Thursday, November 11, 2021

EID Journal: Reassortant Influenza A(H1N1)pdm09 Virus in Elderly Woman, Denmark, January 2021


Nine months ago, in Denmark: Statens Serum Institut (SSI) Reports Detection of A Novel Flu (Jan. 2021), we looked at a barebones report from Denmark's SSI on the detection of a novel (presumably swine-variant) flu virus in a resident without recent contact with pigs.

While the subtype was not specified, The SSI described this novel flu as likely coming from pigs, which suggested a variant H1Nx or H3Nx, with H1N1v, H1N2v, and H3N2v being the most likely subtypes.

And as we've discussed often in the past (see Are Influenza Pandemic Viruses Members Of An Exclusive Club?) - swine flu viruses have a bit of an advantage in the pandemic sweepstakes, as only H1, H2, and H3 influenza subtypes are known to have sparked a human influenza pandemic in the last 130 years. 

Only rarely picked up by surveillance, these swine variant viruses probably jump from pigs to humans more often than we are aware. Last week the CDC reported Three More Novel Influenza Infections (H1N1v & H1N2v)), bringing to 14 the number of novel swine variant viruses detected in the United States during the 2020-21 influenza season, with 1 reported for the 2021-2022 season.

Most, but not all, of these cases had recent direct contract with pigs. The CDC's risk assessment for Swine Variant viruses reads:

Sporadic infections and even localized outbreaks among people with variant influenza viruses may occur. All influenza viruses have the capacity to change and it’s possible that variant viruses may change such that they infect people easily and spread easily from person-to-person. The Centers for Disease Control and Prevention (CDC) continues to monitor closely for variant influenza virus infections and will report cases of H3N2v and other variant influenza viruses weekly in FluView and on the case count tables on this website 

Today we have a follow up report on the Denmark case from last winter, that reveals that virus was a novel reassorted H1N1v, comprised of the human A(H1N1)pdm09 virus with the NS gene from an EA-like H1N1 swine virus. 

Aside from this being Denmark's 1st confirmed swine variant infection of a human, this report is notable because the patient (who had multiple comorbidities) was in a pandemic lockdown at the time of her infection, had very little outside contact, and was one of only 46 confirmed flu cases in Denmark during the 2020-2021 flu season. 

Exactly how she came to be infected with a novel swine variant virus under these conditions isn't known, but the author does dangle a tantalizing possibility; she lived roughly 2 km from a pig farm, and her ". . . residence was downwind of the pig herd most days preceding clinical symptoms.

First, some excerpts from the research letter, then I'll return with a short review what we know about the possibility of long-range airborne spread of influenza  (and other) viruses.  

Volume 27, Number 12—December 2021
Research Letter
Reassortant Influenza A(H1N1)pdm09 Virus in Elderly Woman, Denmark, January 2021

Jakob N. Nissen, Sophie J. George, Charlotte K. Hjulsager, Jesper S. Krog, Xiaohui C. Nielsen, Tina V. Madsen, Klara M. Andersen, Tyra G. Krause, Lasse S. Vestergaard, Lars E. Larsen, and Ramona Trebbien


A case of human infection with influenza A(H1N1)pdm09 virus containing a nonstructural gene highly similar to Eurasian avian-like H1Nx swine influenza virus was detected in Denmark in January 2021. We describe the clinical case and report testing results of the genetic and antigenic characterizations of the virus.

Human infection with swine influenza A virus (IAV) had not previously been detected in Denmark, but sporadic cases have been reported from other countries (1). We report the identification of a case of zoonotic swine influenza infection in Denmark during a low-activity influenza season.

The variant IAV was detected by the National Influenza Center at Statens Serum Institut (Copenhagen, Denmark), as part of routine surveillance. A sputum sample was collected on January 21, 2021, in Zealand, Denmark, from a female patient in her 70s with various concurrent conditions, including a chronic respiratory disease, who was admitted to hospital after 2 days of moderate influenza-like symptoms: fever (39°C), coughing, sore throat, and difficulty breathing. The patient sample was positive for IAV in analyses at the local hospital microbiology laboratory; remaining sample material was submitted to the National Influenza Center, which confirmed it positive for influenza A(H1N1)pdm09 (Appendix).
We performed whole genome sequencing on the virus (2), and named it A/Denmark/1/2021 (vH1N1), and submitted to GISAID (https://www.gisaid.orgExternal Link; accession no. EPI_ISL_909652). BLAST ( Link) and phylogenetic analyses revealed that all segments except the nonstructural gene belonged to influenza A(H1N1)pdm09 clade 1A3.3.2 (3), which is most similar (97%–98% nt identity) to viruses collected from swine in France and Germany in 2014 and 2015 (Table; Figure).
The nonstructural gene was most similar (95%) to Eurasian avian-like H1Nx swine viruses of clade 1C. No segments had a near-exact match to sequences in GenBank or GISAID, and all were distinct from the seasonal vaccine strain, A/Guangdong-Maonan/SWL1536/2019 (Table).

Because of the suspected swine origin of the case virus, we used whole-genome sequencing to retrospectively analyze 68 IAVs with a hemagglutinin (HA) gene belonging to clade 1A.3.3.2 sampled from swine herds in Denmark during 2020–2021. Nine of the samples, collected April 2020–January 2021 from >7 different herds in different parts of Denmark, including Zealand, contained the same gene constellation as the case virus (98.9%–99.4% nt identity). This finding suggests that the virus from the human case originated from swine in Denmark.

The patient and her husband reside in the countryside, <2 km from a medium-sized farm with finisher pigs. Because of coronavirus disease pandemic restrictions, she had not been in close contact with other persons or been close to the pig farm. Both the patient and her husband, who had no signs of illness, were vaccinated against seasonal influenza in October or November 2020. European General Data Protection Regulation ( restrictions on reporting personally identifiable information prevent revealing additional information about the patient or the farm.

Veterinary authorities in Denmark collected nose swab samples from 68 pigs at the neighboring farm on February 1, 2021, according to standard procedures. All samples tested negative by PCR for IAV. Because of the high prevalence of influenza-positive herds in Denmark, we could not be confident potential seropositive swine were infected by the virus in question, so we did not take blood samples. However, we therefore could not exclude previous virus circulation in the herd, because swabs were taken 11 days after virus detection in the patient. According to the Danish Metrological Institute, the patient’s residence was downwind of the pig herd most days preceding clinical symptoms.

Most of the case virus genes were derived from influenza A(H1N1)pdm09, which has been circulating in the human population of Denmark since 2009. However, the HA gene is different from that of the strains currently circulating (4), and it is therefore difficult to predict the level of immunity in the human population against this virus. Antigenic characterization (5) showed no or very poor cross-reactivity to all reference antiserum used for analysis (Appendix Table 1), and the HA gene contained several more mutations at antigenic sites compared with the seasonal vaccine strain (Appendix Figure). Therefore, vaccine effectiveness of the 2020–2021 seasonal influenza vaccine against the variant virus has been assessed as low.

Neuraminidase inhibition tests showed no reduction of oseltamivir or zanamivir inhibition, and the viral genome contains no known antiviral mutations except the V27A mutation in the M2 gene, known from most other H1N1 viruses circulating in human and swine (6,7). We identified no amino acid changes presumed to be related to increased risk of human infection (8), but further in vitro and in vivo analyses are planned to explore this possibility.

Because national coronavirus disease pandemic restrictions limited interpersonal contact, there were only 46 confirmed influenza cases in Denmark during the 2020–2021 season, and transmission of the variant virus was considered negligible. The Danish Patient Authority did not identify any person-to-person swine influenza transmission, and no further public health response measures were enacted.

The effects of the most recent swine influenza pandemic and the extensive diversity and reassortment in swine influenza viruses indicate the obvious zoonotic potential of these viruses (9,10). Therefore, more attention should be given to routine detection and control of swine influenza viruses.

Dr. Nissen is a postdoctoral researcher at the National Influenza Center, Statens Serum Institut, Copenhagen, Denmark. With a background in genomics and bioinformatics, he focuses on bioinformatic tool development and the prediction of the zoonotic potential of influenza viruses.

         (Continue . . . )

Conventional wisdom says that influenza viruses only travel a short distance in the air, are quickly deactivated by desiccation and/or UV rays from the sun, and that they aren't truly `airborne'.  

Like almost every hard-and-fast rule, however, there appear to be some notable exceptions. 

We've seen studies linking infected `dust' (dried feces, feathers, etc.) from poultry farms - often propelled by large exhaust fans - being carried several kilometres by the wind and then infecting other nearby farms. 

And we've seen numerous (mostly anecdotal) reports - particularly out of Asia - of people who either lived near, or simply walked past a live bird market, contracting avian influenza (see J. Infection: Aerosolized H5N6 At A Chinese LBM (Live Bird Market)

The science of all of this has a name; aerobiology – the study of how bacteria, fungal spores, pollen and even viruses can be passively transported in the air. And while some might consider it `fringe' science, we've seen a number of serious studies over they years. 

And while not directly addressing the possibility of wind-borne spread of COVID-19, the ECDC's Rapid Risk Assessment on COVID-19 in mink (LINK) (Nov. 2020) does note:
Mink are housed in adjoining cages made of wire netting, allowing free airflow and contact between animals in adjacent cages, which explains the rapid animal-to-animal transmission. Furthermore, the presence of viral RNA in inhalable dust collected from inside the farms indicates the possibility of workers having been exposed to the virus in mink excretions. 

More recently, in 2020's study Nature Comms: Influenza A Transmission Via `Aerosolized Fomites'we looked at laboratory evidence that influenza A viruses (and probably others) can be transmitted via airborne or `aerosolized fomites'

This potential long-distance carriage of pathogens on the wind isn't limited to avian flu viruses, as reported by a 2014 BMC Veterinary Research article  Evidence of infectivity of airborne porcine epidemic diarrhea virus and detection of airborne viral RNA at long distances from infected herds authors Carmen Alonso, Dane P Goede, Robert B Morrison, Peter R Davies, Albert Rovira, Douglas G Marthaler and Montserrat Torremorell wrote:

Results indicated presence of infectious PEDV in the air from experimentally infected pigs and genetic material of PEDV was detected up to 10 miles downwind from naturally infected farms. Airborne transmission should be considered as a potential route for PEDV dissemination.

The following year (2015), in PLoS One: Concentration, Size Distribution, and Infectivity of Airborne Particles Carrying Swine Viruses, some of the same authors returned with a look at the virus carrying capacity of aerosols from experimentally infected pigs.

Despite these examples, the source of the novel flu infection last January in Denmark remains unknown, and will likely remain so. The proximity of the farm, and prevailing wind direction are interesting factoids, but correlation does not imply causation. 

That said, our understanding of viruses - and how they transmit - continues to evolve. A decade ago, long distance airborne transmission of viable viruses was considered a `fringe' topic.  Today, while its impact in the real world is far from known, it is increasingly a topic of research by serious scientists. 

Who knows? We may even consider it established science a decade from now. 

Stay tuned.