Virus Genes 23:1, 5–16, 2001 © 2001 Kluwer Academic Publishers. Manufactured in The Netherlands. The Genome of Hawaii Virus and its Relationship with other Members of the Caliciviridae MARIA A. PLETNEVA, STANISLAV V. SOSNOVTSEV & KIM Y. GREEN ∗ Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA Received December 2, 2000; Accepted January 19, 2001 Abstract. Hawaii virus (Hu/NLV/GII/Hawaii virus/1971/US), a member of the genus ‘Norwalk-like viruses’ (NLVs) in the family Caliciviridae, has served as one of the reference strains for the fastidious caliciviruses associated with epidemic gastroenteritis in humans. The consensus sequence of the RNA genome of Hawaii virus was deter- mined in order to establish its relatedness with other members of the family. The RNA genome is 7,513 nucleotides (nts) in length, excluding the 3 ′ -end poly (A) tract, and is organized into three major open reading frames (ORF1, nts 5–5,104; ORF2, nts 5,085–6,692; and ORF3, nts 6,692–7,471). Phylogenetic analysis showed the closest relat- edness of Hawaii virus throughout its genome to Lordsdale virus, a Genogroup II NLV. Analysis of the predicted secondary structure of the RNA from the 5 ′ -end of the genome and the putative beginning of the subgenomic RNA showed the presence of two hairpin structures at both ends that are similar to each other and to those of other NLVs. Key words: Hawaii virus, Norwalk-like virus, calicivirus, epidemic gastroenteritis Introduction ‘Norwalk-like viruses’ (NLVs) are members of the family Caliciviridae. They are positive, single-stranded RNA viruses, and are important agents of acute nonbac- terial epidemic gastroenteritis [1,2]. The NLV genome of approximately 7.5 kb is polyadenylated at the 3 ′ -end and contains three open reading frames (ORFs) [3–5]. The first open reading frame (ORF1), begin- ning near the 5 ′ -end of the genome, encodes a large nonstructural polyprotein [6]. The second open read- ing frame (ORF2) encodes the major structural capsid protein [7]; and a small third ORF (ORF3) near the 3 ′ -end of the genome encodes a basic, minor struc- tural protein [8]. Because at least two structural proteins have been identified in the virions of Norwalk virus (NV) [8], feline calicivirus (FCV) [9], and rab- bit hemorrhagic disease virus (RHDV) [10], it has recently been proposed that the major and minor capsid ∗ Author for all correspondence: Tel.: 301 594-1665 (voice mail); Fax: 301 496-8312; E-mail: kgreen@niaid.nih.gov proteins of caliciviruses be designated as VP1 and VP2, respectively [9]. Hawaii virus (HV) was first identified in 1977 in the stool of a volunteer who underwent an oral chal- lenge with a stool filtrate derived from an individual involved in a 1971 family outbreak of gastroenteri- tis that occurred in Honolulu, Hawaii [11]. Hawaii virus (subsequently designated by a cryptogram as Hu/NLV/GII/Hawaii virus/1971/US) assumed promi- nence as a distinct serotype among the group of ‘small round structured viruses’ because it was found to be antigenically distinct from NV by immune elec- tron microscopy (IEM) and in human cross-challenge studies [12]. Sequence analysis of part of the HV genome, including that encoding the major capsid pro- tein, identified it as a member of Caliciviridae that was genetically distinct from NV [13]. Further molec- ular characterization of partial genome sequences from additional NLV strains associated with epidemic gas- troenteritis led to the identification of two major genetic groups that have been designated as Genogroup I (GI, ‘NV-like’) and Genogroup II (GII, ‘HV-like’ or