First report of a persistent oropharyngeal infection of type 2 vaccine-derived poliovirus (iVDPV2) in a primary immune deficient (PID) patient after eradication of wild type 2 poliovirus.

This is the first report of persistent oropharyngeal mucosal infection with type 2 poliovirus (iVDPV2) in a primary immune deficient patient (PID) after wild type 2 poliovirus eradication. The iVDPV2 also established persistence in the gut. iVDPV2 at both loci evolved independently. Persistent oral infections present a potential risk for oral-oral as well as fecal-oral poliovirus transmission during transition to a poliovirus 2-free world.

Prolonged excretion of type-2 poliovirus from a primary immune deficient patient during the transition to a type-2 poliovirus-free world, Israel, 2016.

Wild poliovirus type-2 has been eradicated, use of live type-2 vaccine has been terminated globally, and all type-2 polioviruses are under strict laboratory containment protocols. Re-emergence may arise from prolonged asymptomatic excretion of poliovirus by hospitalised primary immune deficient (PID) patients, as described here, through repeated exposure of close contacts to high titres of infected material. At this transition time, PID patients should be screened and hospital containment protocols updated in parallel with laboratory containment.

Identification by full-genome analysis of a bovine rotavirus transmitted directly to and causing diarrhea in a human child.

The genome of rotaviruses consists of 11 segments of double-stranded RNA, and each genome segment has multiple genotypes. Thus, the genotype constellation of an isolate is often indicative of its host species. Albeit rarely, interspecies transmission occurs either by virions with nonreassorted or reassorted genomic segments. A rotavirus with the G6P[1] genotype, Ro8059, was isolated from the stool of a 1-year-old child during routine characterization of diarrheal specimens from a sentinel clinic in Israel in 1995. Since genotype G6P[1] is generally associated with bovine rotaviruses, and the child developed diarrhea within days of his first contact with calves at an urban farm, the aim of this study was to characterize the whole genomic constellation of Ro8059 and four G6P[1] bovine strains, BRV101, BRV105, BRV106, and CR231/39, by RNA-RNA hybridization and full genome sequencing to determine whether some or all of the segments were of bovine origin. The genome constellations of all four bovine G6P[1] strains were G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3 for VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5, respectively. Ro8059 shared the same genotype constellation with these bovine strains, with high nucleotide sequence identities (95.84 to 100%) for each of the 11 segments indicating that Ro8059 represented a direct interspecies whole-genome transmission of a nonreassorted rotavirus from a calf to a human infant. We conclude that this was the earliest example with a complete epidemiological link in which an entirely bovine rotavirus directly infected a human child and caused a symptomatic diarrheal illness. Thus, not all bovine rotaviruses are always naturally attenuated to the human host.

Genotyping rotavirus RNA from archived rotavirus-positive rapid test strips.

Genotyping circulating rotaviruses before and after introduction of rotavirus vaccine is useful for evaluating vaccine-associated changes in genotype distribution. We determined frequency of rotavirus genotypes among 61 rotavirus-positive children hospitalized in Israel during the 2005-06 rotavirus season. Accurate molecular epidemiologic data were recovered from affinity-concentrated rotavirus immobilized in rotavirus-positive bands from air-dried, diagnostic rotavirus rapid test strips (dipstick) stored at room temperature from 1 week to 5 years. G genotypes were identical for 21 paired dipsticks and suspensions, whereas dipsticks or suspensions detected an additional G genotype in 2 samples. RNA sequences from 7 pairs were identical. Phylogenetic analysis suggested previously unreported G2 sublineages and G9 lineages. The ease with which dipsticks can be stored at local facilities and transported to central reference laboratories can reverse increasing difficulties in obtaining geographically representative stool samples and expand surveillance to regions lacking adequate laboratory facilities.

High frequency and diversity of rearrangements in polyomavirus bk noncoding regulatory regions cloned from urine and plasma of Israeli renal transplant patients and evidence for a new genetic subtype.

Polyomavirus BK (BKV) establishes latent infection in various human tissues, including the kidney. Reactivation following renal transplantation (RT) may cause BKV-associated nephropathy, leading to graft loss. BKV reactivation is often associated with extensive rearrangements in the BKV noncoding regulatory region (NCRR). We explored the formation and predominance of the rearrangements versus the diversity of the rearrangements by cloning and characterizing PCR-amplified NCRR sequences from six Israeli RT patients. We found a high frequency and a high degree of diversity of rearrangements: NCRRs that contained major rearrangements (mrNCRRs), including large insertions and deletions, were detected in 0 to 100% of the clones from individual samples (mean, 50% and 67% in plasma and urine, respectively). In addition, we found a high frequency of mrNCRRs that contained single-nucleotide variations (snvNCRRs) among identical mrNCRRs and archetype clones. mrNCRRs were present in plasma and in concomitantly collected urine samples, but for each patient, only a subset of the mrNCRRs and snvNCRRs were present in both compartments at the same time and/or in subsequent samples from the same compartment. Some mrNCRRs were observed over several months, indicating the continuous replication of the viral genomes carrying them. Phylogenetic analysis based on the snvNCRR in the archetype clones grouped isolates from four of the patients into a new subgroup of genotype IV. Genotypes Ib-1 and Ib-2 were also found. Isolates from two patients had NCRRs from two genotypes, one concurrently with a RT and one after a second RT. Our study prompts further investigation of the functional consequences of NCRR rearrangements to assess their biological significance and their putative role in disease progression and prognosis.