Identification of a Novel Simian Immunodeficiency Virus-Infected African Green Monkey (Chlorocebus tantalus) Confirms that Tantalus Monkeys in Cameroon Are Infected with a Mosaic SIVagm Lineage

MinION nanopore sequencing and assembly of a complete human papillomavirus genome

BACKGROUND

The MinION sequencer belongs to the third generation of sequencing technology that allows for the generation of ultra-long reads, representing a potentially more effective approach to characterize entire viral genome sequences than other time-consuming and low-throughput methodologies.

METHODS

We report the use of the MinION nanopore sequencer to sequence the full-length genome of human papillomavirus (HPV)-ICB2 (7441 bp), which was previously characterized in our laboratory. Three independent MinION libraries were prepared and sequenced using either three consecutive 12 -h runs (Protocol A) or a single run of 48 h starting from a pool of three barcoded DNA libraries (Protocol B). A fully automated bioinformatics pipeline was developed for the reconstruction of the viral genome.

RESULTS

Protocols A and B generated 9,354,933 and 3,255,879 reads, respectively. Read length N50 values ranged between 6976 and 7360 nucleotides over the four sequencing runs. Bioinformatics analysis showed that both protocols allowed for the reconstruction of the whole viral genome, with pairwise percentages of identity to HPV-ICB2 of 100 % for protocol A and 99.98 % for protocol B.

CONCLUSION

Our results show that the use of the MinION nanopore sequencer represents an effective strategy for whole-genome sequencing of HPVs with a minimal error rate.

Broad diversity of simian immunodeficiency virus infecting Chlorocebus species (African green monkey) and evidence of cross-species infection in Papio anubis (olive baboon) in Kenya

BACKGROUND

Simian immunodeficiency virus (SIV) naturally infects African non-human primates (NHPs) and poses a threat of transmission to humans through hunting and consumption of monkeys as bushmeat. This study investigated the as of yet unknown molecular diversity of SIV in free-ranging Chlorocebus species (African green monkeys-AGMs) and Papio anubis (olive baboons) within Mombasa, Kisumu and Naivasha urban centres in Kenya.

METHODS

We collected blood samples from 124 AGMs and 65 olive baboons in situ, and detected SIV by high-resolution melting analysis and sequencing of PCR products.

RESULTS

Simian immunodeficiency virus prevalence was 32% in AGMs and 3% in baboons. High-resolution melting (HRM) analysis demonstrated distinct melt profiles illustrating virus diversity confirmed by phylogenetic analysis.

CONCLUSIONS

There is persistent evolutionary diversification of SIVagm strains in its natural host, AGMs and cross-species infection to olive baboons is occurring. Further study is required to establish pathogenesis of the diverse SIVagm variants and baboon immunological responses.