Mutation rate and genotype variation of Ebola virus from Mali case sequences

Abstract

The occurrence of Ebola virus (EBOV) in West Africa during 2013-2015 is unprecedented. Early reports suggested that in this outbreak EBOV is mutating twice as fast as previously observed, which indicates the potential for changes in transmissibility and virulence and could render current molecular diagnostics and countermeasures ineffective. We have determined additional full-length sequences from two clusters of imported EBOV infections into Mali, and we show that the nucleotide substitution rate (9.6 × 10(-4) substitutions per site per year) is consistent with rates observed in Central African outbreaks. In addition, overall variation among all genotypes observed remains low. Thus, our data indicate that EBOV is not undergoing rapid evolution in humans during the current outbreak. This finding has important implications for outbreak response and public health decisions and should alleviate several previously raised concerns.

Essentials of filoviral load quantification

“…Variability in lethality might also relate to factors such as time from disease onset to presentation for care, quality of care available, patient demographics, or variant of infecting virus. 14,[22][23][24] Accurate viral load measurement is also important in interpreting Ebola virus persistence in and transmission risk from immuneprivileged body compartments and fl uids, 25 including the male gonads or semen, [25][26][27][28] eyes, 29 CNS, 30 breast milk, 31 and the intrauterine space in pregnant women. 32 Additionally, Ebola virus has occasionally been found in sweat and urine, 33 and in atypical or asymptomatic cases.…”

Mapping the clinical outcomes and genetic evolution of Ebola virus in Sierra Leone

“…In the current study, we performed a long-term investigation of EVD patients in Sierra Leone (9) and collected data on residence and definitive clinical outcome of the EVD cases. We also linked our previously sequenced and publicly released EBOV genomes to those patients (3)(4)(5)7).…”

“…Sierra Leone, which was the most severely affected country in the area, reported its first confirmed EVD case on May 25, 2014. Deep sequencing of the viral genome from patient samples and phylogenetic studies have unraveled the evolution and transmission of the Ebola virus (EBOV) in Sierra Leone (2-4), Guinea (5-7), Liberia (8), and Mali (9). In our previous studies, we not only discovered a steady nucleotide substitution rate and diversified evolutionary lineages for EBOV, but also identified the transmission dynamic and intervention effectiveness of EVD in Sierra Leone (10), which may contribute to more closely understanding the epidemic characteristics of EVD and EBOV in Sierra Leone.…”

Genome sequence analysis of Ebola virus in clinical samples from three British healthcare workers, August 2014 to March 2015

“…These SNPs are not expected to affect primer binding, although this is yet to be formally determined, but this reinforces the necessity of regular review of diagnostic detection strategies against available sequence information. A recent analysis of sequences from nine EBOVs from Mali and other available sequences also indicated no effect of SNPs on PCR-based detection assays [12,13].…”