Dr. Niman's Corner

Interview at 10 PM EDT tonight will include MERS camel sequences & update on South Korea THURSDAY Dr. Henry L. Niman, PhD Flu, Flu, Flu

I have recently begun to look at personal DNA testing. Initial observations are for two of the more popular home tests (23andme and ancestry.com). Both services include raw data on over 500,000 snps, which include many predictive markers for a variety of medical conditions, including cancer. Recently, 10 of the 23andme tests have received FDA approval.

NIH launches "All of Us" program to enroll one million diverse US citizens including under-represented populations to create personalized medical applications and interventions. https://www.nih.gov/news-events/news-releases/nih-announces-national-enrollment-date-all-us-research-program-advance-precision-medicine

Following the success of the identification of the Golden State Killer via matches with relatives in a genealogy database, GEDmatch, California law enforcement is targeting the 1960's Zodiac Killer using similar approaches.

Golden State Killer was identified after tracing DNA via personalized DNA kits and the database at GEDmatch.

23andme has received FDA approval on the three most well studied frame shifts in BRCA1 and BRCA2. These frame shifts are founder mutations in Ashkenazi Jews and are present in approximately 2% of the population.

NY Times has a report on 23andme FDA approved test for late onset Alzheimer's disease and impact on long term care heath insurance. However, the determination of APOE4 status can be determined through additional markers on Chromosome 19.

CDC has released 3 full D68 enterovirus sequences from US acute flaccid myelitis cases.

Inaugural 1 hour interview on Zika local transmission in Florida (Wynwood Cluster) with discussion of details in WSJ report (including detail on the index site and why it was an occupational hazard) https://soundcloud.com/thedrnimanshow/august102016

Michigan H3N2v sequence, A/Michigan/84/2016, has H3 that matches 2015 New Jersey case and N2 matching 2012 human cases. This constellation is distinct from recently released 2016 human sequences from Michigan and Ohio.

The CDC has reported H3N2v cases in Michigan and Ohio. In the week 31 Fluview 2 cases in each state were reported. followed by 7 more in week 32 (6 MI & 1 OH). Four sets of full or partial sequences were released at GISAID ( A/Ohio/27/2016, A/Ohio/28/2016, A/Michigan/82/2016, A/Michigan/83/2016 ). The sequences contain a novel constellation with an H3 most closely related to 2010 seasonal H3N2 and an MP related to H1N1pdm09. Other genes were most closely related to earlier human H3N2v sequences from 2012. However, only H3 and N2 were released from a fifth isolate, A/Michigan/84/2016, which matched recent human isolates.

Oswaldo Cruz Institute released a partial sequence from cerebral spinal fluid of Rio de Janeiro case, Zika1697_BR-RJ/2015, collected in mid-2015.http://www.ncbi.nlm.nih.gov/nuccore/KT381874

LOCUS KU921608 10823 bp RNA linear VRL 20-JUN-2016 DEFINITION Yellow fever virus isolate CNYF01/2016, complete genome. ACCESSION KU921608 VERSION KU921608.1 GI:1036436399 KEYWORDS . SOURCE Yellow fever virus (YFV) ORGANISM Yellow fever virus Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus; Yellow fever virus group. REFERENCE 1 (bases 1 to 10823) AUTHORS Liu,L. TITLE Complete Genome Sequence of Yellow Fever virus isolate CNYF01/2016 from First Imported Case in China mainland, March 2016 JOURNAL Unpublished REFERENC…

Beijing CDC has released four full 2016 Yellow Fever Virus (YFV) sequences from infected travelers returning from Angola.

USDA release January 2016 Iowa swine, A/swine/Iowa/A01729543/2016, which matches 2012 H3N2v cases. http://www.ncbi.nlm.nih.gov/nuccore/KU666891

Isolate name: A/Hong Kong/VB16021618/2016 Isolate ID: EPI_ISL_212471 Passage details/history: Original Type: A / H7N9 Lineage: Sample information Collection date: 2016-02-12 Host Human Additional host information: Zip code: Patient status: In-patient Last vaccinated: In-vivo pathogenicity test: Location: Hong Kong (SAR) Additional location information: Patient age: 60 Year(s) Gender: Male Outbreak: Treatment: Specimen source: Nasopharyngeal Institute information Originating lab: Public Health Laboratory Services Branch, Centre for Health Protection Sample ID given by the sample provider: Address: Public Health Laboratory Se…

LOCUS KU497555 10793 bp RNA linear VRL 18-FEB-2016 DEFINITION Zika virus isolate Brazil-ZKV2015, complete genome. ACCESSION KU497555 VERSION KU497555.1 GI:985578255 KEYWORDS . SOURCE Zika virus ORGANISM Zika virus Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus. REFERENCE 1 (bases 1 to 10793) AUTHORS Calvet,G., Aguiar,R.S., Melo,A.S.O., Sampaio,S.A., de Filippis,I., Fabri,A., Araujo,E.S.M., de Sequeira,P.C., de Mendonca,M.C.L., de Oliveira,L., Tschoeke,D.A., Schrago,C.G., Thompson,F.L., Brasil,P., dos…

LOCUS KU179098 1148 bp RNA linear VRL 19-FEB-2016 DEFINITION Zika virus isolate JMB-185 nonstructural protein 5 gene, partial cds. ACCESSION KU179098 VERSION KU179098.1 GI:998491569 KEYWORDS . SOURCE Zika virus ORGANISM Zika virus Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus. REFERENCE 1 (bases 1 to 1148) AUTHORS Perkasa,A., Yudaputri,F., Haryanto,S., Hayati,R.F., Ma'roef,C.N., Antonjaya,U., Yohan,B., Myint,K.S.A., Ledderman,J.P., Rosenberg,R., Powers,A.M. and Sasmono,R.T. TITLE Isolation o…

LOCUS KM014700 281 bp RNA linear VRL 06-FEB-2015 DEFINITION Zika virus polyprotein gene, partial cds. ACCESSION KM014700 VERSION KM014700.1 GI:734568018 KEYWORDS . SOURCE Zika virus ORGANISM Zika virus Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus. REFERENCE 1 (bases 1 to 281) AUTHORS Musso,D., Roche,C., Robin,E., Nhan,T., Teissier,A. and Cao-Lormeau,V.M. TITLE Potential sexual transmission of zika virus JOURNAL Emerging Infect. Dis. 21 (2), 359-361 (2015) PUBMED 25625872 REFERENCE 2 (bases 1 to 281) …

InDRE released a partial Zika sequences collected in October 2015 in Queretaro from a 26M. http://www.ncbi.nlm.nih.gov/nuccore/KU556802.1

CDC has released sequences for 6 segments on the New Jersey case announced in week 52 (which did not have direct swine contact) http://www.cdc.gov/flu/weekly/weeklyarchives2015-2016/Week52.htm The N2 links back to seasonal flu from the mid 1990's,in contrast to recent human H3N2v cases which link back to seasonal flu from 2003. In late 2011 (West Virginia day care center) the N2 lineage changed and this change was subsequently found in all human H3N2v in the United States.

LOCUS KU232301 692 bp RNA linear VRL 10-FEB-2016 DEFINITION Zika virus isolate 072ZV_PEBR15 NS5 protein gene, partial cds. ACCESSION KU232301 VERSION KU232301.1 GI:987895001 KEYWORDS . SOURCE Zika virus ORGANISM Zika virus Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus. REFERENCE 1 (bases 1 to 692) AUTHORS Pessoa,R. and Sanabani,S. TITLE Investigation into an Outbreak of Dengue-like Illness in Pernambuco, Brazil Revealed a Co-circulation of Zika, Chikungunya, and Dengue Virus Type 1

LOCUS KU707826 10648 bp RNA linear VRL 12-FEB-2016 DEFINITION Zika virus isolate SSABR1, complete genome. ACCESSION KU707826 VERSION KU707826.1 GI:992324757 KEYWORDS . SOURCE Zika virus ORGANISM Zika virus Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus. REFERENCE 1 (bases 1 to 10648) AUTHORS Alcantara,L.C.J., Giovanetti,M., Nunes,M.R.T., Vasconcelos,J.M., Vianez,J.L. Jr. and da Silva,S.P. TITLE Zika virus genome from Salvador, Bahia, Brazilhttp://www.ncbi.nlm.nih.gov/nuccore/KU707826.1

University of Ljubljana full Zika sequence, Bahia2015, collected October 2015 from aborted fetal brain from case with microcephaly. http://www.ncbi.nlm.nih.gov/nuccore/KU527068

Veterinary Services is making the HPAI genomic sequence, as well as the HPAI virus courtesy of the Indiana State Board of Animal Health, available to facilities to encourage disease research and development to benefit the U.S. poultry industry. The complete genomic sequence for the HPAI can be found in the attached file. Sequence information has also been submitted to GenBank and will be available for both HPAI and LPAI viruses soon under accessions as follows: H7N8 HPAI KU558903-8910; H7N8 LPAI KU585905-12 and KU585913-20. https://www.aphis.usda.gov/animal_health/vet_biologics/publications/notice_16_02.pdf