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Withheld Novel Human H5N1 Sequences in Indonesia

Recombinomics Commentary

May 17, 2006

The latest cluster in Indonesia again raises the question of human-to-human (H2H) transmission. As in most familial clusters, there is a 5–10 day gap between the disease onset date (April 27) of the index case, and other family members (May 3–4). In addition, the family members were at an April 29 BBQ, suggesting they were infected there by the index case.  The number of clusters in Indonesia remains high.  In addition to the familial clusters, there is a geographical cluster in Bekasi. 

These clusters are cause for concern, as is Indonesia’s testing procedures.  Samples for testing are collected at infectious disease hospitals.  Thus, milder cases that recover are not tested for H5N1.  Moreover, most tested are first asked about contact with poultry, thereby limiting testing of patients infected by mammals, including humans and cats.

Only one human H5N1 HA sequence has been made public and it has a novel cleavage sit, RESRRKKR. This sequence is not found in any of the many bird H5N1 sequences released from Indonesia and it is not in any H5N1 sequence at GenBank.

There are now over 30 confirmed human cases in Indonesia, and H5N1 has been isolated and sequenced from many. However, these sequences are being withheld and some comments have suggested that many of the human sequences have RESRRKKR, suggesting the source of infection is not avian.

The withholding of these mammalian H5N1 sequences from Indonesia should not be tolerated.  The evidence for H2H in Indonesia continues to increase, as do the number of human sequences that are being withheld.  Below are some of the recent avian HA sequences made public.  None have the RESRRKKR cleavge site found in the Indonesian cluster from July, 2005.

Recent avian H5N1 sequences from Indonesia:

DQ497642.1 A/chicken/Malang/BBVet-IV/2004(H5N1)
DQ497643.1 A/chicken/Magetan/BBVW/2005(H5N1)
DQ497644.1 A/chicken/Ngawi/BPPV4/2004(H5N1)
DQ497645.1 A/chicken/Pekalongan/BPPV4/2003(H5N1)
DQ497646.1 A/chicken/Sragen/BPPV4/2003(H5N1)
DQ497647.1 A/quail/Boyolali/BPPV4/2004(H5N1)
DQ497648.1 A/chicken/Purworejo/BBVW/2005(H5N1)
DQ497649.1 A/quail/Yogjakarta/BBVet-IX/2004(H5N1)
DQ497650.1 A/chicken/Kulon Progo/BBVet-XII-2/2004(H5N1)

DQ497651.1 A/chicken/Gunung Kidal/BBVW/2005(H5N1)
DQ497652.1 A/chicken/Kulon Progo/BBVW/2005(H5N1)
DQ497653.1 A/chicken/Purwakarta/BBVet-IV/2004(H5N1)

DQ497654.1 A/quail/Tasikmalaya/BPPV4/2004(H5N1)
DQ497655.1 A/chicken/Bangli Bali/BBPV6-1/2004(H5N1)

DQ497656.1 A/chicken/Bangli Bali/BPPV6-2/2004(H5N1)
DQ497657.1 A/chicken/Jembrana/BPPV6/2004(H5N1)
DQ497658.1 A/chicken/Mangarai-NTT/BPPV6/2004(H5N1)
DQ497659.1 A/duck/Parepare/BBVM/2005(H5N1)
DQ497660.1 A/chicken/Kupang-2-NTT/BPPV6/2004(H5N1)
DQ497661.1 A/chicken/Kupang-3-NTT/BPPV6/2004(H5N1)
DQ497662.1 A/chicken/Kupang-1-NTT/BPPV6/2004(H5N1)

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