Viral forensic genomics reveals the relatedness of classic herpes simplex virus strains KOS, KOS63, and KOS79

Abstract

Herpes simplex virus 1 (HSV-1) is a widespread global pathogen, of which the strain KOS is one of the most extensively studied. Previous sequence studies revealed that KOS does not cluster with other strains of North American geographic origin, but instead clustered with Asian strains. We sequenced a historical isolate of the original KOS strain, called KOS63, along with a separately isolated strain attributed to the same source individual, termed KOS79. Genomic analyses revealed that KOS63 closely resembled other recently sequenced isolates of KOS and was of Asian origin, but that KOS79 was a genetically unrelated strain that clustered in genetic distance analyses with HSV-1 strains of North American/European origin. These data suggest that the human source of KOS63 and KOS79 could have been infected with two genetically unrelated strains of disparate geographic origins. A PCR RFLP test was developed for rapid identification of these strains.

Subclinical Herpes Simplex Virus Type 1 Infections Provide Site-Specific Resistance to an Unrelated Pathogen

“…Strain identity was confirmed by sequencing the viral DNA at key sites, including a marker diagnostic for KOS [24] and the US9 regions (see GenBank: KF498959.1). Pseudorabies virus (PRV) used in this study were generated using a Becker-strain bacterial artificial chromosome (BAC) (kind gift from Lynn Enquist, Princeton University NH).…”

Shared ancestry of herpes simplex virus 1 strain Patton with recent clinical isolates from Asia and with strain KOS63

“…There is a similar geographic disconnect for KOS63, which was also isolated at Baylor, albeit a number of years earlier, but also clusters with genotypes of Asian rather than North American/European origin (Bowen et al, 2016; Smith, 1964). Numerous sequence differences clearly indicate that Patton and KOS63 are distinct viruses and in fact only 15 of the 74 predicted protein products are identical at the amino acid level (Fig.…”

“…The most surprising finding of this study is the unexpected relationship of Patton to strain KOS63, a virus with clear affinities to East Asian rather than North American isolates (Bowen et al, 2016). Although the published details are limited, the indications are that the Patton virus was isolated at Baylor University College of Medicine in Houston, Texas prior to 1973 (Duff and Rapp, 1973).…”

“…Despite extensive engineering and passage within the laboratory, only eight single nucleotide polymorphisms (SNPs) were found in non-repetitive regions of the recombinant virus compared to the parental sequence and of these, only two SNPs are predicted to change the corresponding protein sequence. Unexpectedly, lineage analysis showed that strain Patton is related to strain KOS (referred to here as KOS63, (Bowen et al, 2016)) another widely used laboratory strain first isolated at Baylor College of Medicine, Texas in the early 1960’s (Smith, 1964). Numerous differences in the genomic sequences as well as previously reported differences in biological properties such as neurovirulence confirm that KOS63 and Patton are distinct viruses.…”

Genotypic and phenotypic diversity within the neonatal HSV-2 population

“…Viral nucleocapsid gDNA was sheared using a Covaris M220 sonicator/disruptor under the following conditions: 60s duration, peak power 50, 10% duty cycle, at 4°C. Barcoded sequencing libraries were prepared using the Illumina TruSeq low-throughput protocol according to manufacturer's specifications and as previously described (75,76). The quality of sequencing libraries was evaluated by Qubit (Invitrogen, CA), Bioanalyzer (Agilent), peer-reviewed) is the author/funder.…”