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December 10, 2024
Technical Update: Summary Analysis of the Genetic Sequence of a Highly Pathogenic Avian Influenza A(H5N1) Virus Identified in a Child in California
AT A GLANCE
Although the genetic data generated were insufficient to classify the virus as a specific genotype, the virus gene segments sequenced most closely resemble those segments from recent B3.13 viruses detected in California in humans, dairy cattle and poultry. This analysis supports the conclusion that the overall risk to the general public associated with the ongoing HPAI A(H5N1) outbreak in U.S. dairy cattle and poultry has not changed and remains low at this time
What to Know
This is a technical summary of an analysis of the genomic sequence data for an influenza A(H5N1) virus from a pediatric case in California that was confirmed by CDC on November 22. This analysis supports the conclusion that the overall risk to the general public associated with the ongoing HPAI A(H5N1) outbreak in U.S. dairy cattle and poultry has not changed and remains low at this time.
CDC Update
December 10, 2024 – As previously reported, CDC, in partnership with the California Department of Public Health (CDPH), confirmed a human infection with avian influenza A(H5N1) virus (H5N1 bird flu) in a child in California on November 22, 2024. The patient was initially detected as a suspected case of A(H5N1) through influenza testing and reported to CDPH through influenza surveillance, with initial subtyping conducted by the Stanford Medicine Clinical Virology Laboratory and presumptive positive test results reported by CDPH on November 19, 2024.
Based on real-time RT-PCR cycle threshold (Ct) values determined during diagnostic testing, the nasopharyngeal specimen from the patient was found to have very low levels of influenza viral RNA. Initial attempts to sequence the viral RNA by both Stanford Medicine and CDC using standard Next Generation Sequencing methodologies produced weak amplicons resulting from the PCR process that were challenging to sequence using both Nanopore and Illumina sequencing methodologies. Additionally, efforts to isolate virus from the specimen were not successful. By employing nucleic acid enrichment techniques, CDC and Stanford Medicine were able to generate the following viral RNA sequence data: full-length neuraminidase (NA) and nucleoprotein (NP) genes and partial hemagglutinin (HA), polymerase basic 2 (PB2), and polymerase basic 1 (PB1) genes. CDC and Stanford Medicine have submitted these data for A/California/192/2024 to both the GISAID and GenBank databases with accession numbers EPI_ISL_19597300 and PQ724471-PQ724473, respectively.
The initial sequence analysis, which was based on short fragments of the HA and NA genes, indicated that the virus was a clade 2.3.4.4b A(H5N1) virus similar to viruses causing outbreaks in dairy cattle and poultry in the United States. Upon obtaining full-length NA and NP genes, CDC was able to perform a comprehensive phylogenetic analysis, which showed that the virus was very similar to viruses detected in both dairy cattle and poultry as well as to A(H5N1) viruses from previous human infections in dairy workers in California. Although the genetic data generated were insufficient to classify the virus as a specific genotype, the NA and NP sequences shared close nucleotide identity and phylogenetic clustering with NA and NP genes from recent B3.13 viruses detected in California in humans, dairy cattle and poultry. Epidemiologic and environmental investigations did not clearly identify a possible source of exposure. Given that additional sequence data from the case could not be generated, it is unlikely that the source of the child's exposure to A(H5N1) virus will be identified, thus completing the investigation into genotype and exposure.
In addition to the phylogenetic analysis of the NA and NP genes, CDC conducted an assessment of the sequences of the virus specimen for molecular changes that might impact infectivity or transmissibility in humans or reduce susceptibility to antivirals, such as oseltamivir. The partial HA sequence, despite lacking portions of the 5' end of the gene, did not have additional changes in predicted antigenic sites compared to available clade 2.3.4.4b candidate vaccine viruses (CVVs). Nor were changes identified in the receptor binding domain of the virus, indicating that the virus retained avian receptor binding properties with no mutations that would impact changes in infectivity or transmissibility in humans. The PB2 and PB1 genes did not have genetic changes associated with mammalian adaptation, nor were there any genetic changes identified in NA sequence data that have been associated with reduced susceptibility to neuraminidase inhibitors, such as oseltamivir. Lastly, the sequence data confirmed that the virus from this case is not closely related to the virus that caused severe illness in a human in British Columbia, Canada. Collectively, these data indicate that the virus detected in this pediatric case is very similar to the majority of other influenza A(H5N1) viruses detected in the United States and bears no signs of concerning mutations.
While the sequence data obtained do not allow for definitive determination of the viral genotype, and no specific animal exposure source has been identified, these findings provide important contextual information and help to inform CDC's overall risk assessment. They also highlight the value of a collaborative approach to this response, including virologic risk assessments based on genetic data.
Follow-up Actions
Sporadic human infections with a novel influenza virus where animal exposure is not identified are not uncommon and have occurred during the current H5N1 bird flu outbreak in U.S. dairy cattle and poultry and in past outbreaks around the world. This case does not change CDC’s assessment of the immediate risk to the general public, which remains low at this time.
There is no evidence of human-to-human transmission of H5N1 virus in California or elsewhere in the United States. However, persons with occupational exposure to infected animals, such as poultry cullers, poultry workers, and dairy farm workers, are at higher risk of influenza A(H5N1) virus infection. Public health surveillance and investigations of all identified cases will continue at the local, state, and federal levels to monitor for concerning changes in the epidemiology of human cases or changes to influenza A(H5N1) viruses that could signal an increased public health threat – potentially including more severe outcomes in those currently at risk of exposure and infection, or increased risk to the general public.
https://www.cdc.gov/bird-flu/spotlig...-12092024.html
December 10, 2024
Technical Update: Summary Analysis of the Genetic Sequence of a Highly Pathogenic Avian Influenza A(H5N1) Virus Identified in a Child in California
AT A GLANCE
Although the genetic data generated were insufficient to classify the virus as a specific genotype, the virus gene segments sequenced most closely resemble those segments from recent B3.13 viruses detected in California in humans, dairy cattle and poultry. This analysis supports the conclusion that the overall risk to the general public associated with the ongoing HPAI A(H5N1) outbreak in U.S. dairy cattle and poultry has not changed and remains low at this time
What to Know
This is a technical summary of an analysis of the genomic sequence data for an influenza A(H5N1) virus from a pediatric case in California that was confirmed by CDC on November 22. This analysis supports the conclusion that the overall risk to the general public associated with the ongoing HPAI A(H5N1) outbreak in U.S. dairy cattle and poultry has not changed and remains low at this time.
CDC Update
December 10, 2024 – As previously reported, CDC, in partnership with the California Department of Public Health (CDPH), confirmed a human infection with avian influenza A(H5N1) virus (H5N1 bird flu) in a child in California on November 22, 2024. The patient was initially detected as a suspected case of A(H5N1) through influenza testing and reported to CDPH through influenza surveillance, with initial subtyping conducted by the Stanford Medicine Clinical Virology Laboratory and presumptive positive test results reported by CDPH on November 19, 2024.
Based on real-time RT-PCR cycle threshold (Ct) values determined during diagnostic testing, the nasopharyngeal specimen from the patient was found to have very low levels of influenza viral RNA. Initial attempts to sequence the viral RNA by both Stanford Medicine and CDC using standard Next Generation Sequencing methodologies produced weak amplicons resulting from the PCR process that were challenging to sequence using both Nanopore and Illumina sequencing methodologies. Additionally, efforts to isolate virus from the specimen were not successful. By employing nucleic acid enrichment techniques, CDC and Stanford Medicine were able to generate the following viral RNA sequence data: full-length neuraminidase (NA) and nucleoprotein (NP) genes and partial hemagglutinin (HA), polymerase basic 2 (PB2), and polymerase basic 1 (PB1) genes. CDC and Stanford Medicine have submitted these data for A/California/192/2024 to both the GISAID and GenBank databases with accession numbers EPI_ISL_19597300 and PQ724471-PQ724473, respectively.
The initial sequence analysis, which was based on short fragments of the HA and NA genes, indicated that the virus was a clade 2.3.4.4b A(H5N1) virus similar to viruses causing outbreaks in dairy cattle and poultry in the United States. Upon obtaining full-length NA and NP genes, CDC was able to perform a comprehensive phylogenetic analysis, which showed that the virus was very similar to viruses detected in both dairy cattle and poultry as well as to A(H5N1) viruses from previous human infections in dairy workers in California. Although the genetic data generated were insufficient to classify the virus as a specific genotype, the NA and NP sequences shared close nucleotide identity and phylogenetic clustering with NA and NP genes from recent B3.13 viruses detected in California in humans, dairy cattle and poultry. Epidemiologic and environmental investigations did not clearly identify a possible source of exposure. Given that additional sequence data from the case could not be generated, it is unlikely that the source of the child's exposure to A(H5N1) virus will be identified, thus completing the investigation into genotype and exposure.
In addition to the phylogenetic analysis of the NA and NP genes, CDC conducted an assessment of the sequences of the virus specimen for molecular changes that might impact infectivity or transmissibility in humans or reduce susceptibility to antivirals, such as oseltamivir. The partial HA sequence, despite lacking portions of the 5' end of the gene, did not have additional changes in predicted antigenic sites compared to available clade 2.3.4.4b candidate vaccine viruses (CVVs). Nor were changes identified in the receptor binding domain of the virus, indicating that the virus retained avian receptor binding properties with no mutations that would impact changes in infectivity or transmissibility in humans. The PB2 and PB1 genes did not have genetic changes associated with mammalian adaptation, nor were there any genetic changes identified in NA sequence data that have been associated with reduced susceptibility to neuraminidase inhibitors, such as oseltamivir. Lastly, the sequence data confirmed that the virus from this case is not closely related to the virus that caused severe illness in a human in British Columbia, Canada. Collectively, these data indicate that the virus detected in this pediatric case is very similar to the majority of other influenza A(H5N1) viruses detected in the United States and bears no signs of concerning mutations.
While the sequence data obtained do not allow for definitive determination of the viral genotype, and no specific animal exposure source has been identified, these findings provide important contextual information and help to inform CDC's overall risk assessment. They also highlight the value of a collaborative approach to this response, including virologic risk assessments based on genetic data.
Follow-up Actions
Sporadic human infections with a novel influenza virus where animal exposure is not identified are not uncommon and have occurred during the current H5N1 bird flu outbreak in U.S. dairy cattle and poultry and in past outbreaks around the world. This case does not change CDC’s assessment of the immediate risk to the general public, which remains low at this time.
There is no evidence of human-to-human transmission of H5N1 virus in California or elsewhere in the United States. However, persons with occupational exposure to infected animals, such as poultry cullers, poultry workers, and dairy farm workers, are at higher risk of influenza A(H5N1) virus infection. Public health surveillance and investigations of all identified cases will continue at the local, state, and federal levels to monitor for concerning changes in the epidemiology of human cases or changes to influenza A(H5N1) viruses that could signal an increased public health threat – potentially including more severe outcomes in those currently at risk of exposure and infection, or increased risk to the general public.
https://www.cdc.gov/bird-flu/spotlig...-12092024.html
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