H5N1

WHO: Influenza A(H1N2)v-United States of America

A WHO DON: Influenza A(H1N2)v-United States of America. Excerpt:

Situation at a glance:  

On 4 August 2023, the United States International Health Regulations (IHR) National Focal Point informed PAHO/WHO of a human infection with a novel influenza A(H1N2) variant virus identified in the State of Michigan. This was confirmed by Reverse Transcription Polymerase Chain Reaction at the United States (US) Centers for Disease Control and Prevention (CDC) on August 2.  

The case was not hospitalized and is recovering from the illness. Investigations by local public health officials identified swine exposure by the patient at an agricultural fair.  

Additional public health response efforts including enhanced surveillance for cases is undergoing. Given the potential impact on public health, human infections with these viruses need to be monitored closely. In this event, there was no reported evidence of sustained human-to-human transmission, the illness was mild and no further influenza variant virus transmission in the community has been identified.  

Description of the case:  

On 4 August 2023, the United States IHR National Focal Point informed PAHO/WHO of a human infection with a novel influenza A(H1N2) variant virus identified in the State of Michigan and confirmed by the US CDC.   

According to the report, the case is under 18 years old, with no comorbidities, resident in the State of Michigan, who developed respiratory illness on 29 July 2023. The case presented with fever, cough, sore throat, muscle aches, headache, shortness of breath, diarrhea, nausea, dizziness, and lethargy. On 29 July, the case sought medical care at an emergency department, and an upper respiratory tract specimen was collected on 30 July. The specimen tested positive for influenza A virus on the same day. On 1 August, the patient received influenza antiviral treatment (Oseltamivir).  

On 31 July, the specimen was tested at the Michigan Department of Health and Human Services (MDHHS), and RT-PCR results were positive for influenza A virus but lacked reactivity with diagnostic tests for contemporary human influenza viruses representing either (H1) pdm09 or (H3) subtypes. The specimen was then sent to the US CDC for further testing and received on 2 August. On the same day, RT-PCR analysis of the specimen indicated an influenza A(H1N2) variant (v) virus. The virus was isolated and subsequent analysis including genetic sequencing is underway.  

The case was not hospitalized. Investigation by local public health officials identified swine exposure by the patient at an agricultural fair, that took place between 23 and 29 July, within 10 days prior to illness onset. Additional investigation did not identify respiratory illness in any of the patient’s close contacts or household contacts. No additional cases were identified related to this agriculture fair. No person-to-person transmission of influenza A(H1N2)v virus associated with this case has been identified. No additional cases of human infection with A(H1N2)v virus have been identified as of 10 August 2023.  

This is the first influenza A(H1N2)v virus infection identified in the United States this year. Since 2005, there have been 512 influenza A variant virus infections (all subtypes), including 37 (human infections with influenza A (H1N2)v viruses reported in the United States.

WHO: Weekly epidemiological update on COVID-19 - 3 August 2023

WHO has published Weekly epidemiological update on COVID-19 - 3 August 2023. Click or tap through to download the full report. The overview:

Globally, over one million new COVID-19 cases and over 3100 deaths were reported in the last 28 days (3 to 30 July 2023). While five WHO regions have reported decreases in the number of both cases and deaths, the Western Pacific Region has reported an increase in the number of cases and a decrease in the number of deaths. 

As of 30 July 2023, over 768 million confirmed cases and over 6.9 million deaths have been reported globally. Currently, reported cases do not accurately represent infection rates due to the reduction in testing and reporting globally. 

During this 28-day period, 46% (107 of 234) of countries and territories reported at least one case to WHO – a proportion that has been declining since mid-2022. 

In this edition, we include:  

• The COVID-19 epidemiological update at the global and the regional levels  

• An update on hospitalizations and ICU admissions  

• An update on the SARS-CoV-2 variants of interest (VOI) and variants under monitoring (VUM)   

• An update on the vaccine effectiveness of primary series and booster vaccination against the Omicron and its descendant lineages

WHO: Weekly epidemiological update on COVID-19 - 3 August 2023

Via WHO: Weekly epidemiological update on COVID-19 - 3 August 2023. Click or tap through to download the full report. The overview:

Globally, over one million new COVID-19 cases and over 3100 deaths were reported in the last 28 days (3 to 30 July 2023). While five WHO regions have reported decreases in the number of both cases and deaths, the Western Pacific Region has reported an increase in the number of cases and a decrease in the number of deaths. 

As of 30 July 2023, over 768 million confirmed cases and over 6.9 million deaths have been reported globally. Currently, reported cases do not accurately represent infection rates due to the reduction in testing and reporting globally. During this 28-day period, 46% (107 of 234) of countries and territories reported at least one case to WHO – a proportion that has been declining since mid-2022.

WHO: Middle East Respiratory Syndrome Coronavirus –United Arab Emirates

WHO has published a DON: Middle East Respiratory Syndrome Coronavirus –United Arab Emirates. Excerpt:

Situation at glance:  

On 10 July 2023, the United Arab Emirates (UAE), notified WHO of a case of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in a 28-year-old male from Al Ain city in Abu Dhabi. The case had no history of direct or indirect contact with dromedaries, goats, or sheep. The patient was admitted to the hospital on 8 June. A nasopharyngeal swab was collected on 21 June and tested positive for MERS-CoV by polymerase chain reaction (PCR) on 23 June 2023. All 108 identified contacts were monitored for 14 days from the last date of exposure to the MERS-CoV patient. No secondary cases have been detected to date.  

Since July 2013, when the UAE reported the first case of MERS-CoV, 94 confirmed cases (including this new case) and 12 deaths have been reported. Globally, the total number of confirmed MERS-CoV cases reported to WHO since 2012 is 2605, including 936 associated deaths.  

WHO continues to monitor the epidemiological situation and conducts risk assessments based on the latest available information. WHO expects that additional cases of MERS-CoV infection will be reported from the Middle East and/or other countries where MERS-CoV is circulating in dromedaries.  

WHO re-emphasizes the importance of strong surveillance by all Member States for acute respiratory infections, including MERS-CoV, and to carefully review any unusual patterns.  

Description of the case:  

On 10 July 2023, the International Health Regulations National Focal Point (IHR NFP) of the United Arab Emirates (UAE) notified WHO of a confirmed case of MERS-CoV in Abu Dhabi. The patient is a 28-year-old male, non- Emirati national living in Al Ain city, a non-healthcare worker.  The case visited a private medical center multiple times between 3 and 7 June 2023, complaining of vomiting, right flank pain, and dysuria (pain when passing urine). On 8 June, the case presented to a government hospital with vomiting, and gastrointestinal symptoms including diarrhea, and was given an initial diagnosis of acute pancreatitis, acute kidney injury, and sepsis.  

On 13 June, he was in critical condition and referred to an intensive care unit (ICU) at a specialized government tertiary hospital where he was put on mechanical ventilation. He deteriorated and a nasopharyngeal swab was collected on 21 June and tested positive for MERS-CoV by PCR on 23 June 2023.  

The case has no known co-morbidities, no history of contact with MERS-CoV human cases, and no recent travel outside the UAE. The patient has no known history of direct contact with animals including dromedary camels, nor consumption of their raw products.  

All 108 contacts that were identified have been monitored for 14 days from the last date of exposure to the MERS-CoV patient, no secondary case was identified. The case has no family members or household contacts identified in the UAE.  

Prior to this notification, the last MERS-CoV infection reported from the UAE was in November 2021. The first laboratory-confirmed case of MERS-CoV in UAE was in July 2013. Since then, the UAE has reported 94 cases of MERS-CoV (including this current case) and 12 associated deaths (Case Fatality Ratio (CFR): 13%).

ECDC: Enhanced surveillance of severe avian influenza virus infections in hospital settings in the EU/EEA

ECDC has published Enhanced surveillance of severe avian influenza virus infections in hospital settings in the EU/EEA. Click or tap through to download the PDF. The executive summary:

Avian influenza virus outbreaks are continuing during the summer months, causing mass mortality in sea-breeding bird colonies, including gulls. A larger exposure of human population to sick or dead birds and mammals is expected to occur. Transmission to humans cannot be excluded when avian influenza is circulating in wild birds and mammals and people are directly exposed without wearing protective equipment. 

During the summer months, infections with seasonal influenza viruses are considered to be very limited, and only a few patients with severe disease caused by the seasonal influenza virus are expected to be admitted to hospitals. 

 To identify sporadic severe human infections with avian influenza virus in hospital settings, the following approach is proposed: People admitted to hospitals with respiratory symptoms should be asked about exposure to birds (wild birds or poultry) or other wild animals (dead or alive) in the two weeks before admission. 

Consider testing for influenza virus hospitalised patients with unexplained viral encephalitis/ meningoencephalitis lacking the aetiological agent diagnosis. All influenza A-positive samples from hospitalised patients should be subtyped for seasonal influenza viruses A(H1)pdm09 and A(H3). Samples positive for influenza type A virus but negative for A(H1)pdm09 or A(H3) should be immediately sent to national influenza reference laboratories for further analysis and H5 testing.

Uganda: Second suspected Ebola victim dies

Uganda's new Ebola outbreak hit the news yesterday, but it seems to have started several weeks ago. Via New Vision: Second suspected Ebola victim dies.

Another man suspected to be infected with Ebola has died at Mubende Regional Referral Hospital.  

He was part of the 14 people who checked into Mubende Regional Referral Hospital with symptoms of Ebola on September 20, 2022.  

Emmanuel Ainebyoona, the health ministry spokesperson, confirmed the death of suspected victim.  

"Yes, there is a child who died yesterday but we are waiting for test results  from UVRI. It is a suspected death at the moment," he said.  

According to Mubende RDC Rosemary Byabashaijja, a man from Madudu Sub County in Mubende died yesterday (September 20) after he was admitted at Mubende Regional Referral Hospital.  

The RDC is heading the Mubende Rapid Response team, which is working with Ministry of Health to track down contacts for the person who died on Monday and investigate the six deaths that occurred earlier in the month.  

The six deaths occurred suddenly and the local people say they died of strange illness.  

Byabashaijja said they had identified 14 contacts of the person who died on September 19, 2022. They included 10 people from Madudu Sub county including the one who passed on yesterday (September 20) and four people from neighbouring Kyegegwa district in Toro.  

“Since we registered the first case, we sent a surveillance team which goes around where they even sensitize the people. In Madudu, we have been asking those who were in touch with first victims to willingly come up and be tested and we are happy that some are turning up,” she said.  

On September 20, the team of medics took away the body of the first victims from Mubende hospital and buried. The body of the person who died on September 20 is awaiting burial today (September 21), according to sources.  

Byabashaijja noted that the six people expected to have died of Ebola form Madudu died because of self-medication.  

An isolation center has been set up at Mubende Regional Referral Hospital where suspected cases are being quarantined pending the results from samples picked from them.

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.

Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy

Via ScienceDirect, a report in Environmental Research that could change the origin story of SARS-CoV-2: Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy. The abstract:

As a reference laboratory for measles and rubella surveillance in Lombardy, we evaluated the association between SARS-CoV-2 infection and measles-like syndromes, providing preliminary evidence for undetected early circulation of SARS-CoV-2. 

Overall, 435 samples from 156 cases were investigated. RNA from oropharyngeal swabs (N = 148) and urine (N = 141) was screened with four hemi-nested PCRs and molecular evidence for SARS-CoV-2 infection was found in 13 subjects. Two of the positive patients were from the pandemic period (2/12, 16.7%, March 2020–March 2021) and 11 were from the pre-pandemic period (11/44, 25%, August 2019–February 2020). 

Sera (N = 146) were tested for anti-SARS-CoV-2 IgG, IgM, and IgA antibodies. Five of the RNA-positive individuals also had detectable anti-SARS-CoV-2 antibodies. No strong evidence of infection was found in samples collected between August 2018 and July 2019 from 100 patients. 

The earliest sample with evidence of SARS-CoV-2 RNA was from September 12, 2019, and the positive patient was also positive for anti-SARS-CoV-2 antibodies (IgG and IgM). Mutations typical of B.1 strains previously reported to have emerged in January 2020 (C3037T, C14408T, and A23403G), were identified in samples collected as early as October 2019 in Lombardy. One of these mutations (C14408T) was also identified among sequences downloaded from public databases that were obtained by others from samples collected in Brazil in November 2019. 

We conclude that a SARS-CoV-2 progenitor capable of producing a measles-like syndrome may have emerged in late June-late July 2019 and that viruses with mutations characterizing B.1 strain may have been spreading globally before the first Wuhan outbreak. Our findings should be complemented by high-throughput sequencing to obtain additional sequence information. 

We highlight the importance of retrospective surveillance studies in understanding the early dynamics of COVID-19 spread and we encourage other groups to perform retrospective investigations to seek confirmatory proofs of early SARS-CoV-2 circulation.

Health officials link four pneumonia deaths in Tucumán to Legionnaires' disease

Via the Buenos Aires Times: Health officials link four pneumonia deaths in Tucumán to Legionnaires' disease. Excerpt:

Tucumán health officials said Saturday that four people in a clinic in northwestern province had died of Legionnaires' disease, a relatively rare bacterial affliction of the lungs.  

Health Minister Carla Vizzotti told reporters that Legionnaires' had been identified as the underlying cause of double pneumonia in the four, who had suffered high fevers, body aches and trouble breathing.   

The deaths, all since Monday, occurred in a single clinic in the city of San Miguel de Tucumán.  

The latest, on Saturday morning, was that of a 48-year-old man with underlying health problems. A 70-year-old woman who had undergone surgery in the clinic was also a victim.

Seven other non-fatal cases have been identified, all in the same establishment and nearly all involving clinic personnel, provincial officials said.  

The disease, which first appeared at a 1976 meeting of the American Legion veterans group in the US city of Philadelphia, has been linked to contaminated water or unclean air-conditioning systems.  

When the outbreak in Tucumán was first detected, doctors tested the afflicted for Covid-19, flu and the hantavirus, but ruled all of them out.   

Samples were then sent to the prestigious ANLIS-Malbran Institute in Buenos Aires. Tests at the research body pointed to Legionnaires'.

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.