BackgroundA chikungunya virus outbreak of unprecedented magnitude is currently ongoing in Indian Ocean territories. In Réunion Island, this alphavirus has already infected about one-third of the human population. The main clinical symptom of the disease is a painful and invalidating poly-arthralgia. Besides the arthralgic form, 123 patients with a confirmed chikungunya infection have developed severe clinical signs, i.e., neurological signs or fulminant hepatitis.Methods and FindingsWe report the nearly complete genome sequence of six selected viral isolates (isolated from five sera and one cerebrospinal fluid), along with partial sequences of glycoprotein E1 from a total of 127 patients from Réunion, Seychelles, Mauritius, Madagascar, and Mayotte islands. Our results indicate that the outbreak was initiated by a strain related to East-African isolates, from which viral variants have evolved following a traceable microevolution history. Unique molecular features of the outbreak isolates were identified. Notably, in the region coding for the non-structural proteins, ten amino acid changes were found, four of which were located in alphavirus-conserved positions of nsP2 (which contains helicase, protease, and RNA triphosphatase activities) and of the polymerase nsP4. The sole isolate obtained from the cerebrospinal fluid showed unique changes in nsP1 (T301I), nsP2 (Y642N), and nsP3 (E460 deletion), not obtained from isolates from sera. In the structural proteins region, two noteworthy changes (A226V and D284E) were observed in the membrane fusion glycoprotein E1. Homology 3D modelling allowed mapping of these two changes to regions that are important for membrane fusion and virion assembly. Change E1-A226V was absent in the initial strains but was observed in >90% of subsequent viral sequences from Réunion, denoting evolutionary success possibly due to adaptation to the mosquito vector.ConclusionsThe unique molecular features of the analyzed Indian Ocean isolates of chikungunya virus demonstrate their high evolutionary potential and suggest possible clues for understanding the atypical magnitude and virulence of this outbreak.

Prochlorococcus marinus. The purification and properties of the axenic strain PCC 9511, derived from the same primary culture (SARG) as the type species, are reported here. Prochlorococcus PCC 9511 differs from the latter in possessing horseshoeshaped thylakoids, exhibiting a low chlorophyll b 2 content and lacking phycoerythrin, but shares these phenotypic properties with Prochlorococcus strain CCMP 1378. This relationship was confirmed by 16S rRNA sequence analyses, which clearly demonstrated that the axenic isolate is not co-identic with the nomenclatural type. Strain PCC 9511 has a low mean DNA base composition (32 mol % GMC) and harbours the smallest genome of all known oxyphotobacteria (genome complexity 13 GDa l 2 Mbp). Urea and ammonia are the preferred sources of nitrogen for growth, whereas nitrate is not utilized. Several different organic phosphorus compounds efficiently replace phosphate in the culture medium, indicative of ecto-phosphohydrolase activity. In order to distinguish strain PCC 9511 from the nomenclatural type, a new subspecies is proposed, Prochlorococcus marinus Chisholm et al. 1992 subsp. pastoris subsp. nov. This paper is dedicated in gratitude to Professor Germaine Cohen-Bazire on the occasion of her 80th birthday. Together with her late husband, Professor R. Y. Stanier, Germaine gave the members of the Physiologie Microbienne (Institute Pasteur, Paris) generous scientific guidance and spiritual support over many years (1971)(1972)(1973)(1974)(1975)(1976)(1977)(1978)(1979)(1980)(1981)(1982)(1983)(1984)(1985)(1986)(1987)(1988) Abbreviations : chl, chlorophyll ; HL, high light ; LL, low light ; PPFD, photosynthetic photon flux density ; PE, phycoerythrin ; T m , temperature mid-point of denaturation. Keywords :The GenBank accession numbers for the 16S rRNA sequences of PCC 9511, CCMP 1426 and NATL1 are AF180967, AF133833 and AF133834, respectively. INTRODUCTIONIn the last edition of Bergey's Manual of Systematic Bacteriology, the class Oxyphotobacteria was subdivided into the Cyanobacteria, whose ordinal recognition still awaits validation, and the order Prochlorales Lewin 1977(Castenholz & Waterbury, 1989. In the light, like algae and plants, these photosynthetic prokaryotes use H # O for the generation of chemical energy and reducing power and liberate molecular O # as a by-product. The demand for cellular carbon is met by CO # fixation. Cyanobacteria synthesize monovinyl chlorophyll a (chl a " ) and harvest light by aid of watersoluble multimeric complexes, the phycobilisomes, composed of biliproteins and linker polypeptides R. Rippka and others (Glazer, 1987(Glazer, , 1989Sidler, 1994). In contrast, oxyphotobacteria of the order Prochlorales Lewin 1977 either lack phycobiliproteins entirely, or synthesize only trace amounts (Lewin, 1977(Lewin, , 1989 BurgerWiersma et al., 1986 ;Chisholm et al., 1992 ;Hess et al., 1996). Their light-harvesting complexes are membrane-associated proteins containing chlorophyll a (a " or a # ) and chlorophyll b (b " or b # ) as the major photosyntheti...

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PCR amplification of the internal transcribed spacer (ITS) between the 16SrRNA and 23S rRNA genes of the cyanobacterium Nostoc PCC 7120 gave three products. Two represented true ITS regions of different sizes, while the third was a heteroduplex. The longer spacer (ITS-L) contained 512 nucleotides and carried tRNA Ile and tRNA Ala genes, separated by a large stem-loop structure (V2) composed of short tandemly repeated repetitive sequences. Both tRNA genes, and the 5' half of the intervening stem, were absent from the shorter spacer (ITS-S), of length 283 nucleotides, which was otherwise almost completely identical to ITS-L. The two spacer regions of Nostoc PCC 7120 were aligned to published ITS sequences of cyanobacteria, the cyanelle of Cyanophora paradoxa and Escherichia coli. Although the ITS regions of cyanobacteria vary in length from 283 to 545 nucleotides and contain either both tRNA Ile and tRNA Ala genes, only the tRNA Ile gene, or neither, there is no correlation between ITS size and coding capacity for tRNAs. Putative secondary structures were determined for the deduced transcripts of the rrn operons of several cyanobacteria and were compared to that of E. coli. Highly conserved motifs important for folding and for maturation of the rRNA transcripts were identified, and regions homologous to bacterial antiterminators (box B-box A) were located. The conserved and variable regions of the cyanobacterial ITS are potential targets of PCR primers and oligonucleotide probes for detection and identification of cyanobacteria at different taxonomic levels.