Occasionally, molecular typing based on M13 fingerprinting, AFLP and RFLP analysis is misleading.
An aliquot of DNA from all episodes of HAdV was designated for molecular typing based on nested PCR amplification and sequencing of a partial region of the HAdV hexon gene [31], [32]; 116 such samples were submitted to the Centers for Disease Control and Prevention laboratory performing these assays.
Prospective molecular typing based on spoligotyping and 5-loci VNTRs showed that evolutionary recent Euro-American lineages predominated in Guadeloupe (91.5% of isolates).
To directly type HRVs in nasal secretions of infants with frequent respiratory illnesses, we developed a sensitive molecular typing assay based on phylogenetic comparisons of a 260-bp variable sequence in the 5' noncoding region with homologous sequences of the 101 known serotypes.
Molecular typing assays based on PCR amplification and sequencing of the AdV hexon and fibre genes were used.
More recently, molecular typing methods based on variable number tandem repeats (VNTRs) of genetic elements named mycobacterial interspersed repetitive units (MIRUs) (17 ) have been developed (18, 19 ).
Traditional molecular typing studies based on pulsed-field gel electrophoresis (PFGE), arbitrarily primed PCR (AP-PCR) and multi-locus sequence typing (MLST) have been employed to distinguish among isolates [ 5- 9].
In the United States, the exchange of molecular data has been addressed by the establishment of PulseNet, a national molecular typing scheme based on a standard method for PFGE; a similar network is being set up for the major Salmonella reference laboratories in Europe with research funding from the European Commission.
Molecular typing methods based on reverse transcription PCR (RT-PCR) amplification, nucleotide sequencing of the complete or the 3′ portion of the viral protein (VP) 1 gene, and comparison of the derived sequences with those of prototype and variant HEVs in the databases are widely used to identify EV types in clinical samples (9, 10 ).
In this study, an approach based on whole genome sequencing by NGS technology, comparative genomics, and gene function prediction was set up and applied to investigate N. meningitidis isolates, collected during an outbreak, that appeared identical by standard molecular typing methods based on PFGE, MLST, and porA VR1/VR2 sequencing.
Because HRV was the predominant pathogen detected, we genotyped all HRV isolates directly from the specimens using a molecular typing assay based on phylogenetic comparisons of a 260-bp variable sequence (P1 P2) in the 5′-noncoding 5′-noncodinghomologous sequences of the 101 known seregions (3, 4 ).
