H5N1 in carnivore brains

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   DJ A NL study did find out carnivores eating H5N1-infected birds had the H5N1-virus in their brain..One question I have is does that mean H5N1 now may be in rats, cats, mice their brains as well ? Did we miss a lot of spread by only looking at respitory system for H5N1 in carnivores ? (If that is what "we" did most of the time ?)
The study [url]https://www.mdpi.com/2076-0817/12/2/168[/url] or https://www.mdpi.com/2076-0817/12/2/168 ;
Abstract
Wild carnivore species infected with highly pathogenic avian influenza (HPAI) virus subtype H5N1 during the 2021–2022 outbreak in the Netherlands included red fox (Vulpes vulpes), polecat (Mustela putorius), otter (Lutra lutra), and badger (Meles meles). 

Most of the animals were submitted for testing because they showed neurological signs.

 In this study, the HPAI H5N1 virus was detected by PCR and/or immunohistochemistry in 11 animals and was primarily present in brain tissue, often associated with a (meningo) encephalitis in the cerebrum. In contrast, the virus was rarely detected in the respiratory tract and intestinal tract and associated lesions were minimal. Full genome sequencing followed by phylogenetic analysis demonstrated that these carnivore viruses were related to viruses detected in wild birds in the Netherlands. 

The carnivore viruses themselves were not closely related, and the infected carnivores did not cluster geographically, suggesting that they were infected separately. 

The mutation PB2-E627K was identified in most carnivore virus genomes, providing evidence for mammalian adaptation. 

This study showed that brain samples should be included in wild life surveillance programs for the reliable detection of the HPAI H5N1 virus in mammals. Surveillance of the wild carnivore population and notification to the Veterinary Authority are important from a one-heath perspective, and instrumental to pandemic preparedness.
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3. Results
3.1. Virological Analysis of Infected Carnivores
During the period December 2021–February 2022, 21 wild carnivores suspected of HPAI H5N1 infection based on neurological signs or evidence of viral infection in post-mortem sections were submitted for testing. Of these, 14 animals tested positive for influenza A virus using the M-PCR. Three red foxes (Vulpes vulpes) were analyzed in a previous study [8]. The current study describes the analysis of the 11 other carnivores: red fox (n = 6), polecat (Mustela putorius) (n = 3), badger (Meles meles) (n = 1), and otter (Lutra lutra) (n = 1) (Table 1). The locations where the infected carnivores were found were dispersed over the Netherlands (Figure 1) and the cases did not cluster geographically. When examined, overall viral loads in brain tissues were higher than those in the swabs of the throat and intestinal tract. All viruses detected were of the subtype HPAI H5N1. Virus isolation was performed in eight animals, showing the presence of the infectious virus in five animals (Table S1).
Figure 1. Map of the locations were HPAI H5N1 infected carnivores were found during the 2021–2022 epizootic in the Netherlands. The infected carnivores analyzed in this study are marked in orange, and numbers are corresponding to Table 1. The infected mammals analyzed in previous studies [8] are depicted in grey. The map was generated using the R software package tmap [24].
DJ discussion and results;
4. Discussion
The HPAI H5N1 epizootic in 2021–2022 is the largest that occurred in Europe so far and was associated with massive mortality amongst wild birds. This study showed that at least four different wild carnivore species became infected with HPAI H5N1 viruses in the Netherlands. Within a three-month period, 14 out of 21 carnivores suspected of HPAI H5N1 infection based on ante-mortem behavior or post-mortem indications for viral infection, tested positive for the virus. 
The virus was detected in nine red foxes, three polecats, one otter and one badger. This study confirmed the initial findings in three of the red foxes [8] by greater numbers of animals and across four species. Higher viral RNA loads were consistently detected in the brains of the animals studied compared to those detected in throat or anal swabs. Interestingly, 3 out of 11 animals in this study were negative in anal and throat swab and HPAI diagnosis would have been missed without additional brain samples. 
Other studies also reported the presence of HPAI H5 virus in the brain of various wild carnivore species [3,5,7]. Full genome sequencing of the carnivore viruses, followed by phylogenetic analysis, demonstrated that they belonged to H5N1 clade 2.3.4.4b and that the carnivore viruses were related to viruses detected in wild birds in the Netherlands. 
Consistent with the results from the initial study [8], the carnivore viruses were not genetically closely related among themselves and they did not cluster geographically. This suggests that the animals were infected by separate virus introductions likely originating from wild birds. 

There was no evidence for mammal to mammal spread within this small number of cases. However, there was no active surveillance for the virus in ambulatory or mildly infected mammals without clinical signs, which may also spread the virus. Samples from wildlife harvested for hunting purposes, wildlife culled as a management tool, or culled for intervention of disease control, could be used for that type of surveillance.
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Conclusions
Our study showed that brain samples were needed for the reliable detection of the HPAI H5N1 virus in mammals, and therefore must be routinely included, besides throat and anal swabs, in surveillance programs. HPAI viruses were detected in multiple carnivore species, frequently with mutations indicative of mammalian adaptation. Therefore, detection of HPAI viruses in mammals must be made notifiable to the Veterinary Authorities. Surveillance of the wild carnivore population is important from a one heath perspective, and instrumental to pandemic preparedness.
DJ...in my non expert view this study is very alarming...H5N1 is spreading from infected birds into carnivores...very likely on a large scale. There are mutations enabling better mammal-to-mammal spread...that such spread so far has not been detected does not mean that it is not happening....
Finally, many of the wild carnivores were infested with lung parasites [33]. Especially in red foxes, the presence of A. vasorum larvae in the lungs was a common finding [34] and may have overshadowed changes due to HPAI lung pathology. Furthermore, the lung pathology and the clinical relevance of these parasites is variable in wildlife and it is unclear if these co-infections influenced susceptibility to HPAI. Besides these limitations, our results can be used to improve HPAI wildlife surveillance.
Coinfections may complicate detecting H5N1 spread in mammals...
Minks did show high spread from mink to mink of H5N1..."mink-like animals" in the wild could become the missing gap between H5N1 spread in birds and H2H/ spread in humans...

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Dutch Josh Members Profile Send Private Message Find Members Posts Add to Buddy List Adviser Group Joined: May 01 2013 Location: Arnhem-Netherla Status: Offline Points: 95227	Post Options Post Reply Quote Dutch Josh Report Post Thanks(0) Quote Reply Topic: H5N1 in carnivore brains Posted: February 18 2023 at 10:38pm
	DJ A NL study did find out carnivores eating H5N1-infected birds had the H5N1-virus in their brain..One question I have is does that mean H5N1 now may be in rats, cats, mice their brains as well ? Did we miss a lot of spread by only looking at respitory system for H5N1 in carnivores ? (If that is what "we" did most of the time ?) The study [url]https://www.mdpi.com/2076-0817/12/2/168[/url] or https://www.mdpi.com/2076-0817/12/2/168 ; Abstract Wild carnivore species infected with highly pathogenic avian influenza (HPAI) virus subtype H5N1 during the 2021–2022 outbreak in the Netherlands included red fox (Vulpes vulpes), polecat (Mustela putorius), otter (Lutra lutra), and badger (Meles meles). Most of the animals were submitted for testing because they showed neurological signs. In this study, the HPAI H5N1 virus was detected by PCR and/or immunohistochemistry in 11 animals and was primarily present in brain tissue, often associated with a (meningo) encephalitis in the cerebrum. In contrast, the virus was rarely detected in the respiratory tract and intestinal tract and associated lesions were minimal. Full genome sequencing followed by phylogenetic analysis demonstrated that these carnivore viruses were related to viruses detected in wild birds in the Netherlands. The carnivore viruses themselves were not closely related, and the infected carnivores did not cluster geographically, suggesting that they were infected separately. The mutation PB2-E627K was identified in most carnivore virus genomes, providing evidence for mammalian adaptation. This study showed that brain samples should be included in wild life surveillance programs for the reliable detection of the HPAI H5N1 virus in mammals. Surveillance of the wild carnivore population and notification to the Veterinary Authority are important from a one-heath perspective, and instrumental to pandemic preparedness. - 3. Results 3.1. Virological Analysis of Infected Carnivores During the period December 2021–February 2022, 21 wild carnivores suspected of HPAI H5N1 infection based on neurological signs or evidence of viral infection in post-mortem sections were submitted for testing. Of these, 14 animals tested positive for influenza A virus using the M-PCR. Three red foxes (Vulpes vulpes) were analyzed in a previous study [8]. The current study describes the analysis of the 11 other carnivores: red fox (n = 6), polecat (Mustela putorius) (n = 3), badger (Meles meles) (n = 1), and otter (Lutra lutra) (n = 1) (Table 1). The locations where the infected carnivores were found were dispersed over the Netherlands (Figure 1) and the cases did not cluster geographically. When examined, overall viral loads in brain tissues were higher than those in the swabs of the throat and intestinal tract. All viruses detected were of the subtype HPAI H5N1. Virus isolation was performed in eight animals, showing the presence of the infectious virus in five animals (Table S1). Figure 1. Map of the locations were HPAI H5N1 infected carnivores were found during the 2021–2022 epizootic in the Netherlands. The infected carnivores analyzed in this study are marked in orange, and numbers are corresponding to Table 1. The infected mammals analyzed in previous studies [8] are depicted in grey. The map was generated using the R software package tmap [24]. DJ discussion and results; 4. Discussion The HPAI H5N1 epizootic in 2021–2022 is the largest that occurred in Europe so far and was associated with massive mortality amongst wild birds. This study showed that at least four different wild carnivore species became infected with HPAI H5N1 viruses in the Netherlands. Within a three-month period, 14 out of 21 carnivores suspected of HPAI H5N1 infection based on ante-mortem behavior or post-mortem indications for viral infection, tested positive for the virus. The virus was detected in nine red foxes, three polecats, one otter and one badger. This study confirmed the initial findings in three of the red foxes [8] by greater numbers of animals and across four species. Higher viral RNA loads were consistently detected in the brains of the animals studied compared to those detected in throat or anal swabs. Interestingly, 3 out of 11 animals in this study were negative in anal and throat swab and HPAI diagnosis would have been missed without additional brain samples. Other studies also reported the presence of HPAI H5 virus in the brain of various wild carnivore species [3,5,7]. Full genome sequencing of the carnivore viruses, followed by phylogenetic analysis, demonstrated that they belonged to H5N1 clade 2.3.4.4b and that the carnivore viruses were related to viruses detected in wild birds in the Netherlands. Consistent with the results from the initial study [8], the carnivore viruses were not genetically closely related among themselves and they did not cluster geographically. This suggests that the animals were infected by separate virus introductions likely originating from wild birds. There was no evidence for mammal to mammal spread within this small number of cases. However, there was no active surveillance for the virus in ambulatory or mildly infected mammals without clinical signs, which may also spread the virus. Samples from wildlife harvested for hunting purposes, wildlife culled as a management tool, or culled for intervention of disease control, could be used for that type of surveillance. - Conclusions Our study showed that brain samples were needed for the reliable detection of the HPAI H5N1 virus in mammals, and therefore must be routinely included, besides throat and anal swabs, in surveillance programs. HPAI viruses were detected in multiple carnivore species, frequently with mutations indicative of mammalian adaptation. Therefore, detection of HPAI viruses in mammals must be made notifiable to the Veterinary Authorities. Surveillance of the wild carnivore population is important from a one heath perspective, and instrumental to pandemic preparedness. DJ...in my non expert view this study is very alarming...H5N1 is spreading from infected birds into carnivores...very likely on a large scale. There are mutations enabling better mammal-to-mammal spread...that such spread so far has not been detected does not mean that it is not happening.... Finally, many of the wild carnivores were infested with lung parasites [33]. Especially in red foxes, the presence of A. vasorum larvae in the lungs was a common finding [34] and may have overshadowed changes due to HPAI lung pathology. Furthermore, the lung pathology and the clinical relevance of these parasites is variable in wildlife and it is unclear if these co-infections influenced susceptibility to HPAI. Besides these limitations, our results can be used to improve HPAI wildlife surveillance. Coinfections may complicate detecting H5N1 spread in mammals... Minks did show high spread from mink to mink of H5N1..."mink-like animals" in the wild could become the missing gap between H5N1 spread in birds and H2H/ spread in humans...
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