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Haiti 2016 Zika Recombinant Signals Origin In Americas


niman

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The recently released detail in PLOS NTD confirm that the 2014 Zika sequences in Haiti were due to local transmission.  Although the UF authors note the similarities (identity) with 31 of 51 NS5 sequences from Easter Island (collected between Mach and May,2014), the don't address the 2016 sequence (from a US resident infected in Haiti).

 

The 2016 NS5 sequence is identical to the 2014 Haiti sequences, but most of the 2016 polymorphisms match the 2016 sequences from Natal, Brazil (from the brain of the aborted fetus in Slovenia).

 

The 2016 Haiti sequence ,Haiti/1/2016,is a clear recombinant, which was created by recombination between the 2014 Haiti sequence, Haiti/1225/2014 and the 2016 sequence from Brazil via Slovenia, Natal RGN.

Edited by niman
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The first patient was a 15 year-old boy who presented to the clinic on December 12, 2014, with a history of subjective fever, headache, and generalized arthralgias, myalgias and asthenia. When seen, temperature was 37 degrees C, with a pulse of 92 and respiratory rate of 24, weight 51.5 Kg. He had no rash, and physical exam was unremarkable. The second patient was a 7 year-old girl who was seen on December 15, 2014 at the clinic for subjective nocturnal fever, abdominal pain, anorexia, and cough. Temperature was 37 degrees C, pulse 116, RR 28, and weight 22.8 Kg. There was no rash, and physical exam was again unremarkable. The third patient was an asymptomatic 4 year-old boy who came in December 17, 2014 for follow up after being treated for tonsillitis on November 25, when he had presented with a fever of 39 degrees C. In none of the cases would it have been possible to have identified the illness as a ZIKV infection based on clinical presentation, rather than DENV or CHIKV (and, as indicated, one child was simultaneously infected with DENV).

http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0004687

 

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In tissue culture, viral agents from all three patients induced subtle CPE within 4–8 days post-inoculation of human (A549, HeLa, and MRC-5) and more pronounced CPE in simian (LLC-MK2 and Vero E6) cells incubated at either 33° and 37°C.

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LOCUS       KU509998               10807 bp    RNA     linear   VRL 11-APR-2016
DEFINITION  Zika virus strain Haiti/1225/2014, complete genome.
ACCESSION   KU509998
VERSION     KU509998.3  GI:1016563098
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10807)
  AUTHORS   Lednicky,J.A., Morris,J.G. Jr., Beau De Rochars,V.M., Elbadry,M.A.,
            Okech,B.A. and Loeb,J.C.
  TITLE     Zika virus from a Haitian, December 2014
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10807)
  AUTHORS   Lednicky,J.A., Morris,J.G. Jr., Beau De Rochars,V.M., Elbadry,M.A.,
            Okech,B.A. and Loeb,J.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JAN-2016) Environmental and Global Health, University
            of Florida - Gainesville, 1225 Center Drive, Room 4155,
            Gainesville, FL 32610, USA
REFERENCE   3  (bases 1 to 10807)
  AUTHORS   Lednicky,J.A., Morris,J.G. Jr., Beau De Rochars,V.M., Elbadry,M.A.,
            Okech,B.A. and Loeb,J.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-MAR-2016) Environmental and Global Health, University
            of Florida - Gainesville, 1225 Center Drive, Room 4155,
            Gainesville, FL 32610, USA
  REMARK    Sequence update by submitter
REFERENCE   4  (bases 1 to 10807)
  AUTHORS   Lednicky,J.A., Morris,J.G. Jr., Beau De Rochars,V.M., Elbadry,M.A.,
            Okech,B.A. and Loeb,J.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-APR-2016) Environmental and Global Health, University
            of Florida - Gainesville, 1225 Center Drive, Room 4155,
            Gainesville, FL 32610, USA
  REMARK    Sequence update by submitter
COMMENT     On Apr 11, 2016 this sequence version replaced gi:1012306669.
            
            ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10807
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /strain="Haiti/1225/2014"
                     /isolation_source="plasma"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Haiti"
                     /collection_date="12-Dec-2014"

http://www.ncbi.nlm.nih.gov/nuccore/KU509998

 

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Sequences producing significant alignments:

Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
1852518525100%0.0100%KU509998.3
1850218502100%0.099%KU321639.1
1848018480100%0.099%KX051563.1
1844718447100%0.099%KJ776791.1
1842918429100%0.099%KU991811.1
1842018420100%0.099%KU729218.1
1842018420100%0.099%KU707826.1
1842018420100%0.099%KU365779.1
1840818408100%0.099%KU926309.1
1840818408100%0.099%KU365780.1
1840218402100%0.099%KU940228.1
1840218402100%0.099%KU527068.1
1840218402100%0.099%KU647676.1
1840218402100%0.099%KU365777.1
1839918399100%0.099%KU501217.1
183951839599%0.099%KU497555.1
1839318393100%0.099%KU729217.2
1839318393100%0.099%KU501216.1
1839018390100%0.099%KX087102.1
1839018390100%0.099%KU820897.1
1839018390100%0.099%KU365778.1
1839018390100%0.099%KU312312.1
1838418384100%0.099%KU922960.1
1838118381100%0.099%KU926310.1
1838118381100%0.099%KU922923.1
1838118381100%0.099%KU501215.1
1837518375100%0.099%KX087101.1
1837518375100%0.099%KU870645.1
1837218372100%0.099%KU853013.1
1837018370100%0.099%KU853012.1
1836318363100%0.099%KU820898.1
1835718357100%0.099%KX117076.1
1835718357100%0.099%KX056898.1
1835718357100%0.099%KU955590.1
1835418354100%0.099%KU740184.2
1835418354100%0.099%KU761564.1
1834818348100%0.099%KU963796.1
1834518345100%0.099%KU955589.1
1834518345100%0.099%KU820899.2
183091830999%0.099%KU940224.1
1825818258100%0.099%KU744693.1
1823618236100%0.099%KU866423.1
1810518105100%0.099%KU681081.3
1779817798100%0.098%KU955593.1
177981779899%0.098%JN860885.1
177511775198%0.099%KF993678.1
1764317643100%0.098%EU545988.1
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LOCUS       KX059013                1024 bp    cRNA    linear   VRL 12-APR-2016
DEFINITION  Zika virus isolate Haiti/1227/2014 NS5 gene, partial cds.
ACCESSION   KX059013
VERSION     KX059013.1  GI:1016884666
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 1024)
  AUTHORS   Lednicky,J.A., Morris,J.G. Jr., Beau De Rochars,V.M., Elbadry,M.A.,
            Okech,B.A. and Loeb,J.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-APR-2016) Environmental and Global Health, University
            of Florida - Gainesville, 1225 Center Drive, Room 4155,
            Gainesville, FL 32610, USA
COMMENT     ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..1024
                     /organism="Zika virus"
                     /mol_type="viral cRNA"
                     /isolate="Haiti/1227/2014"
                     /isolation_source="plasma"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Haiti"
                     /collection_date="15-Dec-2014"
                     /identified_by="John Lednicky"

http://www.ncbi.nlm.nih.gov/nuccore/KX059013

 

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LOCUS       KX059014                1024 bp    cRNA    linear   VRL 12-APR-2016
DEFINITION  Zika virus isolate Haiti/1230/2014 NS5 gene, partial cds.
ACCESSION   KX059014
VERSION     KX059014.1  GI:1016884668
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 1024)
  AUTHORS   Lednicky,J.A., Morris,J.G. Jr., Beau De Rochars,V.M., Elbadry,M.A.,
            Okech,B.A. and Loeb,J.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-APR-2016) Environmental and Global Health, University
            of Florida - Gainesville, 1225 Center Drive, Room 4155,
            Gainesville, FL 32610, USA
COMMENT     ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..1024
                     /organism="Zika virus"
                     /mol_type="viral cRNA"
                     /isolate="Haiti/1230/2014"
                     /isolation_source="plasma"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Haiti"
                     /collection_date="17-Dec-2014"
                     /identified_by="John Lednicky"

http://www.ncbi.nlm.nih.gov/nuccore/KX059014

 

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Sequences producing significant alignments:

Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
17611761100%0.0100%KX059014.1
17611761100%0.0100%KX059013.1
17611761100%0.0100%KX051563.1
17611761100%0.0100%KU509998.3
17611761100%0.0100%KM078936.1
17611761100%0.0100%KJ776791.1
17571757100%0.099%KM078961.1
17551755100%0.099%KU497555.1
17551755100%0.099%KU647676.1
17551755100%0.099%KM078930.1
17541754100%0.099%KM078971.1
17541754100%0.099%KM078970.1
17541754100%0.099%KM078933.1
17521752100%0.099%KX087102.1
17521752100%0.099%KU870645.1
17521752100%0.099%KU926310.1
17521752100%0.099%KU729217.2
17521752100%0.099%KU820897.1
17521752100%0.099%KU321639.1
17521752100%0.099%KM078929.1
17461746100%0.099%KX087101.1
17461746100%0.099%KU991811.1
17461746100%0.099%KU926309.1
17461746100%0.099%KU922960.1
17461746100%0.099%KU922923.1
17461746100%0.099%KU853013.1
17461746100%0.099%KU853012.1
17461746100%0.099%KU707826.1
17461746100%0.099%KU527068.1
17461746100%0.099%KU501217.1
17461746100%0.099%KU501216.1
17461746100%0.099%KU501215.1
17461746100%0.099%KU365780.1
17461746100%0.099%KU365779.1
17461746100%0.099%KU365777.1
17431743100%0.099%KX117076.1
17431743100%0.099%KU940228.1
17431743100%0.099%KU940224.1
17431743100%0.099%KU820898.1
17431743100%0.099%KU729218.1
17431743100%0.099%KU312312.1
17371737100%0.099%KX056898.1
17371737100%0.099%KU963796.1
17371737100%0.099%KU955590.1
17371737100%0.099%KU955589.1
17371737100%0.099%KU740184.2
17371737100%0.099%KU820899.2
17371737100%0.099%KU761564.1
17371737100%0.099%KU744693.1
17371737100%0.099%KU365778.1
17341734100%0.099%KF993678.1
17191719100%0.099%KU866423.1
17191719100%0.099%KU681081.3
1710171098%0.099%KU179098.1
16891689100%0.098%KU955593.1
16891689100%0.098%JN860885.1
16891689100%0.098%EU545988.1
16651665100%0.098%KU681082.3
1611161191%0.0100%KJ873160.1
15301530100%0.095%HQ234499.1
1429142981%0.0100%KJ873161.1
1353135377%0.099%KU985087.1
1348134878%0.099%KM851039.1
1346134676%0.099%KU556802.1
1312131278%0.098%KM851038.1
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LOCUS       KX051563               10807 bp    cRNA    linear   VRL 19-APR-2016
DEFINITION  Zika virus isolate Haiti/1/2016, complete genome.
ACCESSION   KX051563
VERSION     KX051563.1  GI:1016884664
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10807)
  AUTHORS   Lednicky,J.A., Crooke,H.R., White,S.K., Loeb,J.C., Iovine,N.M. and
            Morris,J.G. Jr.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-APR-2016) Environmental and Global Health, University
            of Florida - Gainesville, 1225 Center Drive, Room 4155,
            Gainesville, FL 32610, USA
COMMENT     ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10807
                     /organism="Zika virus"
                     /mol_type="viral cRNA"
                     /isolate="Haiti/1/2016"
                     /isolation_source="saliva and urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="USA"
                     /collection_date="05-Feb-2016"
                     /identified_by="John Lednicky and Sarah White"
                     /note="passage details: one passage in LLC-MK2 cells"

http://www.ncbi.nlm.nih.gov/nuccore/KX051563

 

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Sequences producing significant alignments:

Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
1896918969100%0.0100%KX051563.1
1891418914100%0.099%KU509998.3
1888618886100%0.099%KU321639.1
1886418864100%0.099%KU527068.1
1885318853100%0.099%KJ776791.1
1883118831100%0.099%KU991811.1
1882018820100%0.099%KU729218.1
1882018820100%0.099%KU707826.1
1882018820100%0.099%KU365779.1
1880318803100%0.099%KU926309.1
1880318803100%0.099%KU365780.1
1879818798100%0.099%KU940228.1
1879818798100%0.099%KU647676.1
1879818798100%0.099%KU365777.1
1879218792100%0.099%KU501217.1
187881878899%0.099%KU497555.1
1878718787100%0.099%KU729217.2
1878718787100%0.099%KU501216.1
1878118781100%0.099%KX087102.1
1878118781100%0.099%KU820897.1
1878118781100%0.099%KU365778.1
1878118781100%0.099%KU312312.1
1877618776100%0.099%KU922960.1
1877018770100%0.099%KU926310.1
1877018770100%0.099%KU922923.1
1877018770100%0.099%KU501215.1
1876418764100%0.099%KX087101.1
1876418764100%0.099%KU870645.1
1875918759100%0.099%KU853013.1
1875718757100%0.099%KU853012.1
1874818748100%0.099%KU820898.1
1874218742100%0.099%KX117076.1
1874218742100%0.099%KX056898.1
1874218742100%0.099%KU955590.1
1873718737100%0.099%KU740184.2
1873718737100%0.099%KU761564.1
1873118731100%0.099%KU963796.1
1872618726100%0.099%KU955589.1
1872618726100%0.099%KU820899.2
187001870099%0.099%KU940224.1
1859318593100%0.099%KU866423.1
1858718587100%0.099%KU744693.1
1843218432100%0.099%KU681081.3
180631806399%0.098%JN860885.1
1806118061100%0.098%KU955593.1
180461804698%0.099%KF993678.1
1787117871100%0.098%EU545988.1
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LOCUS       KU527068               10808 bp    RNA     linear   VRL 11-FEB-2016
DEFINITION  Zika virus strain Natal RGN, complete genome.
ACCESSION   KU527068
VERSION     KU527068.1  GI:982894594
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10808)
  AUTHORS   Mlakar,J., Korva,M., Tul,N., Popovic,M., Poljsak-Prijatelj,M.,
            Mraz,J., Kolenc,M., Resman Rus,K., Vesnaver Vipotnik,T., Fabjan
            Vodusek,V., Vizjak,A., Pizem,J., Petrovec,M. and Avsic Zupanc,T.
  TITLE     Zika Virus Associated with Microcephaly
  JOURNAL   N. Engl. J. Med. (2016) In press
   PUBMED   26862926
  REMARK    Publication Status: Available-Online prior to print
REFERENCE   2  (bases 1 to 10808)
  AUTHORS   Avsic Zupanc,T. and Korva,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JAN-2016) Institute of Microbiology and Immunology,
            University of Ljubljana, Faculty of Medicine, Vrazov trg 2,
            Ljubljana 1000, Slovenia
FEATURES             Location/Qualifiers
     source          1..10808
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /strain="Natal RGN"
                     /isolation_source="fetus' brain autopsy"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil: Rio Grande do Norte, Natal"
                     /collection_date="2015"

http://www.ncbi.nlm.nih.gov/nuccore/KU527068

 

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Sequences producing significant alignments:

Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
1896918969100%0.0100%KU527068.1
1886418864100%0.099%KX051563.1
1882018820100%0.099%KU509998.3
1880318803100%0.099%KU321639.1
1880318803100%0.099%KJ776791.1
1879218792100%0.099%KU991811.1
1878118781100%0.099%KU729217.2
1878118781100%0.099%KU729218.1
1878118781100%0.099%KU707826.1
1878118781100%0.099%KU365779.1
1877618776100%0.099%KU926310.1
1876418764100%0.099%KU926309.1
1876418764100%0.099%KU501217.1
1876418764100%0.099%KU365780.1
1875918759100%0.099%KU940228.1
1875918759100%0.099%KU647676.1
1875918759100%0.099%KU501216.1
1875918759100%0.099%KU365777.1
1875318753100%0.099%KU853013.1
1875218752100%0.099%KU853012.1
187501875099%0.099%KU497555.1
1874218742100%0.099%KU820897.1
1874218742100%0.099%KU365778.1
1874218742100%0.099%KU312312.1
1873718737100%0.099%KU922960.1
1873118731100%0.099%KU922923.1
1873118731100%0.099%KU501215.1
1872618726100%0.099%KU870645.1
1870918709100%0.099%KU820898.1
1870318703100%0.099%KX056898.1
1870318703100%0.099%KU955590.1
1869818698100%0.099%KU740184.2
1869818698100%0.099%KU761564.1
1868118681100%0.099%KU963796.1
1867618676100%0.099%KU955589.1
1867618676100%0.099%KU820899.2
186611866199%0.099%KU940224.1
1854318543100%0.099%KU866423.1
1851518515100%0.099%KU744693.1
1838218382100%0.099%KU681081.3
180131801399%0.098%JN860885.1
1801118011100%0.098%KU955593.1
179961799698%0.099%KF993678.1
1782117821100%0.098%EU545988.1
1763417634100%0.098%KU681082.3
163771637799%0.095%HQ234499.1
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