Many patients develop severe haemorrhagic symptoms within seven days. The virus is transmitted to people from fruit bats and spreads among humans through direct contact with the bodily fluids of infected people, surfaces and materials.  

There are no vaccines or antiviral treatments approved to treat the virus. However, supportive care – rehydration with oral or intravenous fluids – and treatment of specific symptoms, improves likelihood of survival.

China is flying blind as pandemic rages

Via Science: China is flying blind as pandemic rages. Excerpt:

Most scientists believe China’s decision to end its zero-COVID policy was long overdue. But now they have a new worry: that the country is collecting and sharing far too little data about the rough transition to a new coexistence with the virus.  

China abruptly dropped virtually all controls a month ago, after protests, a sagging economy, and the extreme transmissibility of the virus’ latest variants made clinging to zero COVID untenable. Now, “SARS-CoV-2 has an open goal in front of it: a population with very low levels of standing immunity,” says evolutionary biologist Edward Holmes of the University of Sydney. But how the epidemic is unfolding is a mystery because the country has practically stopped collecting basic epidemiological data.  

Models that predicted a massive wave of infection and death if China ended zero COVID appear to have been correct. Press reports and social media posts have shown intensive care units stretched beyond capacity, with crowds of patients in wheelchairs and on gurneys in hallways. Doctors and nurses are reportedly working while sick. Crematoriums are overwhelmed. 

But China’s official COVID-19 death toll is widely considered laughably low. And some scientists worry a genomic monitoring plan unveiled last month doesn’t have the power to detect new SARS-CoV-2 variants arising as the virus works its way through one-fifth of the world population.

Earlier in the pandemic China’s daily counts of COVID-19 cases and deaths, based partly on its exhaustive testing programs, were generally believed to be accurate. Now, they are anyone’s guess. Patients with mild symptoms are not encouraged to get tested, let alone those who are asymptomatic. People testing positive at home are not asked to report their results.  

The China Center for Disease Control and Prevention (China CDC) put the number of confirmed cases the last week of December 2022 at more than 35,000—a fraction of the official number in the United States. But leaked notes from an internal meeting suggest a very different reality: The agency was told that almost 250 million people in China—roughly 18% of the population—may have caught COVID-19 in the first 20 days of December. Some experts said the number is implausibly large, but Yanzhong Huang, a global health specialist at the Council on Foreign Relations, a U.S. think tank, says it’s “not unreasonable,” given credible reports that 80% of Beijing residents have been infected by now.  

As to the death toll, China’s reporting had long been inconsistent, Huang says, with some regions reporting all fatalities in which SARS-CoV-2 was a factor, as most countries do, and others excluding people who died from other conditions, such as heart attacks, even if they had COVID-19. In early December, China’s government decided the narrower definition should be used nationwide.  

Even then, the official count is astonishingly low: just eight deaths for the entire last week of December, which is “not matching media reports and what is being seen on social media,” says Louise Blair, who tracks China’s COVID-19 outbreak for Airfinity, a London-based health analytics firm that estimates about 9000 people were dying of COVID-19–related causes every day in late December.  

Also missing are data on case fatality rates, the average number of new infections stemming from each case, and hospital and intensive care admissions. “These are critical data” that would help health authorities get a handle on the surge and further the world’s understanding of the pandemic, says Xi Chen, a public health scientist at the Yale School of Public Health.

Impact of surge in China COVID-19 cases on epidemiological situation in EU/EEA

A news report from ECDC: Impact of surge in China COVID-19 cases on epidemiological situation in EU/EEA.

The number of COVID-19 cases has reached a record high in mainland China, peaking on 2 December 2022. In the past three weeks, incidence has fallen, likely also due to a lower number of tests being carried out, resulting in fewer infections being detected.  

ECDC, together with the EU/EEA Member States and the European Commission has increased its monitoring activities and will revise risk assessments and adjust actions if needed. ECDC is working closely with the World Health Organization (WHO)/Europe and WHO/Headquarters and is in regular contact with the Chinese Center for Disease Control and Prevention (China CDC) and major CDCs globally.  

ECDC continues to routinely monitor and report on emerging SARS-CoV-2 variant threats via its Strategic Analysis of Variants in Europe (SAVE) Working Group, where variants and epidemiological trends in countries neighbouring China as well as in the EU/EEA will continue to be evaluated.  

The number of COVID-19 cases has reached a record high in mainland China, peaking on 2 December 2022. In the past three weeks, incidence has fallen, likely also due to a lower number of tests being carried out, resulting in fewer infections being detected. There continues to be a lack of reliable data on COVID-19 cases, hospital admissions, deaths as well as Intensive Care Unit (ICU) capacity and occupancy in China.  

High levels of SARS-CoV-2 infections and increased pressure on healthcare services in China are expected in the coming weeks due to low population immunity and the relaxation of non-pharmaceutical interventions.  

China has started depositing SARS-CoV-2 sequences in GISAID EpiCoV[1] in higher numbers. From 1 to 30 December 2022, China has deposited 592 sequences, out of which 540 sequences were being deposited this week (from 25 December to 30 December 2022). As of 30 December 2022, of the total 592 sequences submitted from China, 437 had recent sample collection dates between 1 and 24 December 2022 in GISAID EpiCoV.  

These sequences mainly belonged to the lineages (including their sub-lineages) BA.5.2 (35%), BF.7 (24%), BQ.1 (18%), BA.2.75 (5%), XBB (4%), BA.2 (2%). In addition, from travel related cases, the variants BA.5.6, BA.4.6, BM.4.1.1 and BA.2.3.20 have also been detected to be circulating in China. No new variant has been detected.  

The variants circulating in China are already circulating in the EU, and as such are not challenging for the immune response of EU/EEA citizens. In addition, EU/EEA citizens have relatively high immunisation and vaccination levels.  

Given higher population immunity in the EU/EEA, as well as the prior emergence and subsequent replacement of variants currently circulating in China by other Omicron sub-lineages in the EU/EEA, a surge in cases in China is not expected to impact the COVID-19 epidemiological situation in the EU/EEA. This is based on the information available as of this week, and the ECDC assessment, as detailed in Communicable Diseases Threat Report of week 51, remains currently unchanged.

Serial cross-sectional estimation of vaccine and infection-induced SARS-CoV-2 sero-prevalence in children and adults, British Columbia, Canada: March 2020 to August 2022

Via medRxiv: Serial cross-sectional estimation of vaccine and infection-induced SARS-CoV-2 sero-prevalence in children and adults, British Columbia, Canada: March 2020 to August 2022. The underestimates of infections are breathtaking. The abstract:

Background  

We chronicle SARS-CoV-2 sero-prevalence through eight cross-sectional sero-surveys (snapshots) in the Lower Mainland (Greater Vancouver and Fraser Valley), British Columbia, Canada from March 2020 to August 2022.  

Methods  

Anonymized-residual sera were obtained from children and adults attending an outpatient laboratory network. Sera were tested with at least three immuno-assays per snapshot to detect spike (S1) and/or nucleocapsid protein (NP) antibodies. Sero-prevalence was defined by dual-assay positivity, including any or infection-induced, the latter requiring S1+NP antibody detection from January 2021 owing to vaccine availability. Infection-induced estimates were used to assess the extent to which surveillance case reports under-estimated infections.  

Results  

Sero-prevalence was ≤1% by the 3rd snapshot in September 2020 and <5% by January 2021 (4th). Following vaccine roll-out, sero-prevalence increased to >55% by May/June 2021 (5th), ∼80% by September/October 2021 (6th), and >95% by March 2022 (7th). In all age groups, infection-induced sero-prevalence remained <15% through September/October 2021, increasing through subsequent Omicron waves to ∼40% by March 2022 (7th) and ∼60% by July/August 2022 (8th). By August 2022, at least 70-80% of children ≤19 years, 60-70% of adults 20-59 years, but ∼40% of adults ≥60 years had been infected. 

Surveillance case reports under-estimated infections by 12-fold between the 6th-7th and 92-fold between the 7th-8th snapshots. 

Interpretation  

By August 2022, most children and adults had acquired SARS-CoV-2 vaccine and infection exposures, resulting in more robust hybrid immunity. Conversely the elderly, still at greatest risk of severe outcomes, remain largely dependent on vaccine-induced protection alone, and should be prioritized for additional doses. 

Competing Interest Statement  

DMS is Principal Investigator on grants from the Public Health Agency of Canada and Michael Smith Foundation for Health Research, paid to her institution, in support of this work and has received grants from the Canadian Institutes of Health Research and the BCCDC Foundation for Public Health, also paid to her institution, for other SARS-CoV-2 work. As the Provincial Health Officer with authority under the emergency provisions of the Public Health Act, BH authorized the access to and analysis of the anonymized sera used in this study; the study was separately reviewed and approved by the University of British Columbia Clinical Research Ethics Board. MK received grants/contracts paid to his institution from Roche, Hologic and Siemens. No other authors have conflicts of interest to disclose.

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.

The prevalence of SARS-CoV-2 infection and uptake of COVID-19 antiviral treatments during the BA.2/BA.2.12.1 surge, New York City, April-May 2022

Via medRxiv: The prevalence of SARS-CoV-2 infection and uptake of COVID-19 antiviral treatments during the BA.2/BA.2.12.1 surge, New York City, April-May 2022. The abstract: 

Importance: Routine case surveillance data for SARS-CoV-2 are incomplete, biased, missing key variables of interest, and may be unreliable for both timely surge detection and understanding the burden of infection.  

Objective: To determine the prevalence of SARS-CoV-2 infection during the Omicron BA.2/BA.2.12.1 surge in relation to official case counts, and to assess the epidemiology of infection and uptake of SARS-CoV-2 antivirals.  

Design: Cross-sectional survey of a representative sample of New York City (NYC) adult residents, conducted May 7-8, 2022. Setting: NYC, April 23-May 8, 2022, during which the official SARS-CoV-2 case count was 49,253 and BA.2.12.2 comprised 20% of reported cases.  

Participants: A representative sample of 1,030 NYC adult residents >18 years.

Exposure(s): Vulnerability to severe COVID-19, including vaccination/booster status, prior COVID, age, and presence of comorbidities.  

Main Outcome(s) and Measure(s): Prevalence of SARS-CoV-2 infection during a 14-day period, weighted to represent the NYC adult population. Respondents self-reported on SARS-CoV-2 testing (including at-home rapid antigen tests), testing outcomes, COVID-like symptoms, and contact with confirmed/probable cases. Individuals with SARS-CoV-2 were asked about awareness/use of antiviral medications.  

Results: An estimated 22.1% (95%CI 17.9%-26.2%) of respondents had SARS-CoV-2 infection during the study period, corresponding to ~1.5 million adults (95%CI 1.3-1.8 million). Prevalence was estimated at 34.9% (95%CI 26.9%- 42.8%) among individuals with co-morbidities, 14.9% (95% CI 11.0%-18.8%) among those 65+ years, and 18.9% (95%CI 10.2%-27.5%) among unvaccinated persons. Hybrid protection against severe disease (i.e., from both vaccination and prior infection) was 66.2% (95%CI 55.7%-76.7%) among those with COVID and 46.3% (95%CI 40.2-52.2) among those without. Among individuals with COVID, 55.9% (95%CI 44.9%- 67.0%) were not aware of the antiviral nirmatrelvir/ritonavir (PaxlovidTM), and 15.1% (95%CI 7.1%-23.1%) reported receiving it.  

Conclusions and Relevance: The true magnitude of NYCs BA.2/BA.2.12.1 surge was vastly underestimated by routine SARS-CoV-2 surveillance. Until there is more certainty that the impact of future pandemic surges on severe population health outcomes will be diminished, representative surveys are needed for timely surge detection, and to estimate the true burden of infection, hybrid protection, and uptake of time-sensitive treatments.

See also this report in The Guardian which discusses the study.

Climate change increases cross-species viral transmission risk

Via Nature, an important new study: Climate change increases cross-species viral transmission risk. The abstract:

At least 10,000 virus species have the capacity to infect humans, but at present, the vast majority are circulating silently in wild mammals. However, climate and land use change will produce novel opportunities for viral sharing among previously geographically-isolated species of wildlife. In some cases, this will facilitate zoonotic spillover—a mechanistic link between global environmental change and disease emergence.  

 

Here, we simulate potential hotspots of future viral sharing, using a phylogeographic model of the mammal-virus network, and projections of geographic range shifts for 3,139 mammal species under climate change and land use scenarios for the year 2070.  

 

We predict that species will aggregate in new combinations at high elevations, in biodiversity hotspots, and in areas of high human population density in Asia and Africa, driving the novel cross-species transmission of their viruses an estimated 4,000 times.  

 

Because of their unique dispersal capacity, bats account for the majority of novel viral sharing, and are likely to share viruses along evolutionary pathways that will facilitate future emergence in humans. Surprisingly, we find that this ecological transition may already be underway, and holding warming under 2°C within the century will not reduce future viral sharing.  

 

Our findings highlight an urgent need to pair viral surveillance and discovery efforts with biodiversity surveys tracking species’ range shifts, especially in tropical regions that harbor the most zoonoses and are experiencing rapid warming.

COVID-19 is in for the long haul

Here's a screenshot of this evening's Johns Hopkins Coronavirus COVID-19 (2019-nCoV) dashboard:

It's notable for several reasons. First, the US is now far back in the 28-day case count—seventh, behind Germany, South Korea, Russia, Vietnam, France, and Brazil.

 

Second, almost all the case and mortality numbers are likely severe undercounts, since so many countries have simply abandoned any pretence of testing and contact tracing. I would not be shocked if the true number of cases were around 1.5 billion, and deaths close to 20 million.

 

The numbers for Russia (3.7 million cases in the last 28 days, 20,000 deaths) and Ukraine (458,000 cases, 3,800 deaths) are especially implausible, given the events of the past 15 days. But we'll surely see an explosive growth in cases as over 2 million Ukrainians move through Europe in search of refuge.

 

The early-success countries have largely succumbed to Omicron. While China pursues its zero-COVID policy, it's still recorded 539,000 cases and 2,600 deaths. Hong Kong has seen 533,000 cases in 28 days, and 2,600 deaths. Vietnam racked up 26 million cases in the last 28 days, and 2,400 deaths. New Zealand had 267,000 cases and 12 deaths; it had only 38,900 cases in the previous 23 months of the official pandemic.

 

The graphs on the right tell us that the Omicron spike has fallen sharply from its peak of 23,333,000 in the week ending January 23; we're now at 10,706,000 as of the week ending March 6. That looks impressive, but it's still about 5 million more than the three previous waves.

 

Omicron also drove a spike in deaths, peaking at 75,000 in the week of February 13 and now fallen to 50,400. Meanwhile, vaccinations have fallen from a recent high of 257,000 in the week of February 6 to 105,600 in the week ending March 6.

 

Yet many countries are effectively declaring the pandemic over, making masks and distancing optional, junking vaccine passports, and dropping regular reports by public health officials. Governments seem to think COVID-19 can now sink back into the background noise with other diseases, while we turn our attention to war and inflation and the next election.

 

On February 1, Johns Hopkins reported 381,232,070 cases, so we have seen almost 72 million cases of COVID-19 in the past six weeks alone. Even if the Omicron spike continue to drop, the next six weeks will see tens of millions more cases, and likely another 40 or 50 thousand people now alive will be dead before May 1. 

 

We are nowhere near the end of the pandemic. In fact, I expect it will in many ways get worse as healthcare systems really do collapse, and as sequelae like Long COVID affect more and more cases. The pandemic that began two years ago really is in the for long haul.

Canada's abandoning of COVID-19 testing leaves us vulnerable to future variants, experts say

As the saying goes, "If you don't count it, it doesn't count." Via CBC News: Canada's abandoning of COVID-19 testing leaves us vulnerable to future variants, experts say. Excerpt:

Canada is entering a period of relative calm as the Omicron-driven fifth wave subsides across much of the country. But our ability to track new and existing variants is in jeopardy with testing access still heavily restricted — leaving us vulnerable to pandemic whiplash.  

Dr. Theresa Tam, Canada's chief public health officer, said Friday that COVID-19 levels have continued to decline in most of Canada, with weekly case counts down 26 per cent and hospitalizations and ICU admissions down 20 per cent compared to the previous week.   

"Nevertheless, as the virus is still circulating widely, some jurisdictions are reporting weekly increases in case counts and others could see additional bumps in the weeks ahead," she said.   

"At the same time, there is a continued high volume of PCR testing being performed and ongoing genetic sequencing of circulating virus variants."   

But the level of COVID-19 testing in Canada has actually dropped off dramatically since the start of the Omicron wave — with more than 100,000 daily tests being performed in early December, about 150,000 in early January, down to just over 50,000 as of Friday.   

That makes it nearly impossible to get a clear sense of what the true number of COVID-19 cases are in Canada, and severely limits the number of testing samples that can undergo genomic sequencing to detect for the presence of variants.

World 'cannot abandon' testing amid threat of variants  

The World Health Organization's leading coronavirus expert Maria Van Kerkhove said this week that while there has been a 20 per cent drop in COVID-19 levels globally in the past week compared to the previous week, the decline "may not be real" due to a lack of testing. 

"We are very concerned about a reduction in testing around the world," she said Tuesday.

A turning point in coverage of COVID data

Via the Columbia Journalism Review, a column by Jon Allsop: A turning point in coverage of COVID data. Click through for the full article and many links. Excerpt:

There's important information down the toilet—and no, I’m not talking about sensitive documents from the Trump White House. Early this month, the Centers for Disease Control and Prevention updated its online COVID data tracker to include wastewater analyses from hundreds of communities across the US, information that can serve as an early indicator of increased viral spread, or the circulation of a new variant, given that people shed the virus via their feces without having to take and report a test result. (Wastewater data is also collective, obviating privacy issues inherent to other forms of medical-data reporting.) 

Wastewater experts who spoke with Apoorva Mandavilli, a reporter at the New York Times, were “understanding” of the fact that it took the CDC so long to publicly share data that it was, in some cases, already collecting. Not everyone shared that assessment, though. Robinson Meyer, a journalist at The Atlantic who co-founded the COVID Tracking Project to fill the gap left by official data shortages early in the pandemic, called the delayed publication “a scandal.”  

It’s not just wastewater—as Mandavilli reported over the weekend, it turns out that the CDC “has published only a tiny fraction of the data it has collected” during the pandemic. The agency has tracked data breaking down hospitalization stats by age, race, and vaccination status for more than a year now but has mostly not published it; when officials shared data on the effectiveness of vaccine boosters recently, they left out the figures for a huge tranche of younger recipients until the Times inquired.  

CDC representatives told Mandavilli that the agency withholds data for a variety of reasons, from the numbers being “not yet ready for prime time” to the agency’s slow and cumbersome bureaucracy as well as a fear that the public might misinterpret certain trends, particularly where the hospitalization of vaccinated people is concerned.  

Jessica Malaty Rivera, who has also worked with the Tracking Project, slammed the latter rationale, in particular, noting that rather than reduce the risk of misinterpretation, “data vacuums” only heighten it. So, too, did Meyer, who called such attitudes not only “counterproductive” but “profoundly undemocratic.” The “approach has now persisted in the CDC across two presidents,” he noted. “It’s an issue with that agency—and with the overweeningly scholastic culture of public health in the US.” 

The availability of good, timely data has been a persistent challenge for the press throughout the pandemic, as I’ve explored many times in this newsletter. So, too, has knowing how best to relay the data that we do have to our audiences. The recent Omicron wave sharpened the challenge again by posing a different type of threat than prior variants: low for most individuals, especially the vaccinated, but sharp for many immunocompromised and unvaccinated people as well as at the collective level of US healthcare infrastructure, given the variant’s high transmissibility.

Even before Omicron, some health officials and experts had urged news outlets to emphasize hospitalization and death rates more than case counts in their coverage, as mass vaccination frayed the previously close link between those numbers; as Omicron further frayed the link, those calls intensified. If Omicron cast fresh doubt on the usefulness of case counts, it also cast fresh doubt on their accuracy, as testing—which was not adequate to make US case counts fully reliable to begin with—became harder to access and many people neglected to report at-home results. The Associated Press, among other outlets, told staffers to be more cautious around case counts, and not to hype supposed new records by writing whole stories about them.