We compared bacterial 16S ribosomal RNA gene sequences recovered from Lake Loosdrecht, the Netherlands, to reported sequences from lakes in Alaska and New York State. In each of the three lake systems, which differ in pH and trophic state, some sequence types were found without related sequences (sequence identity < 90%) in the data sets from the other two systems. Two sequences in the Actinomycetes and Verrucomicrobia radiations were more closely related to sequences from the New York lakes data set than to any other sequence in the global databases. However, the most striking similarities were found in the subdivisions alpha and beta of the Proteobacteria. In these subdivisions three different clusters of highly related bacteria were identified (97-100% sequence identity) that were represented in all three lake regions. The clusters contained no members other than freshwater bacteria. One cluster falls within a monophyletic aquatic supergroup that apparently diverged early in evolution into an exclusive freshwater cluster and an exclusive marine cluster, the so-called SAR11 cluster. The detection of these three bacterial clades in lakes distinguished by geographic distance as well as physical and chemical diversity suggests that these organisms are dispersed globally and that they possess unique functional capabilities enabling successful competition in a wide range of freshwater environments.

Antiretroviral therapy including zidovudine may yield replicating viruses with a two amino-acid insertion in RT in combination with amino-acid changes at codons 67 and 215, which are highly resistant to lamivudine and stavudine on top of zidovudine and have unpredictable susceptibility to didanosine and zalcitabine despite lack of previously reported corresponding resistance-associated amino-acid changes. It is currently unknown what regimens can induce the emergence of this type of multidrug-resistant viruses. This will only be elucidated when resistance assays are capable of detecting these mutants.

Bacterial diversity in the water column of a freshwater lake in the Netherlands was investigated by analysis of 16S rRNA gene sequences recovered through PCR amplification from total community DNA. Among 23 unique cloned sequences, two appeared to belong to the recently described bacterial division Verrucomicrobiales. One of the two sequences was most similar to a group of environmental clones that form a distinct lineage within the division. The other sequence was divergent (less than 85% similarity) from all 16S rRNA gene sequences, both from cultivated species and from environmental clones, known in this division to date. Analysis by denaturing gradient gel electrophoresis (DGGE) and sequencing of DNA recovered through excision from the DGGE gel showed that the two sequence types were present in the lake throughout the year.

Countries of the former Soviet Union are experiencing an emerging HIV-1 epidemic due to a rapid expansion of HIV-1 among injecting drug users (IDUs). To study the molecular epidemiology of HIV-1 among IDUs in St. Petersburg, Russia, virus sequences were obtained from 22 individuals. Phylogenetic analysis of the env and gag regions revealed circulation of two major HIV-1 populations, one belonging to HIV-1 subtype A, and another being a recombinant of subtype A and B viruses (gagA/envB). Both virus populations were highly homogeneous, with a mean pairwise genetic distance of <2%, and similar to viruses obtained earlier from IDUs in other regions of the former Soviet Union. Distribution of the two major HIV-1 genotypes in St. Petersburg correlated with geographical origin of infections. In one individual, a virus type previously unseen among IDUs was found, which demonstrates the possibility that new viruses are entering this risk group.