Jingfen Zhang

Date of origin of the SARS coronavirus strains

BackgroundA new respiratory infectious epidemic, severe acute respiratory syndrome (SARS), broke out and spread throughout the world. By now the putative pathogen of SARS has been identified as a new coronavirus, a single positive-strand RNA virus. RNA viruses commonly have a high rate of genetic mutation. It is therefore important to know the mutation rate of the SARS coronavirus as it spreads through the population. Moreover, finding a date for the last common ancestor of SARS coronavirus strains would be useful for understanding the circumstances surrounding the emergence of the SARS pandemic and the rate at which SARS coronavirus diverge.MethodsWe propose a mathematical model to estimate the evolution rate of the SARS coronavirus genome and the time of the last common ancestor of the sequenced SARS strains. Under some common assumptions and justifiable simplifications, a few simple equations incorporating the evolution rate (K) and time of the last common ancestor of the strains (T0) can be deduced. We then implemented the least square method to estimate K and T0 from the dataset of sequences and corresponding times. Monte Carlo stimulation was employed to discuss the results.ResultsBased on 6 strains with accurate dates of host death, we estimated the time of the last common ancestor to be about August or September 2002, and the evolution rate to be about 0.16 base/day, that is, the SARS coronavirus would on average change a base every seven days. We validated our method by dividing the strains into two groups, which coincided with the results from comparative genomics.ConclusionThe applied method is simple to implement and avoid the difficulty and subjectivity of choosing the root of phylogenetic tree. Based on 6 strains with accurate date of host death, we estimated a time of the last common ancestor, which is coincident with epidemic investigations, and an evolution rate in the same range as that reported for the HIV-1 virus.

AN ITERATIVE ALGORITHM TO QUANTIFY FACTORS INFLUENCING PEPTIDE FRAGMENTATION DURING TANDEM MASS SPECTROMETRY

In protein identification by tandem mass spectrometry, it is critical to accurately predict the theoretical spectrum for a peptide sequence. To date, the widely-used database searching methods adopted simple statistical models for predicting. For some peptide, these models usually yield a theoretical spectrum with a significant deviation from the experimental one. In this paper, in order to derive an improved predicting model, we utilized a non-linear programming model to quantify the factors impacting peptide fragmentation. Then, an iterative algorithm was proposed to solve this optimization problem. Upon a training set of 1803 spectra, the experimental result showed a good agreement with some known principles about peptide fragmentation, such as the tendency to cleave at the middle of peptide, and Pros preference of the N-terminal cleavage. Moreover, upon a testing set of 941 spectra, comparison of the predicted spectra against the experimental ones showed that this method can generate reasonable predictions. The results in this paper can offer help to both database searching and de novo methods.

Phylogeny of SARS-CoV as inferred from complete genome comparison

SARS-CoV, as the pathogeny of severe acute respiratory syndrome (SARS), is a mystery that the origin of the virus is still unknown even a few isolates of the virus were completely sequenced. To explore the genesis of SARS-CoV, the FDOD method previously developed by us was applied to comparing complete genomes from 12 SARS-CoV isolates to those from 12 previously identified coronaviruses and an unrooted phylogenetic tree was constructed. Our results show that all SARS-CoV isolates were clustered into a clique and previously identified coronaviruses formed the other clique. Meanwhile, the three groups of coronaviruses depart from each other clearly in our tree that is consistent with the results of prevenient papers. Differently, from the topology of the phylogenetic tree we found that SARS-CoV is more close to group 1 within genus coronavirus. The topology map also shows that the 12 SARS-CoV isolates may be divided into two groups determined by the association with the SARS-CoV from the Hotel M in Hong Kong that may give some information about the infectious relationship of the SARS.

Using a combination of whole-exome sequencing and homozygosity mapping to identify a novel mutation of SCARB2

To the Editor : Progressive myoclonus epilepsy (PME) is a heterogeneous disorder associated with diverse clinical features and causative genes. When the clinical manifestations do not fit the canonical model, it becomes exceedingly difficult to screen all the known genetic mutations that can cause PME, let alone those that have yet to be revealed. We focused on two patients of related parents with action myoclonus and seizures. Patient 1 (the proband, II:5) was the third child of parents who were related in the third degree of consanguinity (Fig. 1c). She developed tremor in her two hands when writing or fetching things at the age of 21. A gait disorder developed at the age of 22. Since then, she fell easily, especially when scared. The same year, she developed dysarthria and drinking cough. At age 25, she could not walk without aid. In February 2009, when the patient was 25 years old, she suffered a generalized tonic–clonic seizure. Generalized seizures were recurrent since that time, averaging 2–3 times per month. The symptoms could not be controlled even when taking sodium valproate 400 mg t.i.d. However, her intelligence was intact. The patient underwent several examinations. The results of brain MRI scan, electromyography, cerebrospinal fluid examination and renal function were normal. Twenty-four-hour video electroencephalography (EEG) revealed no paradoxical discharge. Brainstem auditory-evoked responses indicated minor bilateral impairment, and the somatosensory-evoked potential and motor-evoked potential were normal. Patient 2 (II:4) was the elder sister of Patient 1. She was in good health until the age of 27, when she developed tremor in her hands. Her action myoclonus, gait problems and dysarthria appeared successively and have progressed in recent years. Now, at age 34, she was able to walk a short distance with aid, and her intelligence was preserved. Unlike her sister, she did not suffer from seizures. The results of her examinations were comparable with her sister’s. To locate the causative mutation, whole-exome sequencing was performed using genomic DNA from Patients 1 and 2. Given that their parents were related, we focused on homozygosity for the same recessive mutant allele and narrowed our range to 23 SNPs and 35 indels. Because disease-linked variants are reported to be concentrated in homozygous regions longer than 5 Mb, the data from whole-exome sequencing were examined for large stretches of homozygous regions of length 5 or more Mb (1). Only two homozygous regions that fulfilled our selection criteria were identified. After comparing the SNPs and indels with the homozygosity regions, we finally identified the homozygous nonsense mutation (c.1270 C>T, p. R424X) in exon 11 of SCARB2 gene which was co-segregating within the family. The siblings’ parents and their older brother were all carriers of the heterozygous mutation with normal phenotypes, as were the children of Patient 1 and her brother (III:1, III:2, III:3). The novel mutation was undetected in nine other PME patients and 500 normal controls using Sanger sequencing (Fig. 1a). To explain the clinical heterogeneity of the affected siblings despite the identical mutation, we examined data from whole-exome sequencing for possible mutations in epilepsy-related genes. A heterozygous mutation (c.1286G>A, p.C429Y) was detected in another epilepsy-related gene, KCNQ2 , in the affected sibling with frequent seizures but was not detected in her older sister without seizures (Fig. 1b). This mutation was inherited from their father (I:1) and absent in 500 normal controls. This is the first report of PME caused by a SCARB2 mutation in China. To date, <20 PME families with SCARB2 mutations have been reported and 16 distinct mutations have been identified worldwide (Fig. 1d). Unlike most other cases that have been reported, our patients had a relatively late age of onset (2, 3). Whole-exome sequencing, combined with homozygosity mapping, is a powerful way of reducing the number of candidate genes. This helped us to attain a clinical diagnosis via molecular diagnosis. This is very useful for diseases such as PME where diagnosis is challenging. The exact genetic diagnoses will lay a solid foundation for further functional study and treatment. In summary, we successfully identified a novel mutation in SCARB2 as a cause of PME and a mutation in KCNQ2 which might impact the phenotype of the