Genetic sequences of highly pathogenic avian influenza A(H5N1) viruses identified in a person in Louisiana | Bird flu

Summary of amino acid mixtures identified in hemagglutinin (HA) in patient clinical samples.

Overall, the hemagglutinin (HA) sequences from the two clinical samples were closely related to HA sequences detected in other D1.1 genotype viruses, including viruses sequenced from samples collected in November and December 2024 in wild birds and poultry in Louisiana. The HA genes of these viruses were also closely related to A/Ezo red fox/Hokkaido/1/2022 candidate vaccinia virus (CVV) with 2 or 3 amino acid changes detected. These viruses have an average of 3 or 4 amino acid changes in HA when compared directly to the A/Astrakhan/3212/2020 CVV sequence. These data indicate that the viruses detected in respiratory samples from this patient are closely related to existing HPAI A(H5N1) CVVs that are already available to manufacturers and could be used to make vaccines if is necessary.

Some differences were detected between the NP/OP and NP samples. Despite the very close similarity between the D1.1 sequences from the Louisiana human case and the avian virus, deep sequence analysis of the HA gene segment from the combined NP/OP sample revealed low-frequency mixed nucleotides corresponding to notable amino acid residues (using mature HA ) sequence numbering):

• A134A/V (Alanine 88%, Valine 12%);
• N182N/K (asparagine 65%, lysine 35%); and
• E186E/D (glutamic acid 92%, aspartic acid 8%).

Notably, the NP sample did not have these low-frequency changes, indicating that they may have been detected from inoculation of the patient’s oropharyngeal cavity. Although these low-frequency changes are rare in humans, they have been reported in previous cases of A(H5N1) in other countries and most often during severe illness2345. For example, the E186E/D mixture was also identified in a sample collected from the severe human case discovered in British Columbia, Canada67.

This summary analysis focuses on mixed nucleotide detections at residues A134V, N182K, E186D, as these changes may result in increased virus binding to α2-6 cell receptors found in the human upper respiratory tract. It is important to note that these changes represent a small fraction of the total virus population identified in the sample analyzed (ie the virus still retains the majority of ‘bird’ amino acids at the residues associated with receptor binding). The observed changes were likely generated by replication of this virus in the patient with advanced disease rather than primarily transmitted at the time of infection. Comparison of influenza A(H5) sequence data from viruses identified in wild birds and poultry in Louisiana, including poultry identified on the patient’s property and other regions of the United States did not identify these changes. Of note, viral sequences from poultry sampled on the patient’s property were nearly identical to the viral sequences from the patient, but did not have the mixed nucleotides identified in the patient’s clinical sample, strongly suggesting that the changes occurred during infection as the virus replicated in the patient. Although of concern and a reminder that A(H5N1) viruses can develop changes during the clinical course of a human infection, these changes would be more concerning if found in animal hosts or in early stages of infection (e.g. .within a few days of symptom onset) when these changes may be more likely to facilitate spread to close contacts. Notably, in this case, no transmission from the patient in Louisiana to other individuals has been identified. The Louisiana Department of Public Health and CDC are collaborating to generate additional sequence data from sequential patient samples to facilitate further genetic and virologic analysis.

Further genomic analysis

The genetic sequences of A(H5N1) viruses from the Louisiana patient did not have the PB2 E627K change or other changes in polymerase genes associated with adaptation to mammals and no evidence of low-frequency changes at critical positions. And like other D1.1 genotype viruses found in birds, the sequences lack PB2 M631L, which is associated with viral adaptation to mammalian hosts and has been detected in >99% of dairy cow sequences, but is only sporadically found in birds. Analysis of N1 neuraminidase (NA), matrix (M) and polymerase acid (PA) genes from the samples showed no changes associated with known or suspected markers of reduced susceptibility to antiviral drugs. The rest of the genetic sequences of A/Louisiana/12/2024 were closely related to sequences detected in wild birds and poultry D1.1 genotype viruses, including poultry identified on the patient’s property, providing further evidence that the human case was most probably infected after exposure to birds infected with D1.1 genotype virus.

Follow-up actions

Overall, CDC assesses that the risk to the general public associated with the ongoing US HPAI A(H5N1) outbreak has not changed and remains low. The detection of a severe human case with genetic alterations in a clinical sample underscores the importance of ongoing genomic surveillance in humans and animals, containment of avian influenza A(H5) outbreaks in dairy cattle and poultry, and prevention measures among humans exposed to infected animals or environments.