GENETIC AND PHENOTYPIC VARIATION OF WEST NILE VIRUS IN NEW YORK, 2000–2003

GREGORY D. EBEL Arbovirus Laboratories, Wadsworth Center, New York State Department of Health, Slingerlands, New York; Department of Biomedical Sciences, The University at Albany, State University of New York, Albany, New York

Search for other papers by GREGORY D. EBEL in
Current site
Google Scholar
PubMed
Close
,
JUSTIN CARRICABURU Arbovirus Laboratories, Wadsworth Center, New York State Department of Health, Slingerlands, New York; Department of Biomedical Sciences, The University at Albany, State University of New York, Albany, New York

Search for other papers by JUSTIN CARRICABURU in
Current site
Google Scholar
PubMed
Close
,
DAVID YOUNG Arbovirus Laboratories, Wadsworth Center, New York State Department of Health, Slingerlands, New York; Department of Biomedical Sciences, The University at Albany, State University of New York, Albany, New York

Search for other papers by DAVID YOUNG in
Current site
Google Scholar
PubMed
Close
,
KRISTEN A. BERNARD Arbovirus Laboratories, Wadsworth Center, New York State Department of Health, Slingerlands, New York; Department of Biomedical Sciences, The University at Albany, State University of New York, Albany, New York

Search for other papers by KRISTEN A. BERNARD in
Current site
Google Scholar
PubMed
Close
, and
LAURA D. KRAMER Arbovirus Laboratories, Wadsworth Center, New York State Department of Health, Slingerlands, New York; Department of Biomedical Sciences, The University at Albany, State University of New York, Albany, New York

Search for other papers by LAURA D. KRAMER in
Current site
Google Scholar
PubMed
Close
Restricted access

West Nile virus (WNV) strains circulating during the first five years of WNV transmission in New York were collected, partial nucleotide sequences were determined, and in vitro and in vivo phenotypic analyses of selected strains were undertaken to determine whether observed increases in the intensity of enzootic and epidemic transmission in New York State during 2002 and 2003 were associated with viral genetic changes. Functionally diverse regions of the WNV genome were also compared to determine whether some regions may be more or less variable than others. The complete envelope coding regions of 67 strains and fragments of the nonstructural protein 5 (NS5) and 3′ noncoding regions of 39 strains collected during 2002 and 2003 were examined. West Nile virus in New York remains relatively genetically homogeneous. Viral genetic diversity was greater in 2002 and 2003 at both the nucleotide and amino acid levels than in previous years due to the emergence of a new WNV genotype in 2002. This genotype persisted and became dominant in 2003. Envelope and NS5 coding regions were approximately two-fold more likely than the 3′ untranslated region to contain nucleotide substitutions, and the envelope region was approximately three-fold more likely to contain amino acid substitutions than the NS5 region. Variation was noted in in vivo mosquito transmission assays, but not in in vitro growth studies. Strains belonging to the epizootiologically dominant clade were transmitted after approximately two fewer days of extrinsic incubation, providing a possible mechanism for the dominance of this clade. The observed increase in the intensity of WNV transmission beginning in 2002 was associated with an increase in viral genetic diversity that was the result of the emergence of an additional phylogenetic clade. This genotype seems to possess an advantage over previously recognized WNV strains in mosquito transmission phenotype.

Author Notes

  • 1

    Anonymous, 1999. From the Centers for Disease Control and Prevention. Update: West Nile virus encephalitis-New York, 1999. JAMA 282 :1806–1807.

  • 2

    Bernard KA, Maffei J, Jones SA, Kauffman EB, Ebel GD, Dupuis AP, Ngo K, Nicholas D, Young D, Shi PY, Eidson M, White DJ, Stone W, Kramer LD, 2001. Comparison of West Nile virus infection in birds and mosquitoes in New York State in 2000. Emerg Infect Dis 7 :679–685.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 3

    Holland J, Spindler K, Horodyski F, Grabau E, Nichol S, Vande-Pol S, 1982. Rapid evolution of RNA genomes. Science 215 :1577–1585.

  • 4

    Kuno G, Chang GJ, Tsuchiya KR, Karabatsos N, Cropp CB, 1998. Phylogeny of the genus Flavivirus. J Virol 72 :73–83.

  • 5

    Lanciotti RS, Gubler DJ, Trent DW, 1997. Molecular evolution and phylogeny of dengue-4 viruses. J Gen Virol 78 :2279–2284.

  • 6

    Weaver SC, Hagenbaugh A, Bellew LA, Gousset L, Mallampalli V, Holland JJ, Scott TW, 1994. Evolution of alphaviruses in the eastern equine encephalomyelitis complex. J Virol 68 :158–169.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 7

    Ebel GD, Dupuis AP, Ngo K, Nicholas D, Kauffman EB, Jones SA, Young D, Maffei J, Shi PY, Bernard KA, Kramer LD, 2001. Partial genetic characterization of WNV strains isolated in New York State during the 2000 transmission season. Emerg Infect Dis 7 :650–653.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 8

    Beasley DW, Davis CT, Guzman H, Vanlandingham DL, Travassos da Rosa AP, Parsons RE, Higgs S, Tesh RB, Barrett AD, 2003. Limited evolution of West Nile virus has occurred during its southwesterly spread in the United States. Virology 309 :190–195.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 9

    Allison SL, Schalich J, Stiasny K, Mandl CW, Heinz FX, 2001. Mutational evidence for an internal fusion peptide in flavivirus envelope protein E. J Virol 75 :4268–4275.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 10

    Holzmann H, Stiasny K, York H, Dorner F, Kunz C, Heinz FX, 1995. Tick-borne encephalitis virus envelope protein E-specific monoclonal antibodies for the study of low pH-induced conformational changes and immature virions. Arch Virol 140 :213–221.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 11

    Mandl CW, Allison SL, Holzmann H, Meixner T, Heinz FX, 2000. Attenuation of tick-borne encephalitis virus by structure-based site- specific mutagenesis of a putative flavivirus receptor binding site. J Virol 74 :9601–9609.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 12

    Rey FA, Heinz FX, Mandl C, Kunz C, Harrison SC, 1995. The envelope glycoprotein from tick-borne encephalitis virus at 2 A resolution. Nature 375 :291–298.

  • 13

    Lanciotti RS, Ebel GD, Deubel V, Kerst AJ, Murri S, Meyer R, Bowen M, McKinney N, Morrill WE, Crabtree MB, Kramer LD, Roehrig JT, 2002. Complete genome sequences and phylogenetic analysis of West Nile virus strains isolated from the United States, Europe, and the Middle East. Virology 298 :96–105.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 14

    Kauffman EB, Jones SA, Dupuis AP, Ngo K, Bernard KA, Kramer LD, 2003. Virus detection protocols for West Nile virus in vertebrate and mosquito specimens. J Clin Microbiol 41 :3661–3667.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 15

    Kumar S, Tamura K, Nei M, 1993. MEGA: Molecular Evolutionary Genetics Analysis. University Park, PA: Pennsylvania State University.

    • PubMed
    • Export Citation
  • 16

    Aitken THG, 1977. An in vitro feeding technique for artificially demonstrating virus transmission by mosquitoes. Mosq News 37 :130–133.

  • 17

    Ebel GD, Dupuis AP, Nicholas D, Young D, Maffei J, Kramer LD, 2002. Detection by enzyme-linked immunosorbent assay of antibodies to West Nile virus in birds. Emerg Infect Dis 8 :979–982.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 18

    Lindsey HS, Calisher CH, Matthews JH, 1976. Serum dilution neutralization test for California group virus identification and serology. J Clin Microbiol 4 :503–510.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 19

    Roehrig JT, Heinz FX, 1990. Flaviviruses. van Regen Mortel MHV, Neurath AR, eds. Immunochemistry of Viruses II, the Basis for Serodiagnosis and Vaccines. New York: Elsevier, 289–305.

    • PubMed
    • Export Citation
  • 20

    You S, Falgout B, Markoff L, Padmanabhan R, 2001. In vitro RNA synthesis from exogenous dengue viral RNA templates requires long range interactions between 5′- and 3′-terminal regions that influence RNA structure. J Biol Chem 276 :15581–15591.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 21

    Blackwell JL, Brinton MA, 1995. BHK cell proteins that bind to the 3′ stem-loop structure of the West Nile virus genome RNA. J Virol 69 :5650–5658.

  • 22

    Hahn CS, Hahn YS, Rice CM, Lee E, Dalgarno L, Strauss EG, Strauss JH, 1987. Conserved elements in the 3′ untranslated region of flavivirus RNAs and potential cyclization sequences. J Mol Biol 198 :33–41.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 23

    Khromykh AA, Sedlak PL, Westaway EG, 2000. cis- and transacting elements in flavivirus RNA replication. J Virol 74 :3253–3263.

  • 24

    Steffens S, Thiel HJ, Behrens SE, 1999. The RNA-dependent RNA polymerases of different members of the family Flaviviridae exhibit similar properties in vitro. J Gen Virol 80 :2583–2590.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 25

    Twiddy SS, Farrar JJ, Vinh CN, Wills B, Gould EA, Gritsun T, Lloyd G, Holmes EC, 2002. Phylogenetic relationships and differential selection pressures among genotypes of dengue-2 virus. Virology 298 :63–72.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 26

    Twiddy SS, Woelk CH, Holmes EC, 2002. Phylogenetic evidence for adaptive evolution of dengue viruses in nature. J Gen Virol 83 :1679–1689.

  • 27

    Ebel GD, Spielman A, Telford SR III, 2001. Phylogeny of North American Powassan virus. J Gen Virol 82 :1657–1665.

  • 28

    Anon., 2002. Provisional surveillance summary of the West Nile virus epidemic-United States, January–November 2002. MMWR Morb Mortal Wkly Rep 51 :1129–1133.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 29

    Bosio CF, Beaty BJ, Black WC, 1998. Quantitative genetics of vector competence for dengue-2 virus in Aedes aegypti. Am J Trop Med Hyg 59 :965–970.

  • 30

    Bosio CF, Fulton RE, Salasek ML, Beaty BJ, Black WC, 2000. Quantitative trait loci that control vector competence for dengue-2 virus in the mosquito Aedes aegypti. Genetics 156 :687–698.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 31

    Ahmed T, Hayes CG, Baqar S, 1979. Comparison of vector competence for West Nile virus of colonized populations of Culex tritaeniorhynchus from southern Asia and the Far East. Southeast Asian J Trop Med Public Health. 10 :498–504.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 32

    Boromisa RD, Rai KS, Grimstad PR, 1987. Variation in the vector competence of geographic strains of Aedes albopictus for dengue 1 virus. J Am Mosq Control Assoc. 3 :378–386.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 33

    Hardy JL, Houk EJ, Kramer LD, Reeves WC, 1983. Intrinsic factors affecting vector competence of mosquitoes for arboviruses. Annu Rev Entomol 28 :229–262.

  • 34

    Reisen WK, Hardy JL, Presser SB, 1997. Effects of water quality on the vector competence of Culex tarsalis (Diptera: Culicidae) for western equine encephalomyelitis (Togaviridae) and St. Louis encephalitis (Flaviviridae) viruses. J Med Entomol 34 :631–643.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 35

    Reisen WK, Hardy JL, Presser SB, Chiles RE, 1996. Seasonal variation in the vector competence of Culex tarsalis (Diptera: Culicidae) from the Coachella Valley of California for western equine encephalomyelitis and St. Louis encephalitis viruses. J Med Entomol 33 :433–437.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 36

    Reisen WK, Reeves WC, Hardy J, Milby MM, 1991. Effects of climatological change on the population dynamics and vector competence of mosquito vectors in California. Proc Calif Mosq Vector Conrtol Assoc 59 :14–20.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 37

    Turell MJ, 1989. Effect of environmental temperature on the vector competence of Aedes fowleri for Rift Valley fever virus. Res Virol 140 :147–154.

  • 38

    Turell MJ, Rossi CA, Bailey CL, 1985. Effect of extrinsic incubation temperature on the ability of Aedes taeniorhynchus and Culex pipiens to transmit Rift Valley fever virus. Am J Trop Med Hyg 34 :1211–1218.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 39

    Hardy JL, Presser SB, Meyer RP, Reisen WK, Kramer LD, Vorndam AV, 1986. Comparison of a 1984 Los Angeles strain of SLE virus with earlier California strains of SLE virus: mouse virulence, chicken viremogenic, RNA oligonucleotide and vector competence characteristics. Proc Calif Mosq Vector Control Assoc 53 :10–15.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 40

    Armstrong PM, Rico-Hesse R, 2001. Differential susceptibility of Aedes aegypti to infection by the American and Southeast Asian genotypes of dengue type 2 virus. Vector Borne Zoonotic Dis 1 :159–168.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 41

    Brault AC, Powers AM, Weaver SC, 2002. Vector infection determinants of Venezuelan equine encephalitis virus reside within the E2 envelope glycoprotein. J Virol 76 :6387–6392.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 42

    Armstrong PM, Rico-Hesse R, 2003. Efficiency of dengue sero-type 2 virus strains to infect and disseminate in Aedes aegypti. Am J Trop Med Hyg 68 :539–544.

  • 43

    Rico-Hesse R, Harrison LM, Salas RA, Tovar D, Nisalak A, Ramos C, Boshell J, de Mesa MT, Nogueira RM, da Rosa AT, 1997. Origins of dengue type 2 viruses associated with increased pathogenicity in the Americas. Virology 230 :244–251.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 44

    Brault AC, Powers AM, Holmes EC, Woelk CH, Weaver SC, 2002. Positively charged amino acid substitutions in the e2 envelope glycoprotein are associated with the emergence of Venezuelan equine encephalitis virus. J Virol 76 :1718–1730.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 45

    Monath TP, Arroyo J, Levenbook I, Zhang ZX, Catalan J, Draper K, Guirakhoo F, 2002. Single mutation in the flavivirus envelope protein hinge region increases neurovirulence for mice and monkeys but decreases viscerotropism for monkeys: relevance to development and safety testing of live, attenuated vaccines. J Virol 76 :1932–1943.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 46

    Reiter P, 1988. Weather, vector biology, and arboviral recrudescence. Monath, TP ed. The Arboviruses: Epidemiology and Ecology. Boca Raton, FL: CRC Press, 245–255.

    • PubMed
    • Export Citation
  • 47

    Lothrop HD, Reisen WK, 2001. Landscape affects the host-seeking patterns of Culex tarsalis (Diptera: Culicidae) in the Coachella Valley of California. J Med Entomol 38 :325–332.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 48

    Meyer RP, Hardy JL, Reisen WK, 1990. Diel changes in adult mosquito microhabitat temperatures and their relationship to the extrinsic incubation of arboviruses in mosquitoes in Kern County, California. J Med Entomol 27 :607–614.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 49

    Reeves WC, Hardy JL, Reisen WK, Milby MM, 1994. Potential effect of global warming on mosquito-borne arboviruses. J Med Entomol 31 :323–332.

  • 50

    Reisen WK, Lothrop HD, Presser SB, Milby MM, Hardy JL, Wargo MJ, Emmons RW, 1995. Landscape ecology of arboviruses in southern California: temporal and spatial patterns of vector and virus activity in Coachella Valley, 1990–1992. J Med Entomol 32 :255–266.

    • PubMed
    • Search Google Scholar
    • Export Citation
  • 51

    Huang C, Slater B, Rudd R, Parchuri N, Hull R, Dupuis M, Hindenburg A, 2002. First isolation of West Nile virus from a patient with encephalitis in the United States. Emerg Infect Dis 8 :1367–1371.

    • PubMed
    • Search Google Scholar
    • Export Citation
Past two years Past Year Past 30 Days
Abstract Views 276 266 16
Full Text Views 383 17 3
PDF Downloads 146 16 1
 
 
 
 
Affiliate Membership Banner
 
 
Research for Health Information Banner
 
 
CLOCKSS
 
 
 
Society Publishers Coalition Banner
Save