The above comments describe a cluster of severe/fatal cases in a family in Bhatkal as well as a “point genetic mutation” in three fatal cases in Pune and Nashik. The “mutation” is almost certainly D225G, which has been reported in prior fatal cases in India in the Pune area. This polymorphism is most easily detected in lung samples because it is frequently transmitted as a mixture and is a minor component in throat swabs, but becomes the major component in lung samples because of the affinity for the 2.3 receptors found on the surface of human lung cells. Thus, the levels of D225G in the tested patients are likely to be markedly higher than the frequency detected in throat or nasopharyngeal samples.

via Fatal / Severe H1N1 Cluster In India.

The isolate was collected a month ago and the genetic background is similar to humans infected by swine H1N1 in 2007 in Ohio. However, the sequence has also acquired pH1N1 sequences that are found in almost all pH1N1 isolates. Moreover, most of these polymorphisms are non-synonymous and at least one polymorphism traces back to 1918. These acquisitions raise concerns that this virus could quickly gain efficient and sustained transmission in humans, leading to a co-circulating H1N1 pandemic.

via Recombination and G158E Duplication In H1N1 Iowa Swine.

There is too little genetic surveillance of last year’s human pandemic flu, which has gone on to infect pigs in China and is readily mixing with other flus there, according to a study released Thursday by researchers in Hong Kong.

No dangerous new strain has emerged, said several experts who saw the study. But in January the researchers found a new strain with one of the pandemic flu’s surface proteins — the outer spikes and knobs it uses to attach to cells. That was a reminder of how easily another swine strain capable of spreading among people could emerge.

“Just because we’ve just had a pandemic does not mean we’ve decreased our chances of having another,” said Dr. Carolyn B. Bridges, an epidemiologist in the flu division of the Centers for Disease Control and Prevention. “We have to stay vigilant.”

via Study Criticizes Swine-Flu Follow-Up – NYTimes.com.

The National Institute of Virology (NIV) here has detected three new variants of the H1N1 virus. Fortunately, all three variants have shown susceptibility to Tamiflu , the drug used in the treatment of swine flu. However, with the virus actively acquiring new properties, NIV scientists are apprehensive that it might develop resistance to the medicines used in treating swine flu. “For now, there is no need to worry. But we are closely monitoring the virus for any change in its virulence ,” NIV assistant director Sarah Cherian told TOI recently.

More via NIV detects three new variants of H1N1 virus – Pune – City – The Times of India.

In 2009 a new swine-origin influenza virus A/H1N1 (A/H1N1 09) emerged, causing the century's first pandemic. Most isolates of the new A/H1N1 09 virus are susceptible to neuraminidase inhibitors, but the H275Y mutation in the neuraminidase gene region associated with high-level oseltamivir resistance has been detected. Using Rolling Circle Amplification (RCA) technology, 96 A/H1N1 09-specific RT-PCR positive clinical samples collected from 80 oseltamivir-treated and untreated patients were screened for the presence of the H275Y mutation. Samples positive for 275Y mutation by RCA were cloned and sequenced for confirmation. From 25 patients who had been treated with oseltamivir and remained A/H1N1 09 RT-PCR positive, we identified three (12%) individuals with the H275Y mutation: one immuno-suppressed adult, one immuno-competent adult and one child. Samples collected at multiple time-points from the two adults showed a switch from wild-type oseltamivir-sensitive 275H to oseltamivir-resistant 275Y population after 9 days of treatment. The child had the 275Y mutation detected after being persistently A/H1N1 09 RT-PCR positive whilst receiving oseltamivir treatment. Resistance was not detected in 17 pre-treatment samples and 54 A/H1N1 09 RT-PCR positive outpatients. RCA demonstrates the rapid emergence of the H275Y resistance mutation in individuals with severe A/H1N1 09 infection receiving neuraminidase inhibitors. Rapid detection of oseltamivir resistance in severe infection is essential for patients to receive maximum therapeutic benefit. In the light of emerging resistance, close monitoring and understanding of the nature and dynamics of resistance mutations in newly emerging strains should be a priority.

via Detection of the rapid emergence of the H275Y muta… [Antiviral Res. 2010] – PubMed result.

In contrast, in lower respiratory tract samples from directly inoculated pigs, with clearly demonstrable pulmonary pathology, there was apparent selection of a virus variant with glycine (225G).

The above comments are from the PLOS paper, “Replication, Pathogenesis and Transmission of Pandemic (H1N1) 2009 Virus in Non-Immune Pigs”, which describes the selection of D225G in swine lung. The swine were initially infected with a pH1N1 mixture at positions 225 and 226. The 226 change, Q226R, was strongly selected against and not found in any of the swine isolates. However the mixture at position 225 was maintained in the upper respiratory tract of the infected swine. Contact swine isolates selected for D225, while the lungs of inoculated swine initially had a mixture, while selection produced D225G at later dates, post infection.

These results match sequence analysis from patients. In the Duke death cluster, isolates from the initial collection had a mixture of D225 and D225G, while a subsequent collection yielded D225G alone.

Much more via Selection of pH1N1 D225G In Swine Lung.

In our study population, we found no evidence for the spontaneous emergence of resistance in untreated patients. This contrasts with very recent findings of resistance in a small number of Chinese and Vietnamese subjects who had not received oseltamivir prophylaxis or treatment [8,10]. These results have been interpreted as showing that spontaneous mutation can occur either before or during infection, or that there is transmission of oseltamivir-resistant virus in some geographical regions.

via Eurosurveillance – View Article.

In our original study, we observed a significantly higher frequency of D222G in patients with severe outcomes (including fatal) compared to patients with mild disease. In fact, in both our data set and the Hong Kong data, mutant viruses were not found among several hundred mild cases. Furthermore, as can be seen from our published data, the frequency may be higher also in fatal outcomes (eight of 27 cases) versus severe non-fatal outcomes (three of 34 cases). Comparing these frequencies results in p=0.078 with Fisher’s exact test (two-sided) and p=0.046 with the Mid-P Exact test (two-sided). It would be interesting to know if the new data from Hong Kong SAR can corroborate this observation. Mak et al. report four fatal D222G cases and five non-fatal severe D222G cases, but one would also need to know the total number of fatal cases versus non-fatal severe cases analysed to make the comparison. Hopefully, this information can be obtained.

via Eurosurveillance – View Article.

In an attempt to understand the relevance of HA D222G substitution among pandemic influenza A (H1N1) causing infections in Hong Kong, HA gene sequences from respiratory specimens and virus isolates of severe and non-severe cases were examined. Cases were individuals who had laboratory confirmed pandemic H1N1 influenza virus by either viral culture or reverse transcription PCR (RT-PCR) of respiratory specimens [5]. The severe cases were individuals classified by the attending physician as being in a serious or critical condition.

From 1 May 2009 to 31 January 2010, 458 respiratory samples were examined. Of 219 severe cases, nine (4.1%) showed D222G substitution while none of the 239 non-severe cases showed D222G substitution. Four of the nine cases died. The association of D222G with severe disease was statistically significant (p=0.002, Fisher’s exact test, doubled one-sided). Other substitutions, of D222N (severe cases, n=3; non-severe cases, n=1) and D222E (only in non-severe cases, n=4) were also found. The first severe case appeared on 6 July 2009 and D222G substitution was detected in July, September, November and December of the same year (Table).

via Eurosurveillance – View Article.

Although the ministry of health initially tried to claim that neither died from the confirmed H1N1 infections, it is widely known and described in the literature that H1N1 infections can lead to kidney failure (as seen in the mother) or Acute Respiratory Distress Syndrome (ARDS), as seen in the daughter. Although diabetes and pregnancies create increased risk, the vast majority of H1N1infections in these risk groups do not lead to hospitalization or death. The rapid death of two members of the same household raises concerns that the H1N1 virus has become more virulent, leading to more severe cases and deaths, as seen in H1N1 that has acquired D225G/N.

via Rapid Death in Malaysia H1N1 Cluster Linked To D225G/N?.