A (H1N1) pdm09 HA D222 variants associated with severity and mortality in patients during a second wave in Mexico
- Joel A Vazquez-Perez1,
- Pavel Isa2,
- Darwyn Kobasa4, 5,
- Christopher E Ormsby1,
- Jose E Ramírez-Gonzalez3,
- Damaris P Romero-Rodríguez1,
- Charlene Ranadheera4, 5,
- Yan Li4, 5,
- Nathalie Bastien4,
- Carissa Embury-Hyatt6,
- Elizabeth González-Duran3,
- Gisela Barrera-Badillo3,
- Yuria Ablanedo-Terrazas1,
- Edgar E Sevilla-Reyes1,
- Marina Escalera-Zamudio2,
- Ana G Cobián-Güemes2,
- Irma Lopez3,
- Joanna Ortiz-Alcántara3,
- Celia Alpuche-Aranda3,
- Jose R Perez-Padilla1 and
- Gustavo Reyes-Terán1, 7Email author
© Vazquez-Perez et al.; licensee BioMed Central Ltd. 2013
Received: 12 September 2012
Accepted: 28 January 2013
Published: 31 January 2013
Pandemic type A (H1N1) influenza arose in early 2009, probably in Mexico and the United States, and reappeared in North America in September for seven more months. An amino acid substitution in the hemagglutinin (HA), D222G, has been reported in a significant proportion of patients with a severe and fatal outcome. We studied the prevalence of HA222 substitutions in patients in Mexico during the second wave and its association with clinical outcome and pathogenicity in a mouse model.
The nucleotide sequences of hemagglutinin (HA) from viruses collected from 77 patients were determined including 50 severe and fatal cases and 27 ambulatory cases. Deep sequencing was done on 5 samples from severe or fatal cases in order to determine the quasispecies proportion. Weight loss and mortality due to infection with cultured influenza viruses were analyzed in a mouse model.
Viruses from 14 out of 50 hospitalized patients (28%) had a non aspartic acid residue at the HA 222 position (nD222), while all 27 ambulatory patients had D222 (p = 0.0014). G222 was detected as sole species or in coexistence with N222 and D222 in 12 patients with severe disease including 8 who died. N222 in coexistence with D222 was detected in 1 patient who died and co-occurrence of A222 and V222, together with D222, was detected in another patient who died. The patients with a nD222 residue had higher mortality (71.4%), compared to the group with only D222 (22.2%, p = 0.0008). Four of the 14 viruses from hospitalized patients were cultured and intranasally infected into mice. Two viruses with G222 were lethal while a third virus, with G222, caused only mild illness in mice similar to the fourth virus that contained D222.
We confirm the elevated incidence of HA222 (H1N1)pdm09 variants in severe disease and mortality. Both clinical and mouse infection data support the idea that nD222 mutations contribute to increased severity of disease but additional determinants in disease outcome may be present.
The first pandemic of this century originated as a novel influenza A/H1N1 virus (pdm09) in 2009. This virus was first detected in March and April in California and several cities of Mexico[1, 2]. A second wave included those cases occurring from late August 2009 and March 2010. As of August 2010, more than 214 countries had reported laboratory confirmed cases of pdm09, including over 18,449 deaths. Although most confirmed cases resulted in uncomplicated influenza illness, some patients required hospitalization due to severe pneumonia and respiratory failure, with a fatal outcome in some cases. The factors that control the generation of pathogenicity in this novel influenza virus remain unknown. However the ability of influenza viruses to activate innate immunity, induce apoptosis mediated by the PB1-F2 protein, and contributions of the viral RNA polymerase proteins, the NS1 and M2 proteins[9, 10], and viral receptor binding preference could be important. The tissue tropism and the binding of influenza viruses to their target cells is mediated by the viral HA protein which recognizes cell surface glycoconjugate receptors that terminate in sialic acid (SA) residues. It has been described that single amino acid changes can alter receptor specificities, and amino acid changes in HA D222G have been associated with acquisition of affinity for N-acetylneuraminic acid with an α-2,3 ketosidic linkage to galactose (SA α2,3Gal), increasing the infection of lower respiratory cells and likelihood of viral pathogenicity.
HA D222G substitution or different variants (D222N, D222S) has been observed in pdm09 viruses isolated from fatal and mild cases in several countries[13, 14]. The first report of substitutions for D222 showed considerable frequency of change at this position (18%) only in fatal and severe cases in Norway. In contrast, two later studies found D222G substitution in mild cases, with Hong Kong and Greece reporting 4% and 15%, respectively[16, 17]. The effect of these substitutions on viral pathogenicity in animal models is also unclear. In the most recent report a recombinant pdm09 with the D222G substitution showed increased virulence in mouse model but was not lethal in the mouse or ferret model.
In the present work we describe a high prevalence (28%) of the D222G substitution in coexistence with D222N and D222S in 50 pdm09 positive patients admitted through the emergency room at the National Institute of Respiratory Diseases in Mexico City during the second pandemic wave. Viruses containing mutations in HA position 222 were associated with higher mortality. In addition, two of three isolated viruses with mutations in this position were lethal in mice. Substitutions at D222 might be associated with increased pathogenicity in humans and also in mice, but the current results suggest that additional unknown determinants also contribute to pathogenicity.
Detection of variants in HA 222 position in severe and fatal cases
Pandemic influenza A (H1N1) viruses characterized by Sanger sequencing for amino acid position 222 of the HA
HA position 222 codon
Mild (n = 27)
Severe (n = 26)
Fatal (n = 24)
84. 6% (22)
58. 2% (14)
222D, 222E, 222G, 222N
222D, 222V, 222A
All 222 variants
Clinical characteristics of hospitalized patients
When considering respiratory illness during an outbreak as our study population, and separating hospitalized patients as cases of severe manifestations and ambulatory patients as mild cases, we found that the proportion of the D222G mutation was significantly higher in the former group (14 of 50, 28%) than in the ambulatory patients (0%, p = 0.001, Table 1). Within the hospitalized patients, the mortality of the patients, which were cases with the mutation, was significantly higher than the patients without (p = 0.0008).
Additionally there was a significantly higher use of mechanical ventilation in the patients with a non D222 residue (p < 0.0001) when comparing with hospitalized patients with D222 only (0.0197). Overall, 41.7% of patients that died and 37.5% of patients that required mechanical ventilation presented variants in residue 222, whereas only 7.5% of the survivors and 4.5% of the patients that did not require mechanical ventilation had these variants.
Clinical characteristics of hospitalized patients and co morbidities identified in hospitalized patients
39.5 (29.5 - 47.5)
30.57 (26.93 - 33.06)
35.77 (27.69 - 38.02)
Evolution time (days)
Heart rate (bpm)
110 (84.5 - 120)
108 (90.5 - 117.5)
O2 saturation (skin)
83 (64.5 - 87)
O2 saturation (blood)
84 (68.9 - 88.6)
73.35 (67.6 - 82.6)
192.14 (116.71 - 235.72)
170.95 (73.5 - 216.43)
8 (6.25 - 11)
4 (3.25 - 6)
105 (78.25 - 136.75)
94 (87.5 - 157.5)
2.9 (2.48 - 3.44)
15.25 (13.3 - 15.85)
12.65 (10.75 - 13.35)
39.5 (29.5 - 47.5)
Systemic arterial hypertension
Acinetobacter baumannii, Klepsiella pneumonie, HIV (2), COPD, pulmonary fibrosis, unspecified mycobacteria
Genetic variations at positions 715–716 of HA nucleotide sequences
The whole genome of four influenza viruses was also determined by Illumina Genome Analyzer IIx for viruses isolated from patients with a severe and fatal outcome, and whose variants at nucleotide position 715–716 had previously been determined by Sanger sequencing (INER047, INER264, INER306 and INER307, GeneBank number accession CY100461-CY10068, CY100519-CY100542). With this strategy, 3.8 ×106 to 8 ×106 total reads per sample were obtained, of which 1.7 ×106 to 4.6 ×106 reads corresponded to the influenza reference genome. The codon at position 222 of HA of INER047 had 5% GAT (D), 32.5% GGT (G) and 62.5% AAT (N). Sample INER306 had 93% GAT (D) and only a few reads of GGT (G) and AAT (N) in the codon for residue 222. These findings were in agreement with the Sanger sequencing in samples INER047 and INER405; however three samples (INER264, INER306 and INER307) were found to contain >93% of the triplet GAT (D) by metagenomic analysis.
Detection of other polymorphisms in influenza viruses of severe and fatal cases
Non-synonymous substitutions* detected in 5 samples with 222 variants (INER047, INER264, INER306, INER307 and INER405)
Pathogenesis of HA 222 variants in mice
All 14 clinical specimens from hospitalized patients were placed in MDCK cell culture in an attempt to derive a stock of virus from each. Four of the viruses (INER047, INER111, INER307 and INER405) were successfully cultured and a stock of virus was generated and titered on MDCK cells. Analysis of the viral variants in each stock from 20 different plaques of each showed that two of four isolates (INER111 and INER405) had only glycine at position 222, while INER047 showed nineteen viruses with glycine and one virus with asparagine. All viruses of sample INER307 had D222. The HA sequencing data suggests that culturing of the clinical isolates on MDCK cells tended to preferentially select one of the variants from each that had been identified in the analysis of HA quasispecies variability in the original clinical isolates. Complete sequencing of all other genes from the INER307, INER405 and INER047 MDCK-grown virus stock (GeneBank number accession KC261306-KC261337) indicated no changes associated with adaptation to cell culture compared to the sequences obtained from the clinical isolates (data not shown). The complete sequence of the MDCK-grown virus INER111 was also determined but the sequence of the clinical isolate was not available for comparison.
D222G is the main substitution found in reports associated with severe or fatal cases of pdm09[15, 19]. Here we found this substitution only in viruses isolated from severe cases; we also found a correlation between the risk of death and HA 222 variants. Low white blood cell (WBC) levels and low hemoglobin levels correlated with the presence of HA 222 variants, and suggested that the viruses harboring variants in HA 222 could be associated with a more severe respiratory disease. Not all severe or fatal cases had this mutation but its emergence could intensify the severity of the disease.
A recent study found a delayed clearance of virus in patients with severe disease, which may represent an opportunity for the accumulation of different variants (including D222G) in patients. However in this study we found no correlation between duration of disease and emergence of D222 variants, supporting the argument that the substitutions appeared spontaneously and sporadically.
Respiratory tract cells expressing α2,3 receptors are more abundant deeper in the human airway, an observation that has led to the hypothesis that viruses with dual receptor specificity can replicate to higher titers in lungs, resulting in a more severe course of disease. Recent studies suggest an increased receptor affinity of the 222G variant for ciliated bronchial epithelial cells, which may have an impact on disease severity. Some studies indicate that such variants were also found more frequently in specimens obtained from the lower respiratory tract than from the nasopharynx. Our findings indicate that the 222 variants including G222, N222, V222 or A222 were present in nasopharynx, showing their presence in the upper respiratory tract. Consistent with the presence of these variants in the upper respiratory tract, transmission of influenza virus with D222G from a patient with severe disease to a family member has been reported. Other studies found that virus with D222G had acquired the ability to bind to SA α2,3Gal, retaining affinity for SA α2,6Gal, the preferential receptor of human viruses that is associated with attachment to cells of the upper respiratory tract. Viruses with G222 do have dual tropism, perhaps resulting in more efficient infection of the lower respiratory tract, causing more severe disease. D222G, D222N, and D222E changes have been found in viruses isolated in different countries[15, 19, 22, 24], but the D222V amino acid change has not been previously reported. A sequence of HA with A222 has been submitted to GenBank, but without any published clinical data. Changes in HA amino acid position 222 located in the receptor-binding cavity might potentially influence receptor binding of the influenza virus. Changing an acidic and polar amino acid (D) to neutral and non-polar (G, V and A) residue could affect the tropism of these new variants. Detection of HA 222 variants has been realized using both pyrosequencing and Sanger methods, resulting in different proportion of polymorphisms in that position, in our case we found discrepancies also between both methodologies, due perhaps an enrichment of minority population during PCR used to amplify metagenomic sequencing library, especially given low amount of RNA used.
We also found that HA substitution G172R, which co-segregated with HA amino acid 222 variants, was present in fatal cases only. This substitution is located in the HA antigenic site Sa that could be implicated in antigenic changes of HA. In fact, future amino acid substitutions in the antigenic sites of pdm09 HA (Gly172Glu) have been anticipated. Furthermore, a HA variant with G172E was found in one fatal case. The biological significance of the presence of both substitutions and their relationship with severity remains unknown.
The severity of the disease observed in human patients was generally consistent with the disease observed in mice. The virus INER047 isolated from a patient with a fatal outcome was lethal at 4 to 6 days PI in mice; and the virus INER111 that caused severe disease in a patient requiring mechanical ventilation was also lethal in mice at 4 and 5 days PI. However, the virus INER405 that had 222G in HA was of limited pathogenicity in mice. This virus was isolated from a patient who recovered after being hospitalized for one month showing an association between the virus and severe infection. However, the mouse study results suggest that additional determinants of pathogenicity in mammals likely exist, aside from 222G in HA, that might be responsible for severe disease in humans but are not determinants of disease in mice. This data suggests that there might be pathogenic factors affecting the clinical course of the disease in humans that have not been described. A recent report in an animal model showed that a pdm09 D222G virus caused more severe disease with fatal outcome in mice, compared with the wild type influenza virus[23, 28], although experiments with ferrets did not support a causal link of D222G substitution with virulence.
Here we report a high prevalence of pdm09 HA codon 222 variants in severe and fatal cases of pneumonia in Mexico City during the second wave of the 2009 influenza pandemic. Recent data confirmed an increase in the overall mortality in Mexico during the pandemic and also mortality due to respiratory and cardiovascular causes, especially in young and middle age individuals. Our results support the suggestion that substitution at HA position 222 is associated with pdm09 pathogenicity, with variants appearing spontaneously during the two pandemic waves in Mexico. Some reports and sequence data have demonstrated that 222 variants appeared in the early phases of the pandemic, increased during 2009–2010 influenza season and have reduced to their present levels during 2010–2011 and 2011–2012 influenza season[30, 31]. Bacterial infection or coexisting conditions do not appear to be major contributing factors to the severity (Table 2). We have identified additional viruses with 222 variants (D222V and D222A) in the same individual, but the biological importance of these substitutions in tropism and pathogenicity remains to be elucidated. The disease observed in animal models was generally concordant with the clinical outcome of patients, but additional determinants of virulence may contribute to the increased severity of disease observed in mammals and is a significant point for further investigation of viral determinants of severe disease in humans caused by pdm09 viruses.
Material and methods
Respiratory samples were obtained from all patients who were hospitalized at the National Institute of Respiratory Diseases in Mexico City, during September 2009 to April 2010. Twenty-seven patients that sought medical care at our institution during the same period of time, but that did not require hospitalization were also included. Nasopharyngeal swabs were collected and infection by pdm09 was assessed by a real-timereverse-transcriptase–polymerase-chain-reaction (RT-PCR). This study was approved by the Bioethics and Research Committee of the National Institute of Respiratory Diseases in Mexico (B-0411). Written informed consent was provided by study participants and/or their legal guardians.
Sanger sequencing of HA
Viral RNA was extracted from 200 μL of respiratory samples using a high throughput system (MagNA Pure®, Roche, Indianapolis, IN, USA). RT-PCR was performed with the one-step RT-PCR kit (QIAGEN, Valencia, CA, USA). The HA gene was partially sequenced; briefly, the initial amplifications were performed using specific primers for pdm09: HA 58F 5′ TTATGTATAGGTTATCATGCGAA 3′ and HA 1676R 5′ ACCCATTAGAGCACATCCAGAAAC 3′, a second round PCR reaction were performed with HA 149F 5′ TAGAAGACAAGCATAACGGGAAA 3′ and HA 865R 5′ CTGGTGTATCTGAAATGATAATA 3′ (608 bp). Nucleotide sequences of PCR products were determined using BigDye® Terminator cycle sequencing kit (Applied Biosystems, Foster City, CA, USA) and were analyzed with the ABI Prism 3100 analyzer sequencer (Applied Biosystems). Nucleotide sequences of PCR products were aligned and analyzed using Clustal X and MEGA 4.0 respectively.
Illumina next generation sequencing and sequence analysis
Whole genome of influenza A isolates was amplified in an one tube multisegment RT-PCR reaction as previously reported. Products obtained were purified and concentrated and used as input material in constructing multiplex libraries using Illuminas Genomic DNA sample Prep Kit with multiplexing primers. Three hundred base-pair sized libraries were loaded in a flow cell (four libraries per lane) from a Genome Analyzer IIx (Illumina, San Diego, CA). Sequencing was performed through 46 cycles of single base pair extensions, followed by acquisition of multiplex code. Image analysis was done using goat.py, and the base calling was done using Bustard.pl, both programs included in Off-Line Basecaller Software v1.6 (Illumina, Hayward, CA). Processing of sequence data was carried out using Maq version 0.7.1 and R/Bioconductor programs. All reads were quality filtered using the Off-Line basecaller Software v1.6 (Illumina, San Diego, CA). Reads were aligned to reference influenza A genome A/Netherlands/602/2009, with maximum of 5 mismatches allowed.
GS Sequencer FLX Titanium platform
For sample INER405, the HA gene was amplified using a pair of specific primers: MBTuni12, HAREV1166 (5′ GGCATTCTGTGTGCTCTTCA 3′) and MBTuni13, HAFW756 (5’ AGCCGGGAGACAAAATAACA 3’). A single stranded DNA library was prepared with the GS Titanium General Library Preparation kit (Roche) as specified by the manufacturer. The DNA library was clonally amplified by emulsion PCR (emPCR) with the GS Titanium emPCR kit (Roche). The amplified beads were recovered and enriched and approximately 340,000 beads were loaded on one line and sequenced in the PicoTiterPlate using a GS Titanium Sequencing reagents kit XLR70. All sequencing reads, were assembled separately in GS De novo Assembler Version 2.0.00. The resulting contigs were analyzed using NCBI megablast program, mapping against an influenza reference sequence (A/Mexico/InDRE4487/2009(H1N1)).
Influenza viruses were isolated from respiratory samples in MDCK cells (ATCC # CCL-34). Titers of each stock virus were determined as the 50% tissue culture infectious dose (TCID50) and reported as the log10 of the TCID50 value. Each of the viruses was plaqued on MDCK cells and 20 plaques of each were picked and stocks were produced in MDCK cells. Viral RNA was isolated from each plaque virus stock and the HA sequenced in the region of amino acid 222. To determine the 50% mouse lethal dose (MLD50), serial 10-fold dilutions of each virus, starting at 6.5 TCID50, were intranasally (i.n.) inoculated in 3 anesthetized (isoflurane) mice/dilution. The MLD50 was expressed as the log10 of the TCID50. Calculations for TCID50 and MLD50 were done according to the method of Reed and Muench.
Groups of twelve 5-6-week-old female BALB/c mice (Charles River) were infected i.n. with 5.5 TCID50 of each virus. Animals were weighed daily for 14 days and monitored for clinical signs. Three mice per group were sacrificed on days 3 and 6 post-infection and lungs were removed aseptically. For determination of viral titers, lung tissues were harvested, weighed, homogenized and supernatants were titrated in 10-fold serial dilutions on MDCK cells. Titers were expressed as log10(TCID50) per gram of tissue.
Pathology and immunohistochemistry
Lung samples were fixed in 10% neutral buffered formalin, embedded in paraffin, sectioned at 5 μm and stained with haematoxylin and eosin for examination by light microscopy. For immunohistochemistry, paraffin tissue sections were quenched for 10 minutes in aqueous 3% H2O2 then pretreated with proteinase K for 15 minutes. Slides were blocked for 30 minutes with Rodent Block M from MM horse radish peroxidase (HRP)-polymer kit (Biocare Medical, USA) then rinsed with TBST. The primary antibody was a mouse monoclonal antibody specific for influenza A nucleoprotein (NP) (F26NP9, produced in-house) and was used at a 1:10,000 dilution for one hour. They were then incubated for 15 minutes with MM polymer-HRP (Biocare Medical, USA) and reacted with the chromogen diaminobenzidine (DAB). The sections were then counter stained with Gill’s hematoxylin.
All animal experiments were performed with strict adherence to the recommendations of the Canadian Council on Animal Care (CCAC). The animal use document was approved by the Animal Care Committee (AAC) of the National Microbiology Laboratory, Canada.
Effects were evaluated by Wilcoxon’s Rank Sum test, odds ratio (ORs) estimated by normal approximation for small samples, and significance assessed by Fisher´s exact method. Correlations were calculated with Spearman’s Rho. Data analysis was conducted using R statistical software, version 2.10.1. All tests were two sided and not controlled for multiple comparisons.
We thank Dr. Ricardo Grande and MS Veronica Jimenez, of the next generation sequencing core facility of the National University of Mexico for their technical support in Illumina sequencing. This work was supported by grant PICDSI09-209 and PICDSI09-208 from the Instituto de Ciencia y Tecnologia del Distrito Federal, grant 141849 from CONACYT and funding provided by the Public Health Agency of Canada. Marina Escalera-Zamudio and Georgina Cobian-Güemes were supported by a scholarship from CONACYT-Mexico. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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