Correction: When I first loaded the article, the Veterinary Quarterly logo appeared at the top. I've amended the title to the proper journal.
#18,268
Up until a couple of months ago, rodents had never been included in the USDA's list of mammalian wildlife infected with H5N1 (see USDA Adds House Mouse To Mammals Affected by H5N1). Since early June we've seen nearly 100 rodents (house mouse, deer mice) added to the list, and they now comprise over 25% of all of the confirmed mammals on the list.
Over the past few months we've also seen the addition of domestic cats (n=37), prairie voles (n=1), and desert cottontails (n=1) to the list. HPAI H5 continues to expand its host range in mammals, and surveillance likely only picks up a small fraction of these spillover events.
Earlier this month, in Nature: Decoding the RNA Viromes in Shrew Lungs Along the Eastern Coast of China, we looked at a study that found a wide range of zoonotic viruses - including HPAI H5N6 - in shrews. Previously, in 2015's Taking HPAI To The Bank (Vole), we looked at that species' susceptibility to both H5N1 and H7N1.
While they haven't gotten the attention they probably deserve, rodents - which are often abundant around poultry and dairy farms - likely contribute to the spread of HPAI viruses (see 2016's The role of rodents in avian influenza outbreaks in poultry farms: a review).
All of which makes it less-than-surprising that researchers have now reported finding HPAI H5N1 in wild rats in Egypt. Given recent detections in deer mice in the U.S., it is probably safe to assume this is not a rare occurrence.
Due to its length, I've only posted some excerpts. Follow the link to read the full report. I'll have a brief postscript after you return.
Highly Pathogenic Avian Influenza Virus H5N1 clade 2.3.4.4b in Wild Rats in Egypt during 2023
Omnia Kutkat,Mokhtar Gomaa,Yassmin Moatasim,Ahmed El Taweel,Mina Nabil Kamel,Mohamed El Sayes, show all
Article: 2396874 | Accepted author version posted online: 28 Aug 2024
Cite this article https://doi.org/10.1080/22221751.2024.2396874
Main text
Avian influenza viruses (AIVs) pose continuous challenges to human and animal health worldwide. Wild birds are considered the natural reservoir for AIVs and play a major role in spreading influenza viruses over long distances [1]. Highly pathogenic avian influenza (HPAI) H5N1 activity has increased globally causing mass mortality in wild birds and poultry and incidental infections in mammals. H5 clade 2.3.4.4 of the H5N1 subtype emerged in China in 2014 due to reassortment and then diversified into several clades [2]. Clade 2.3.4.4b A(H5N1) viruses were detected in birds across the five continents [3, 4]. The spread of clade 2.3.4.4b of A(H5N1) viruses caused high mortality among domestic and wild birds. H5N1 clade 2.3.4.4b viruses have spilled over to several non-avian species, they were detected and isolated from domestic dogs and cats [5] and from different species of marine mammals and minks [6]. Epidemiological investigations based on serological testing showed that H5-specific antibodies were detected in foxes, polecats, and stone martens. These data showed that undetected and clinically mild HPAIV infections have occurred in wild carnivores in the Netherlands [7].
Some influenza viruses can propagate in rodents without adaptation [8]. Previous studies showed the detection of (HPAI) H5N8 virus in a mouse that was found dead in a depopulated poultry house [9] and antibodies against HPAI H5N1 virus were detected in rat sera during the initial outbreak of HPAI H5N1 virus in Hong Kong in 1997 [10]. Rodents can be abundant around poultry houses and share their habitat and may be contributing to the transmission of AIVs across poultry production sectors and across species [11]. The recent outbreak of clade 2.3.4.4b of A(H5N1) viruses in dairy cattle across several states in the United States has raised significant concern nationally and globally [12, 13]. Human cases of H5N1 clade 2.3.4.4b virus infection from dairy farm workers were reported [14]. Transmission of the virus from dairy cattle to other mammals including domestic cats was reported [15].
In 2021, the first HPAI H5N1 clade 2.3.4.4b viruses were detected in wild birds and domestic ducks from live bird markets in Egypt [16]. Based on the genetic analysis of HPAI viruses isolated in Egypt in winter 2021–2022, most H5N1 HPAI viruses were genetically close to H5 HPAI circulating in Europe, Africa, and the Middle East. Here, we report the first detection of HPAI H5N1 clade 2.3.4.4b viruses in wild rats in Egypt.
In July 2023, we collected oropharyngeal and paw swab samples from wild rats from a rural area in Giza near poultry farms, markets, and backyard flocks and performed influenza A virus detection via reverse transcription PCR (universal M-gene) [17]. This work was approved by the Medical Research Ethics Committee of the National Research Centre, Egypt (protocol number 1-4-6). A total of 20 rodents, eight Rattus norvegicus, nine Rattus rattus, and three Acomys cahirinus, were trapped alive, euthanized, and then sampled.
Four oropharyngeal samples from Rattus norvegicus and four oropharyngeal samples from Rattus rattus were positive for influenza A virus but none of the paw swabs (Table S1). The eight positive samples were inoculated into the allantoic cavity of 10-day-old embryonated chicken eggs (ECEs) and incubated for 48 h post-injection at 37 °C, and then chilled at 4 °C overnight, and analysed by hemagglutination assay (HA) using 0.5% chicken red blood cells (RBCs). From the four positive oropharyngeal samples from Rattus norvegicus, two were HA positive and confirmed by reverse transcription PCR of M gene (Table S1). Whole genome sequencing was attempted on RNA from the two isolates using Illumina's Nextera XT DNA Sample Preparation kit as previously described [16].
The two positive samples were confirmed to be positive for H5N1 using the whole genome sequencing and their full genomes (A/Rat/Egypt/STK001/2023 and A/Rat/Egypt/STK003/2023) were generated and submitted to GISAID under accession numbers EPI3276046-EPI3276053 and EPI3276054-EPI3276061. We compared the complete sequence of the HPAI H5N1 virus found in the rats (A/Rat/Egypt/STK001/2023 and A/Rat/Egypt/STK003/2023) with other highly pathogenic avian influenza (HPAI) H5N1 virus sequences available in GISAID selected based on a BLAST search. Sequence analysis to determine nucleotide identity between the two isolates of HPAI A(H5N1) viruses revealed that the eight segments had 99.9% to 100% sequence similarity. Also, the two viruses had a high nucleotide identity (99%–100%) with the HPAI A(H5N1) viruses of clade 2.3.4.4b from Egypt circulating since 2021 (Table S2).
(SNIP)
Low biosecurity measures, especially in backyards and markets, provide more chances for close contact between backyard birds and different animal species, creating an opportunity for interspecies transmission of influenza viruses. Dead birds infected with H5N1 are frequently discarded in open surfaces and consumed by stray animals. Such practices typically increase the chances of virus endemicity and increase viral loads on farms and surrounding environments.
Here, we characterized HPAI viruses from rodents. This has important implications on the management and control of the disease as rodents may be a potential route of virus transmission. To reduce the dissemination of AIV on poultry farms or backyard flocks, control measures including facilities’ maintenance, habitat management, removal of food sources, and pest control must be applied. This applies to Egypt and other countries with similar issues especially that the species sampled are wide spread almost globally.
Limitations of this study include the small sample size, variation of the types of wild mammals sampled, and the data’s inadequacy to distinguish infection from contamination. HPAI H5N1 cases in mammals continue to be reported globally. Enhanced active surveillance in wild animals and understanding the role of wild mammals in the maintenance and spread of influenza viruses are needed.
While it hits the main points, the ecology of H5N1 is far more complex than the CDC graphic below would suggest.
Given the amount of HPAI H5 virus already circulating in birds, cattle, and an array of mammalian species, the addition of rats (in Egypt) or deer mice in Colorado is probably not a game changer, but it is another sign that the virus is becoming increasingly entrenched in our environment.
What that will look like a year or two from now is anyone's guess.
But we ignore this trend at considerable risk to our food supply, our economy, and potentially to our public health.
