Mexico Evaluates Upper Respiratory Swabs from Fatal and Severe Cases with 225A, 225G, 225N & 225V

Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked spreadsheet for completeness in citation.

Last Update
2011-11-03

On 2011-10-27, the Instituto Nacional de Enfermedades Respiratorias from the Centro de Investigacion en Enfermedades Infecciosas of Mexico deposited a group of human pH1N1 sequences at GenBank and GISAID.  The deposit is composed of HA segments, 14 sequence fragments of 232 amino acids (aa38 to aa269), each documenting roughly 41% of a full pH1N1 Hemagglutinin segment.  Various homology to Clade1.Upsilon exists on 5 of the sequences.

This Mexican genetic data supports an investigation entitled, H1N1pdm HA D222 variants associated with severity and mortality in patients during a second wave in Mexico and their pathogenicity in mouse model.  Mexico City, Mexico is the geography indicated on the sequence names.  Each sequence is annotated with gender and isolation source (nasopharyngeal swab), while 12 of the 14 also indicate the subject age.  Subject ages range from 23 to 54 years old, all outside the general severity range for seasonal influenza (under 2 years old or over 60 years old).  The sample dates span 2009-10-01 to 2010-04-05 with no case-level specification of treatment protocol, clinical progression or clinical outcome.

The severity and fatality correlation in cases with polymorphisms at amino acid position 222 (aa225 in H3 numbering) was established very early in the pandemic.  The issue of sample location has been repeatedly posed, with ongoing discussion that samples taken from the lower respiratory tract are more probable to produce valid evidence of aa225 revisions.  This INER deposit, relying entirely on upper respiratory swabs, documents cases where aa225 revisions are found in the upper airway.  The individual details of clinical progression and outcome (severe v. fatal) will establish measurable correlation to the upper respiratory sample location.

Four of the samples show multi-nucleotide ambiguity at amino acid position 225 (contiguous mixed traces, residues 715 and 716) producing a codon of rrT.  That sequencing outcome of rrT demonstrates the presence of wild type D225 with both 225G and 225N, hypermorphism at a single amino acid position.  Overall, ten of the fourteen sequences demonstrate a mixed peak (ambiguity) at one or more nucleotides that build aa225.  MexicoCityINER3_NP_47M_2009_10_15 [EPI341034] illustrates the highly variant nature of the pH1N1 reservoir Receptor Binding Site aa225 with two rare values, 225A and 225V, in a mixture without wild type (D225) and with no additional polymorphisms.

Sequences

. . . . MexicoCityINER14_NP_xF_2010_04_05 (
. . . . . . . . Clade1.Upsilon Potential Precursor
. . . . . . . . GISAID HA EPI341023
. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . syn71E (GAg) mix wt [H6N1],
. . . . . . . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . syn100D (GAc) [H1N1 Avian Farm],
. . . . . . . . 165N,
. . . . . . . . 181S,
. . . . . . . . 189T,
. . . . . . . . syn198A (GCg) mix wt,
. . . . . . . . syn213F (TTt),
. . . . . . . . 225G mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER13_NP_48F_2010_03_25 (
. . . . . . . . Clade1.Upsilon Potential Precursor
. . . . . . . . GISAID HA EPI341024
. . . . . . . . 6 Polymorphisms (5 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 225G mix wt,
. . . . . . . . 225N mix wt,
. . . . . . . . 225S mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER12_NP_37M_2010_03_23 (
. . . . . . . . GISAID HA EPI341025
. . . . . . . . 2 Polymorphisms (2 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 122R,
. . . . . . . . 225N,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER11_NP_34F_2010_02_09 (
. . . . . . . . GISAID HA EPI341026
. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . syn214K (AAa) [H9N2],
. . . . . . . . . . . . . . . . . . [H13N2 Avian],
. . . . . . . . 225G mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER10_NP_39M_2010_02_09 (
. . . . . . . . Clade1.Upsilon Potential Precursor
. . . . . . . . GISAID HA EPI341027
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . syn58C (TGc) [H2N3, H3N8, H4, H6],
. . . . . . . . . . . . . . . . . [H7N3, H7N7],
. . . . . . . . . . . . . . . . . [H9N2, H11],
. . . . . . . . . . . . . . . . . [H13N2, H13N3, H13N6, H13N8, H13N9 Avian],
. . . . . . . . . . . . . . . . . [H1N1 Avian],
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 225G,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER8_NP_23F_2009_11_23 (
. . . . . . . . GISAID HA EPI341029
. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . syn106E (GAa) [H1N1 Avian],
. . . . . . . . syn189A (GCc),
. . . . . . . . 225G,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER9_NP_49M_2010_01_18 (
. . . . . . . . GISAID HA EPI341028
. . . . . . . . 1 Polymorphisms (1 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 225G mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER7_NP_54F_2009_11_09 (
. . . . . . . . Clade1.Upsilon Potential Precursor
. . . . . . . . GISAID HA EPI341030
. . . . . . . . 3 Polymorphisms (3 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 157T,
. . . . . . . . 165N,
. . . . . . . . 225G,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER6_NP_22F_2009_11_06 (
. . . . . . . . GISAID HA EPI341031
. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . syn106E (GAa) [H1N1 Avian],
. . . . . . . . syn189A (GCc),
. . . . . . . . 225G mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER5_NP_52F_2009_10_27 (
. . . . . . . . GISAID HA EPI341032
. . . . . . . . 1 Polymorphisms (1 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 225G mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER4_NP_xM_2009_10_16 (
. . . . . . . . GISAID HA EPI341033
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . syn145K (AAg),
. . . . . . . . 225G mix wt,
. . . . . . . . 225N mix wt,
. . . . . . . . 225S mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER3_NP_47M_2009_10_15 (
. . . . . . . . GISAID HA EPI341034
. . . . . . . . 2 Polymorphisms (2 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 225A mix,
. . . . . . . . 225V mix,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER2_NP_44F_2009_10_12 (
. . . . . . . . GISAID HA EPI341035
. . . . . . . . 3 Polymorphisms (3 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 225G mix wt,
. . . . . . . . 225N mix wt,
. . . . . . . . 225S mix wt,
. . . . . . . . HA Truncated after aa269)

. . . . MexicoCityINER1_NP_40M_2009_10_01 (
. . . . . . . . Clade1.Upsilon Potential Precursor
. . . . . . . . GISAID HA EPI341036
. . . . . . . . 4 Polymorphisms (4 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa38,
. . . . . . . . 165N,
. . . . . . . . 225G mix wt,
. . . . . . . . 225N mix wt,
. . . . . . . . 225S mix wt,
. . . . . . . . HA Truncated after aa269)

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