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  • #16
    Please see:

    Nature Dispatch: Risk Assessment On HPAI H5N1 From Mink

    Comment


    • #17
      Technical Update: Summary Analysis of the Genetic Sequence of a Highly Pathogenic Avian Influenza A(H5N1) Virus Identified in a Human in Michigan


      Español | Other Languages
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      Updated May 24, 2024

      This is a technical summary of an analysis of the genomic sequence of the virus identified in the Michigan case of highly pathogenic avian influenza (HPAI) A(H5N1) virus infection. This analysis supports the conclusion that the overall risk to the general public associated with the ongoing HPAI A(H5N1) outbreak has not changed and remains low at this time. The genome of the virus identified from the patient in Michigan (A/Michigan/90/2024) is publicly posted in GISAID (EPI_ISL_19162802) and has been submitted to GenBank.

      May 24, 2024 – CDC has sequenced the influenza virus genome identified in a conjunctival specimen collected from the person in Michigan who was identified to be infected with HPAI A(H5N1) virus and compared each gene segment with HPAI A(H5N1) sequences from cows, wild birds and poultry and the first human case in Texas. The virus HA was identified as clade 2.3.4.4b with each individual gene segment closely related to genotype B3.13 viruses detected in dairy cows available from USDA testing. No amino acid changes were identified in the HA gene sequence from the Michigan patient specimen compared to the HA sequence from the case in Texas and only minor changes were identified when compared to sequences from cows. These data indicate viruses detected in both cows and the two human cases maintain primarily avian genetic characteristics and lack changes that would make them better adapted to infect or transmit between humans. The genome of the human virus from Michigan did not have the PB2 E627K change detected in the virus from the Texas case, but had one notable change (PB2 M631L) compared to the Texas case that is known to be associated with viral adaptation to mammalian hosts, and which has been detected in 99% of dairy cow sequences but only sporadically in birds[i]. This change has been identified as resulting in enhancement of virus replication and disease severity in mice during studies with avian influenza A(H10N7) viruses[ii]. The remainder of the genome of A/Michigan/90/2024 was closely related to sequences detected in infected dairy cows and strongly suggests direct cow-to-human transmission. Further, there are no markers known to be associated with influenza antiviral resistance found in the virus sequences from the Michigan specimen and the virus is very closely related to two existing HPAI A(H5N1) candidate vaccine viruses that are already available to manufacturers, and which could be used to make vaccine if needed. Overall, the genetic analysis of the HPAI A(H5N1) virus detected in a human in Michigan supports CDC’s conclusion that the human health risk currently remains low. More details of this and other viruses characterized in association with the dairy cow outbreak are available in a previous technical summary.

      [i] Thao-Quyen Nguyen, Carl Hutter, Alexey Markin, Megan Thomas, Kristina Lantz, Mary Lea Killian, Garrett M. Janzen, Sriram Vijendran, Sanket Wagle, Blake Inderski, Drew R. Magstadt, Ganwu Li, Diego G. Diel, Elisha Anna Frye, Kiril M. Dimitrov, Amy K. Swinford, Alexis C. Thompson, Kevin R. Snevik, David L. Suarez, Erica Spackman, Steven M. Lakin, Sara C. Ahola, Kammy R. Johnson, Amy L. Baker, Suelee Robbe-Austerman, Mia Kim Torchetti, Tavis K. Anderson Emergence and interstate spread of highly pathogenic avian influenza A(H5N1) in dairy cattle bioRxiv 2024.05.01.591751; doi: https://doi.org/10.1101/2024.05.01.591751

      [ii]Zhang X, Xu G, Wang C, Jiang M, Gao W, Wang M, Sun H, Sun Y, Chang KC, Liu J, Pu J. Enhanced pathogenicity and neurotropism of mouse-adapted H10N7 influenza virus are mediated by novel PB2 and NA mutations. J Gen Virol. 2017 Jun;98(6):1185-1195. doi: 10.1099/jgv.0.000770. Epub 2017 Jun 8. PMID: 28597818.

      Last Reviewed: May 24, 2024​

      Last edited by sharon sanders; May 25, 2024, 07:23 AM. Reason: added bolding

      Comment


      • #18



        Raj Rajnarayanan
        @RajlabN
        ·
        7h


        #H5N1 Updates The virus sequence from the patient in Michigan is now publicly available in GISAID (EPI_ISL_19162802) Comparing w/ the sequence from Texas: No changes in HA Michigan sequence has PB2 M631L but no E627K​


        Raj Rajnarayanan
        @RajlabN
        ·
        7h


        #H5N1 #DairyCattleOutbreak Updates PB2 mutations (Sequences from Texas and Michigan human cases)
        Image

        Raj Rajnarayanan
        @RajlabN
        ·
        7h


        Replying to
        @RajlabN
        Key differences: Presence of PB2 E362G & M631L and the absence of PB2 E627K




        ​​

        Comment


        • #19
          Post




          See new posts Conversation


          Bloom Lab
          @jbloom_lab


          In new study led by
          @bdadonaite
          , we measure how all mutations to H5 influenza HA affect four molecular phenotypes relevant to pandemic risk: https://biorxiv.org/content/10.1101/2024.05.23.595634v1… Results can inform surveillance of ongoing evolution of H5N1.
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          9:46 AM · May 25, 2024
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          Bloom Lab
          @jbloom_lab
          ·
          4h


          To measure how all HA mutations affect those phenotypes, we created pseudovirus libraries of HA from WHO clade 2.3.4.4b vaccine strain. Pseudoviruses encode no genes other than HA, so can only do a single cycle of infection making them safe for biosafety-level-2.
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          Bloom Lab
          @jbloom_lab
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          First, we measured how all mutations affected HA-mediated cell entry, which is essential for viral fitness See heatmap below, which is easily visualized interactively at https://dms-vep.org/Flu_H5_American-Wigeon_South-Carolina_2021-H5N1_DMS/… Some sites constrained (orange); others w many well tolerated mutations (white/blue)
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          Bloom Lab
          @jbloom_lab
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          Here is constraint (average cell entry effect of mutations at each site) on HA structure. These measurements define ideal targets for new approaches (eg https://biorxiv.org/content/10.1101/2024.03.14.585103v1…) to develop antibodies targeting constrained regions of virus.
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          Bloom Lab
          @jbloom_lab
          ·
          4h


          Next, we measured how mutations affect HA’s usage of a2-6 vs a2-3 sialic acid receptors (thanks
          @PeacockFlu
          for idea how to do this) Important because human-transmissible viruses use a2-6. Below are mutations that improve a2-6 usage, and should be monitored for in surveillance
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          Bloom Lab
          @jbloom_lab
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          8 Bloom Lab
          @jbloom_lab
          ·
          4h


          Airborne-transmissible influenza viruses tend to have higher HA stability, so we also measured how all mutations affect stability. As seen below, stability enhancing mutations tend to be located in helices in fusion machinery and interfaces between head & stalk domains.
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          Bloom Lab
          @jbloom_lab
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          823
          Bloom Lab
          @jbloom_lab
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          In addition to relevance of stability-enhancing mutations for pandemic-risk surveillance, these mutations could be useful to introduce into vaccine immunogens as stabilizing mutations have improved immunogenicity of other viral vaccines.


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          Bloom Lab
          @jbloom_lab
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          4h


          We next measured how all HA mutations affected neutralization by sera from vaccinated mice (from
          @ScottEHensley
          ) or ferrets (from Richard Webby). This is important because WHO recommends candidate vaccine strains to H5, which may need to be updated as virus evolves.


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          Bloom Lab
          @jbloom_lab
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          4h


          Below are sites in HA where mutations reduce neutralization by mouse or ferret sera (see https://dms-vep.org/Flu_H5_American-Wigeon_South-Carolina_2021-H5N1_DMS/for… interactive plots w per-mutation effects) These data make it possible to rapidly identify new viral mutants that are mismatched to current candidate vaccine strains.
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          Bloom Lab
          @jbloom_lab
          ·
          4h


          To use these experimental datasets to inform surveillance, Jordan Ort &
          @LouiseHMoncla
          to integrated them into an interactive Nextstrain tree (https://nextstrain.org/groups/moncla-lab/h5nx/h5-dms/clade-2344b…) that allows you to color nodes by phenotypes (see dropdown at left)


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          Bloom Lab
          @jbloom_lab
          ·
          4h


          Such trees make it possible to immediately identify when new viral mutants have potentially relevant HA phenotypic changes; for instance, see below for examples of mutations in dairy cattle cluster that reduce neutralization, or viruses w increased HA stability.
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          Bloom Lab
          @jbloom_lab
          ·
          4h


          The datasets are so rich that we recommend viewing interactive plots rather than static figures: - Homepage w all data: https://dms-vep.org/Flu_H5_American-Wigeon_South-Carolina_2021-H5N1_DMS/… - Data mapped on HA structure: https://dms-viz.github.io/v0/?data=https%3A%2F%2Fraw.githubusercontent.com%2Fdm s-vep%2FFlu_H5_American-Wigeon_South-Carolina_2021-H5N1_DMS%2Fmain%2Fresults%2Fdms-viz%2Fdms-viz.json… - Data mapped on phylogenetic trees: https://nextstrain.org/groups/moncla-lab/h5nx/h5-dms/clade-2344b…


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          Bloom Lab
          @jbloom_lab
          ·
          4h


          In addition, we have made a page to help convert between the many confusing numbering schemes used to name HA mutations: https://dms-vep.org/Flu_H5_American-Wigeon_South-Carolina_2021-H5N1_DMS/numbering.html… (Throughout we use H3 numbering, but other studies use other schemes)


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          Bloom Lab
          @jbloom_lab
          ·
          4h


          Finally, as we discuss in paper, our ability to safely do deep mutational scanning of H5 HA enabled by switch from live-virus to pseudovirus. I thank
          @mlipsitch
          & others for thoughtful discussion that prompted switch; we welcome continued input on those aspects of our work.
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          Bloom Lab
          @jbloom_lab
          ·
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          Thanks to all who contributed to this study:
          @bdadonaite
          ,
          @Jenny_Ahn0
          , Jordan Ort, Jin Yu, Colleen Furey,
          @anniedosey
          , Will Hannon, Amy Baker, Richard Webby,
          @KingLabIPD
          , Yan Liu,
          @ScottEHensley
          ,
          @PeacockFlu
          ,
          @LouiseHMoncla
          Pre-print is here:

          biorxiv.org
          Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance
          H5 influenza is considered a potential pandemic threat. Recently, H5 viruses belonging to clade 2.3.4.4b have caused large outbreaks in avian and multiple non-human mammalian species. Previous...






          Comment


          • #20
            Preprint: Massive outbreak of Influenza A H5N1 in elephant seals at Peninsula Valdes, Argentina: increased evidence for mammal-to-mammal transmission






            #18,096

            Although we are closely watching a distinct genotype (B3.13) of H5N1 clade 2.3.4.4b running rife in American dairy cattle, in South America another genetically distinct H5N1 virus is causing mass mortality in sea lions and seals.

            Unlike the American cattle genotype, this H5 virus has spread across multiple countries, killing tens of thousands of its mammalian hosts.

            A few of many past blogs on these events include:
            Marine mammals have been long known to be susceptible to influenza A infection (see here, here, here, and here), but previous outbreaks have tended to be smaller, shorter-lived, and geographically limited.

            The spread in marine mammals from Peru on the Pacific coast to southern Brazil on the Atlantic side is unprecedented, leading some researchers to suspect mammal-to-mammal transmission.

            Today we've a preprint (published June 1st) that presents even more evidence suggestive of mammal-to-mammal transmission, including the identification of a marine-mammal specific clade.

            The authors wrote:

            Across the genome, we identified more than 64 amino acid changes in the H5N1 HPAI viruses from Península Valdés when compared viruses from birds and mammals from Argentina, other South American countries, Antarctica, North America (genotype B3.2 from 2022–2023) and the original Goose/Guangdong (Gs/Gd) (Supplementary Table 4).
            Of the 64 mutations, 18 are potentially associated with increased virulence, transmission or adaptation to mammalian hosts, and fifteen are present in H5N1 viruses from Argentina’s coastal outbreaks in marine mammals and terns but absent in H5N1 (B3.2 genotype) strains from North America and from goose/poultry strains from Argentina (Supplementary Table 4). Of note, eleven of the fifteen common mutations were also present in the human case in Chile (Supplementary Table 5).


            This is, as you might imagine, a lengthy (33 Pages) and at times technical report, and while I've posted some excerpts below, is well worth reading in its entirety. I'll have postscript after the break.
            Massive outbreak of Influenza A H5N1 in elephant seals at Peninsula Valdes, Argentina: increased evidence for mammal-to-mammal transmission

            Marcela M Uhart, Ralph E. T. Vanstreels, Martha I. Nelson, Valeria Olivera, Julieta Campagna, Victoria Zavattieri, Philippe Lemey, Claudio Campagna, Valeria Falabella, Agustina Rimondi
            doi: https://doi.org/10.1101/2024.05.31.596774+

            PDF
            Abstract

            H5N1 high pathogenicity avian influenza (HPAI) viruses of the cla(SNIP)de 2.3.4.4b have killed thousands of marine mammals in South America since 2022. In October 2023, following outbreaks in sea lions in Argentina, we recorded unprecedented mass mortality (~17,000 individuals) in southern elephant seals (Mirounga leonina) at Peninsula Valdes. +


            Seal pups were disproportionately affected. Adult seals departed early, disrupting social and breeding structure. Frequent interactions with sea lions and scavenging by seagulls were observed. Deaths of terns concurred with seals but peaked weeks later. HPAI H5N1 was confirmed in seals and terns. Moreover, genomic characterization showed viruses from pinnipeds and terns in Argentina form a distinct clade with marine mammal viruses from Peru, Chile and Brazil.

            These mammal-clade viruses share an identical set of mammalian adaptation mutations which are notably also found in the terns. Our combined ecological and phylogenetic data support mammal-to-mammal transmission and occasional mammal-to-bird spillover.

            To our knowledge, this is the first multinational transmission of H5N1 viruses in mammals ever observed globally. The implication that H5N1 viruses are becoming more evolutionary flexible and adapting to mammals in new ways could have global consequences for wildlife, humans, and/or livestock.

            (SNIP)

            From a public health perspective, mammal-to-mammal transmission could be a critical stepping-stone in the evolutionary pathway for these viruses to become capable of human-to-human transmission and thus potentially pandemic 67. As mentioned previously, some of the mutations found in the strains of the marine mammal clade are already known to be of concern.

            Specifically, the mutation D701N in PB2 has been shown to compensate for the lack of the E627K mutation in PB2 in terms of improved viral growth in mammalian cells and enhanced aerosol transmission of H3N2 and H5N1 viruses68 .

            On the other hand, the phenotypic effects of mutations in other gene segments found in the H5 viruses from our study(Supplementary Table 5) are not yet known, and the possibility that some of them may also open evolutionary pathways that enhance the virulence or transmission of these viruses to mammals (including humans) cannot be ruled out.


            The fact that the H5N1 HPAI virus detected in a human case in Chile 69 belongs to the marine mammal clade described in this study, highlights the potential risk to public health.

            Moreover, given pinniped susceptibility to multiple IAVs (including human-like strains 38–40 ), and their frequent intermingling with other avian and mammalian hosts, co-infections could occur, potentially enabling the emergence of reassorted strains 36,70 .

            Hence, while there is no evidence for genomic reassortment occurring in pinnipeds at this time, the broad circulation of H5N1 HPAI viruses in marine mammals is a warning we must not ignore.

            In conclusion, as recently demonstrated by the detection of HPAI H5N1 viruses in ruminants 71 , few if any compartments and species are outside the scope of the clade 2.3.4.4b strains. Thus, moving forward, HPAI management requires holistic strategies that recognize the interconnectedness of human, animal, and environmental health and safeguard biodiversity, promote sustainable practices, and enhance resilience globally to emerging infectious diseases.

            (Continue . . . )




            Although we still don't know if H5N1 is actually capable of sparking a human pandemic (see Are Influenza Pandemic Viruses Members Of An Exclusive Club?), the number of ongoing field experiments around the globe grows with each passing day.

            And it is fair to say we are probably only vaguely aware of a fraction of them.

            Even in our own backyard - after > 2 months - we still don't know how widespread genotype B3.13 is in American livestock. After more than a year, there are still no answers to the massive die off of seals in the Caspian sea, and we know very little about what is happening with H5N1 in China, Russia, and most of Africa.

            Most of these field experiments will be failures. If it were easy for nature to cobble together a pandemic virus, we'd be hip deep with them all the time.

            But with growing diversity, comes more opportunities for the virus to get `lucky'. And that applies not only to H5N1, but also to a panoply of other subtypes, all embarked on their own evolutionary journeys.

            A few recent blogs include:
            We live in a threat-rich environment. While the following quote is nearly 20 years old, it sums up the pandemic preparedness dilemma in a nut shell.

            Everything you say in advance of a pandemic seems alarmist. Anything you’ve done after it starts is inadequate."- Michael Leavitt, Former Secretary of HHS


            All medical discussions are for educational purposes. I am not a doctor, just a retired paramedic. Nothing I post should be construed as specific medical advice. If you have a medical problem, see your physician.

            Comment


            • sharon sanders
              sharon sanders commented
              Editing a comment

              Tom Peacock
              @PeacockFlu
              ·
              36m


              A reminder that, although there is a (probably heavily human-assisted) mammal to mammal in the American cows, theres whats probably respiratory mammal to mammal transmission throughout the whole of South America in seals/sealions thats been going on for over a year now...

              Quote



              bioRxiv Microbiology
              @biorxiv_micrbio
              ·
              19h
              Massive outbreak of Influenza A H5N1 in elephant seals at Peninsula Valdes, Argentina: increased evidence for mammal-to-mammal ... https://biorxiv.org/cgi/content/shor...31.596774v1… #biorxiv_micrbio



          • #21

            Also commented by:


            Roland Baker

            @RolandBakerIII
            ·
            1h


            Phylogenetic data support mammal-to-mammal transmission of H5N1 & Adaptation Massive outbreak of Influenza A H5N1 in elephant seals at Peninsula Valdes, Argentina: increased evidence for mammal-to-mammal transmission

            biorxiv.org
            Massive outbreak of Influenza A H5N1 in elephant seals at Peninsula Valdes, Argentina: increased...
            H5N1 high pathogenicity avian influenza (HPAI) viruses of the clade 2.3.4.4b have killed thousands of marine mammals in South America since 2022. In October 2023, following outbreaks in sea lions in...


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            Roland Baker

            @RolandBakerIII
            ·
            1h


            SNPs specific to the marine mammal clade: * Q591K and D701N in PB2 * L548F in PB1 * A20T, M86I, and M548I in PA * R21Q and I226T in NS1


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            Roland Baker

            @RolandBakerIII
            ·
            58m


            "We believe that the high mortality rate in elephant seal pups is also consistent with mammal-to-mammal transmission, as pups are toothless and nurtured exclusively through nursing from their mothers."


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            Roland Baker

            @RolandBakerIII
            ·
            57m


            "Some newborns may have been infected before birth, as transplacental transmission of H5N1 HPAI viruses has been reported in humans and high virus loads were detected in aborted sea lion fetuses."


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            Roland Baker

            @RolandBakerIII
            ·
            51m


            "Mammal-to-mammal transmission is also supported by our regional phylogenetic analysis, which identified a novel H5N1 2.3.4.4b clade with viruses that appear to be specific to marine mammals. This marine mammal clade comprises strains with mutations..."


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            Roland Baker

            @RolandBakerIII
            ·
            51m


            "...that were not present in H5N1 2.3.4.4b viruses in birds (wild and domestic) from Peru, Chile, Argentina, Uruguay and Brazil, excepting occasional spillovers from marine mammals to coastal birds (terns and sanderling)."


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            Roland Baker

            @RolandBakerIII
            ·
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            They authors note that ecologically it is unlikely adults are getting H5N1 infections via food sources or interactions with birds. South American sea lions regularly visit multiple rookeries and haul-outs and likely spread H5N1 directly throughout Venezuela, Uruguay and Brazil.


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            Roland Baker

            @RolandBakerIII
            ·
            46m


            Some of these mutations (such as Q591K and D701N in PB2) are associated with increased virulence, transmission, or adaptation to mammalian hosts and have been maintained since they first emerged in H5N1 HPAI viruses in marine mammals in Chile.


            ​more....

            Comment


            • #23
              More from the study posted above:
              ...
              Within the Americas branches, the cattle derived H5N1viruses form a distinct group within the 2.3.4.4b clade (Fig. 1). The new group shows a cluster of H5N1 strains isolated from various hosts in the United States in 2024, including dairy cows, domestic cats, raccoons, skunks, mountain lions, and several bird species. The clustering of sequences from the recent dairy cow outbreak indicates a common ancestor and suggests a potential transmission link between these species. Together, these data demonstrate that the recent outbreak of H5N1 in dairy cows is distinct from other circulating 2.3.4.4b H5N1 viruses.
              ...
              H5N1 viruses circulating in the Americas have acquired mutations near the RBS

              Several mutations have arisen in 2.3.4.4b viruses since 2022, particularly at L111M, T199I, and V214A (Fig. 3A). Notably, these three mutations lie outside of the traditional RBS, which is comprised of the 130-loop, 190-helix, and 220-loop23 143 . Analysis of these mutations based on location and outbreak revealed that all three mutations are specific to H5N1 viruses in the Americas (Fig. 3B). Importantly, we observed T199I was found in all H5N1 viruses from the dairy cow outbreak, as well as some H5N1 viruses circulating in the Americas not related to the ongoing dairy cow outbreak (Fig. 3B)...
              We observed that the T199I mutation arose in the second half of 2023, with I199 becoming dominate by November 2023 (Fig. 3D-E). Notably, A/Texas/37/2024 HA NT sequence clusters more closely with an HA sequence collected from a mountain lion, also known as a cougar (Puma concolor) in Montana than sequences related to the ongoing dairy outbreak (Fig. 3E). Interestingly, the mountain lion isolate was collected in January 2024 and it was recently proposed that the dairy cow outbreak has been ongoing since late 2023 .. These data would suggest a closely related common ancestor from the mountain lion case to the ongoing dairy cow outbreak. Together, these data show that H5N1 viruses in the Americas have accumulated mutations within the RBS, with T199I being the only mutation specific to the ongoing dairy cow outbreak.
              ...
              Our glycan binding data shows that 2.3.4.4b H5N1 viruses, including those related to the ongoing dairy cow outbreak, have not gained binding to α2,6 sialic acids, the most abundant human receptor for influenza viruses, despite the presence of α2,6 sialic acids within the cow mammary glands17,18 220 .​...

              Comment


              • Pathfinder
                Pathfinder commented
                Editing a comment
                According to APHIS, a mountain lion collected on January 30, 2024 in Granite County was confirmed positive for EA H5N1 on February 27, 2024.

                Detections of Highly Pathogenic Avian Influenza in Mammals
                ...
                state county date_collected date_detected hpai_strain species

                Montana Gallatin 2022-10-20 2022-10-28 EA H5N1 Skunk (unidentified)
                Montana Madison 2022-11-22 2022-12-02 EA H5N1 Red fox
                Montana Teton 2022-10-31 2022-12-06 EA/AM H5N1 Grizzly bear
                Montana Flathead 2022-12-16 2022-12-20 EA/AM H5N1 Grizzly bear
                Montana Cascade 2022-12-16 2022-12-20 EA H5N1 Striped skunk
                Montana Sanders 2023-02-09 2023-02-22 EA H5N1 Raccoon
                Montana Lake 2023-02-28 2023-03-08 EA/AM H5N1 Raccoon
                Montana Custer 2023-02-28 2023-03-13 EA/AM H5N1 Striped skunk
                Montana Custer 2023-02-28 2023-03-13 EA/AM H5N1 Striped skunk
                Montana Park 2023-03-14 2023-03-17 EA H5N1 Striped skunk
                Montana Gallatin 2023-03-17 2023-03-23 EA/AM H5N1 Striped skunk
                Montana Madison 2023-04-14 2023-04-20 EA/AM H5N1 Mountain lion
                Montana Rosebud 2023-04-13 2023-04-20 EA/AM H5N1 Striped skunk
                Montana Mineral 2023-04-25 2023-08-04 EA/AM H5N1 Mountain lion
                Montana Granite 2024-01-30 2024-02-27 EA H5N1 Mountain lion
                Montana Yellowstone 2024-03-19 2024-04-26 EA/AM H5N1 Domestic cat

                View the latest information on detections of highly pathogenic avian influenza (HPAI) in mammals.

              • Pathfinder
                Pathfinder commented
                Editing a comment
                Excerpt from the WOAH report:
                ...
                PREVIOUSLY REPORTED OUTBREAKS
                ...
                OB_132896 - GRANITE COUNTY
                ...
                START DATE
                2024/01/30
                ...
                FIRST ADMINISTRATIVE DIVISION
                Montana
                ...
                LOCATION
                Granite County
                ...
                AFFECTED POPULATION DESCRIPTION
                Wild mountain lion (Puma concolor). Samples were collected from a sub-adult female found dead.
                ...

            • #24
              Raj Rajnarayanan
              @RajlabN
              ·
              3m


              #H5N1 updates PB2 of the house mouse sequences contain the recent “cattle outbreak adaptation signature” M631L H/T
              @nextstrain
              Special thanks to Karthik and Praneeth & Anderson Lab
              Image
              Image
              Quote

              Nextstrain
              @nextstrain
              ·
              55m
              Image
              Replying to @0bFuSc8 @USDA_APHIS and 2 others
              Thanks to quick work by Karthik G and Praneeth G to update SRA assemblies at https://github.com/andersen-lab/avian-influenza/…, we now have house mouse sequences up at the live site at https://nextstrain.org/avian-flu/h5n...82-003/2024…


              Comment


              • #25
                Please see:

                Pathogenicity and transmissibility of bovine H5N1 influenza virus (Nature, July 08, 2024)

                Comment


                • #26

                  Raj Rajnarayanan
                  @RajlabN


                  #H5N1 #AvianFlu updates Quick Analysis of the sequence of H5N1 (clade 2.3.4.4b) #Colorado human case uploaded to
                  @GISAID
                  PB2 mutations: T58A, V109I, V139I, E249G, E362G, K389R, D441N, V478I, V495I, M631L*, V649I, M676A * Dairy cattle outbreak signature 1/n​

                  Raj Rajnarayanan
                  @RajlabN
                  ·
                  11h


                  Sequence uploaded from Colorado contains unique PB2 E249G & NS1 R21Q mentioned in Singh et al. Detection and characterization of H5N1 HPAIV in environmental samples from a dairy farm. Virus Genes (2024) https://link.springer.com/article/10.1007/s11262-024-02085-4… 2/n
                  Content cover image
                  Detection and characterization of H5N1 HPAIV in environmental samples from a dairy farm
                  From link.springer.com


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                  Raj Rajnarayanan
                  @RajlabN
                  ·
                  10h


                  Big thanks to all the associated laboratories from sample collection to sequence submission Awaiting Chicken sequences! 3/n


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                  Raj Rajnarayanan
                  @RajlabN
                  ·
                  7h


                  Summary of HA mutations 4/n
                  Image


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                  Raj Rajnarayanan
                  @RajlabN
                  ·
                  7h


                  Summary of NA mutations 5/n
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                  ​​

                  Comment


                  • #27
                    Please see:

                    GISAID: The Plot Thickens

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                    • #28

                      Tom Peacock
                      @PeacockFlu
                      ·
                      Jul 16


                      suggests the US have created a new reservoir of H5N1 that can keep spilling over into poultry all year round. Also these cattle viruses are partially mammalian-adapted which makes them better at jumping into people than normal poultry H5N1 - poultry can act as amplifying hosts​

                      Comment


                      • #29
                        GSAID
                        July 19, 2024

                        H5N1 Bird Flu Circulating in Dairy Cows in the United States


                        The clade of highly pathogenic avian influenza (HPAI) viruses causing outbreaks in wild and domestic birds around the world, is appearing in dairy farms across several U.S. states since at least April 2024. These viruses recently caused morbidity and mortality in over 60 mammalian species, mostly carnivores, after consuming infected carcasses. Although cows were until recently not considered to be at risk of infection, the current outbreak demonstrates influenza remains unpredictable.

                        The route of exposure of these dairy cows and the mode of virus transmission remains unknown. The virus RNA was found at high concentrations in raw milk. Several animal species at dairy and poultry farms, as well as a growing number of farm workers were affected. Initial data released by the USDA’s Animal and Plant Health Inspection Service on GISAID show that the viruses in these cows, other animals and the farm workers are closely related. A mammalian adaptation marker (E627K) was noted in only one farm worker so far, and all farm workers suffered from conjunctivitis. In recent human cases, workers have developed mild eye symptoms alongside respiratory symptoms. GISAID teams continue to facilitate the work of their U.S. based colleagues and assist with the timely sharing of the latest genomic data that will help to monitor the outbreak and stop it..

                        Hundreds of full virus genome sequences from this outbreak have been made available in GISAID’s EpiFlu database, from mammalian and avian host samples collected in at least 13 States. Since the previous update on 16 July 2024, genetic sequence data from 24 new samples collected in U.S. were made available by the USDA, without detailed location and complete collection date. The latest trees, based on representative subsamples, are dated to 19 July 2024.

                        This collection includes many virus sequences from dairy cows, but also closely related viruses detected in poultry and wild birds and in mice, cats and other mammals as well as the recent human infections. Although metadata such as sampling date and location are unfortunately missing from recent datasets, the available data allow a close watch on mutations that may arise as a consequence of virus adaptation to new hosts.

                        [Pictured but not posted]
                        Subsampled phylogenetic trees with focus on recent U.S. H5N1 samples shown for HA, NA or PB2, respectively
                        (as of 19. July 2024)​



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