Analysis of Puumala hantavirus genome in patients with nephropathia epidemica and rodent carriers from the sites of infection

Reverse transcription-polymerase chain reaction (RT-PCR) followed by sequen ce and phylogenetic analyses were used to study specimens from nine Finnish nephropathia epidemica (NE) patients admitted to hospital during the epide mic in winter 1996-1997. Blood samples from six patients were found to be p ositive for the partial M- and/or S-segment sequences of Puumala hantavirus (PUUV). Analyses of these sequences (nt 2168-2610 for the M segment, and n t 819-1082 for the S segment) revealed six distinct PUUV strains showing hi ghest similarity to previously described PUUV strains from Finland: 90-95% for the S segment, and 90-99% for the M segment. Accordingly, on the phylog enetic trees calculated for both viral segments, all six human strains were placed within the Finnish genetic lineage of PUUV. Attempts were made to t race five RT-PCR-positive patients to local bank voles (Clethrionomys glare olus) infected with wildtype PUUV, and for two patients a comparative analy sis of human- and rodent-originated viral sequences was undertaken. Whereas in the first case the differences between the sequences were substantial ( 5.7% for the S segment, and 10.8%, for the M segment), in the other case th e M segment sequence recovered from the clinical specimen was 100% identica l to three sequences recovered from rodent lungs, and the S sequences diffe red by one silent substitution only. This is the first finding of virtually identical PUUV sequences in an NE patient and a natural rodent host from t he site of infection. (C) 1999 Wiley-Liss, Inc.