Atypical presentations in an RTD patient and report of novel SLC52A3 and SLC52A2 mutations.

INTRODUCTION: Riboflavin Transporter Deficiency (RTD) is a rare neurological disorder characterized by pontobulbar palsy, hearing loss, and motor cranial nerve involvement. SLC52A3 and SLC52A2 mutations are causes of RTD. SLC52A2 mutations are usually found in childhood onset cases. Fifteen Iranian RTD diagnosed patients without SLC52A2 mutations have been previously described. We aimed to identify causative mutations in two childhood cases. METHODS: We recruited patients with diagnosis of BVVL. Comprehensive clinical evaluations were performed on the patients. SLC52A3 and SLC52A2 genes were PCR-amplified and Sanger sequenced. Candidate disease causing variations were screened for segregation with disease status in the respective families and control individuals. RESULTS: A novel homozygous SLC52A3 mutation (p.Met1Val) and a heterozygous SLC52A2 mutation (p.Ala288Val) were both observed in one proband with typical RTD presentations. The aggregate of presentations in the early stages of disease in the second patient that included weakness in the lower extremities, absence of bulbar or hearing defects, prominent sensory polyneuropathy as evidenced in electrodiagnostic studies, and absence of sensory symptoms including sensory ataxia did not prompt immediate RTD diagnosis. Dysarthria and decreased hearing manifested later in the disease course. A novel homozygous SLC52A2 (p.Val314Met) mutation was identified. CONCLUSION: A literature search found recent reports of other atypical RTD presentations. These include MRI findings, speech understanding difficulties accompanied by normal hearing, anemia, and left ventricular non-compaction. Knowledge of unusual presentations lessens the chance of misdiagnosis or delayed RTD diagnosis which, in light of favorable effects of riboflavin supplementation, is of immense importance.

Identification of a mutation in TNRC18 in a patient with clinical features of Fazio-Londe disease.

Fazio-Londe disease and Brown-Vialetto-Van Laere syndrome are rare related neurological disorders. Although SLC52A3 and SLC52A2 that encode riboflavin transporters are their only known causative genes, many patients without mutations in these genes have been reported. Clinical and genetic data of a patient with features suggestive of Fazio-Londe disease are presented. Neurological examination revealed significant involvement of cranial nerves and weakness in the lower extremities. Pontobulbar presentations were prominent. EDX study suggested motor neuronopathy. Hearing was normal. She was diagnosed with FL disease. Response to riboflavin supplementation was not favorable. The patient's pedigree suggested recessive inheritance. SLC52A3 and SLC52A2 were screened and mutations were not observed. Results of exome sequencing and segregation analysis suggested that a mutation in TNRC18 is a candidate cause of disease in the patient. The three dimensional structure of the TNRC18 protein was predicted and it was noted that its two conserved domains (BAH and Tudor) interact and that the valine residue affected by the mutation is positioned close to both domains. A mutation in TNRC18 is cautiously reported as the possible cause of FL disease in the patient. The finding warrants further inquiries on TNRC18 about which little is presently known.

A comparison between the effects of two liposome-encapsulated bevacizumab formulations on ocular neovascularization inhibition.

Bevacizumab (BVZ), an anti-VEGF antibody, has demonstrated reliable outcomes in the treatment of irritating ocular neovascularization. Frequent intravitreal injections are necessitated due to rapid clearance and short local accessibility. We recruited liposome as a highly prevailing drug delivery system to enhance drug availability. Two liposome formulations were characterized and their in vitro stability was analyzed. The toxicity of the formulations on some ocular cell lines was also evaluated. In addition, the anti-angiogenic effects of formulations were examined. Drug permeation was measured across ARPE-19 and HCE cell lines as in vitro cellular barrier models. Results revealed that NLP-DOPE-BVZ acquired high stability at 4 °C, 24 °C, and 37 °C for 45 days. It also showed more capacity to entrap BVZ in NLP-DOPE-BVZ (DEE% 69.1 ± 1.4 and DLE% 55.66 ± 1.15) as compared to NLP-BVZ (DEE% 43.57 ± 14.64, and DLE% 37.72 ± 12.01). Although both formulations inhibited the migration and proliferation of HUVECs, NLP-DOPE-BVZ was more effective at inhibiting angiogenesis. Furthermore, NLP-DOPE-BVZ better crossed our established barrier cellular models. Based on the findings, the inclusion of DOPE in NLPs has significantly enhanced the features of drug carriers. This makes them a potential candidate for treating ocular neovascularization and other related ailments.

Adding the Molecular Diversity Information of the Common Fouling Barnacle Amphibalanus amphitrite (Darwin, 1854) (Crustacea: Cirripedia) from the Persian Gulf and Gulf of Oman to the Global Diversity Pattern.

The balanid barnacle, Amphibalanus amphitrite, is known as one of the most common fouling species in the world. A phylogenetic study using material from around the world recovered three distinct clades for this species. Material from the Persian Gulf (PG) and the Gulf of Oman (GO) were not included in that survey. In the present study, we aimed to assess the genetic diversity of the balanid barnacles of these two gulfs and to evaluate their phylogeography. In total, 94 COI DNA sequences were obtained from the PG and the GO material. Most of these sequences clustered into a single clade, corresponding to clade I of the previous global study. However, two sequences, one from the PG and one from the GO, fell into a separate clade corresponding to clade III of the previous study. These two gulfs share some common haplotypes, but host several unique ones that are separated from the most common haplotype mainly by a single mutation. Based on various indices, the genetic diversity of the PG material was higher than that of the GO. Low values of ΦST show a regular gene flow among the stations and the two gulfs. The Bayesian skyline plots and the mismatch distribution analyses both showed signs of a recent population expansion in the PG and the GO. We also modeled the potential distribution areas for A. amphitrite to reveal the separate suitable habitats for the clades. The current phylogeographic status and genetic diversity of A. amphitrite in the PG and GO appears to have been shaped by both historical events and recent human activities.

Identification of UBA1 as the causative gene of an X-linked non-Kennedy spinal-bulbar muscular atrophy.

BACKGROUND AND PURPOSE: Spinal-bulbar muscular atrophy (SBMA) (Kennedy's disease) is a motor neuron disease. Kennedy's disease is nearly exclusively caused by mutations in the androgen receptor encoding gene (AR). The results of studies aimed at identification of the genetic cause of a disease that best approximates SBMA in a pedigree (four patients) without mutations in AR are reported. METHODS: Clinical investigations included thorough neurological and non-neurological examinations and testing. Genetic analysis was performed by exome sequencing using standard protocols. UBA1 mutations were modeled on the crystal structure of UBA1. RESULTS: The clinical features of the patients are described in detail. A missense mutation in UBA1 (c.T1499C; p.Ile500Thr) was identified as the probable cause of the non-Kennedy SBMA in the pedigree. Like AR, UBA1 is positioned on chromosome X. UBA1 is a highly conserved gene. It encodes ubiquitin-like modifier activating enzyme 1 (UBA1) which is the major E1 enzyme of the ubiquitin-proteasome system. Interestingly, UBA1 mutations can also cause infantile-onset X-linked spinal muscular atrophy (XL-SMA). The mutation identified here and the XL-SMA causative mutations were shown to affect amino acids positioned in the vicinity of UBA1's ATP binding site and to cause structural changes. CONCLUSION: UBA1 was identified as a novel SBMA causative gene. The gene affects protein homeostasis which is one of most important components of the pathology of neurodegeneration. The contribution of this same gene to the etiology of XL-SMA is discussed.

Identification of RNF13 as cause of recessively inherited ALS in a multi-case pedigree.

BACKGROUND: Amyotrophic lateral sclerosis (ALS) is the most common motor neuron disease. The approximately 50 known ALS-associated genes do not fully explain its heritability, which suggests the existence of yet unidentified causative genes. We report results of studies aimed at identification of the genetic cause of ALS in a pedigree (three patients) without mutations in the common ALS-causative genes. METHODS: Clinical investigations included thorough neurological and non-neurological examinations and testings. Genetic analysis was performed by exome sequencing. Functional studies included identification of altered splicing by PCR and sequencing, and mutated proteins by western blot analysis. Apoptosis in the presence and absence of tunicamycin was assessed in transfected HEK293T cells using an Annexin-PE-7AAD kit in conjunction with flow cytometry. RESULTS: Clinical features are described in detail. Disease progression in the patients of the pedigree was relatively slow and survival was relatively long. An RNF13 mutation was identified as the cause of the recessively inherited ALS in the pedigree. The gene is highly conserved, and its encoded protein (RING finger protein 13) can potentially affect various neurodegenerative-relevant functions, including protein homeostasis. The RNF13 splice site mutation caused expression of two mis-spliced forms of RNF13 mRNA and an aberrant RNF13 protein, and affected apoptosis. CONCLUSION: RNF13 was identified as a novel causative gene of recessively inherited ALS. The gene affects protein homeostasis, which is one of most important components of the pathology of neurodegeneration. The contribution of RNF13 to the aetiology of another neurodegenerative disease is discussed.

Multi-stage analysis of FOXM1, PYROXD1, hTERT, PPARA, PIM3, BMI1 and MCTP1 expression patterns in colorectal cancer.

Aim: To explore biomarkers with a tumor stage-dependent expression pattern in patients with colorectal cancer (CRC). Background: The fourth most common cancer in the world is colorectal cancer (CRC). A variation in the gene expression rate is a common change in cancers initiation and the accumulation of these variation changes the behavior of normal cells and turns them into cancer cells. Methods: Real-time RT-PCR was used to investigate the expression patterns of the FOXM1, PYROXD1, hTERT, BMI, PPARA, PIM3 and MCTP1 genes in 54 patients with stage I to IV CRC and their relation with clinicopathological features of CRC were analyzed. Results: FOXM1, hTERT and MCTP1 genes are overexpressed in CRC tumor tissues when compared to normal adjacent tissues in all the stages. Results: FOXM1, PYROXD1, hTERT, PIM3, BMI1, PPARA and MCTP1 had-stage dependent expression. Investigation of the association between clinicopathological features and expression pattern of the studied genes revealed; a) a significant relationship between FOXM1 gene expression level and tumor stage, tumor size and lymph node involvement, b) a considerable association between alterations in PPARA and PIM3 expression and lymph node involvement, c) a notable correlation between hTERT expression level and the tumor stage and d) a strong correlation between MCTP1 expression and patient's age only. Conclusion: Our study indicates that expression profiles of these genes either individually or together can be applied as potential biomarkers for prognosis of CRC.

Erratum: Carrier Status for p.Gly61Glu and p.Arg368His CYP1B1 Mutations Causing Primary Congenital Glaucoma in Iran.

[This corrects the article DOI: 10.18502/jovr.v16i4.9747.].

Genetic screening of TGFBI in Iranian patients with TGFBI-associated corneal dystrophies and a meta-analysis of global variation frequencies.

PURPOSE: Transforming growth factor beta-induced (TGFBI)-associated corneal dystrophies (CDs) are a clinically heterogeneous group of CDs caused by mutations in the TGFBI gene. Nucleotide sequences encoding two arginine residues at positions 124 and 555 in TGFBI protein are mutation hotspots. We screened regions of TGFBI that include the hotspots in a cohort of Iranian patients with TGFBI-associated CDs. We also performed a meta-analysis for frequencies of all reported TGFBI mutations. METHODS: Twenty-four TGFBI-associated CD-diagnosed patients were recruited. Exons 4 and 12 of TGFBI were amplified by the polymerase chain reaction and sequenced by Sanger protocol. A meta-analysis on reported TGFBI sequence data was done by reviewing all published relevant articles available in NCBI. RESULTS: Twenty-two out of 24 patients had mutations in exons 4 or 12 of TGFBI. The most frequent mutations were p.Arg124Cys, p.Arg124His, and p.Arg555Trp; each of these was found in six families. Three other missense mutations including p.Arg555Gln, p.Ile522Asn, and p.Ala546Thr were also identified. The data suggested a fairly tight genotype/phenotype correlation for the most common CDs. Literature review evidenced that the reported mutations affected less than 30% of the amino acids of the TGFBI protein and that p.Arg124His, p.Arg124Cys, p.Arg555Trp, p.Arg124Leu, p.Arg555Gln, and p.His626Arg were the most frequent mutations. CONCLUSION: TGFBI mutation profile of Iranian patients is very similar to that of the rest of the world. The meta-analysis confirmed the worldwide prevalence of p.Arg124 and p.Arg555, showed that p.His626Arg is also relatively frequent, and evidenced the value of screening exons 4 and 12 of TGFBI.

Mutation Screening of Six Exons of ABCA4 in Iranian Stargardt Disease Patients.

PURPOSE: Stargardt disease type 1 (STGD1) is a recessively inherited retinal disorder that can cause severe visual impairment. ABCA4 mutations are the usual cause of STGD1. ABCA4 codes a transporter protein exclusively expressed in retinal photoreceptor cells. The genecontains 50 exons. Mutations are most frequent in exons 3, 6, 12, and 13, and exons 10 and 42 each contain two common variations. We aimed to screen these exons for mutations in Iranian STGD1 patients. METHODS: Eighteen STGD1 patients were recruited for genetic analysis. Diagnosis by retina specialists was based on standard criteria, including accumulation of lipofuscin. The six ABCA4 exons were PCR amplified and sequenced by the Sanger method. RESULTS: One or more ABCA4-mutated alleles were identified in 5 of the 18 patients (27.8%). Five different mutations including two splice site (c.1356+1G > A and c.5836-2A > G) and three missense mutations (p.Gly1961Glu, p.Gly1961Arg, and p.Gly550Arg) were found. The p.Gly1961Glu mutation was the only mutation observed in two patients. CONCLUSION: As ABCA4 mutations in exons 6, 12, 10, and 42 were identified in approximately 25% of the patients studied, these may be appropriate exons for screening projects. As in other populations, STDG1 causative ABCA4 mutations are heterogeneous among Iranian patients, and p.Gly1961Glu may be relatively frequent.

Evolution of the SARS-CoV-2 genome and emergence of variants of concern.

The high transmission and mortality rates associated with SARS-CoV-2 have led to tragic consequences worldwide. Large-scale whole-genome sequencing of the SARS-CoV-2 genome since its identification in late 2019 has identified many sequence changes and the emergence of novel strains, each described by co-segregation of a particular set of sequence variations. Variants designated G, alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617.2) are important lineages that emerged sequentially and are considered variants of concern. A notable feature of the last four, each of which ultimately evolved from clade G, is the large number (≥ 20) of co-segregating sequence variations associated with them. Several variations are in the spike gene, and some variations are shared among or between strains. Meanwhile, observation of recurrent infections with the same or different SARS-CoV-2 lineages has raised concerns about the duration of the immune responses induced by the initial infection or the vaccine that was administered. While the alpha strain is sensitive to immune responses induced by earlier strains, the beta, gamma, and delta strains can escape antibody neutralization. Apart from random replication errors, intra-host RNA editing, chronic infections, and recombination are processes that may promote the accumulation of sequence changes in the SARS-CoV-2 genome. The known contribution of recombination to coronavirus evolution and recent data pertaining to SARS-CoV-2 suggest that recombination may be particularly important. Continued surveillance of the SARS-CoV-2 genome is imperative.

Carrier Status for p.Gly61Glu and p.Arg368His CYP1B1 Mutations Causing Primary Congenital Glaucoma in Iran.

PURPOSE: To estimate carrier frequencies of CYP1B1 mutations p.Gly61Glu and p.Arg368His, respectively, in Talesh and the east of Guilan province in Iran with a maximum error of 2%. Previously, it was shown that these CYP1B1 mutations may be relatively prevalent in these regions. METHODS: Population-based screenings were performed. DNA was extracted from saliva samples of 1036 individuals from Talesh and 3029 individuals from the east of Guilan. P.Gly61Glu and p.Arg368His screenings were performed, respectively, by RFLP and ARMS-based PCR protocols. For confirmation, the DNA of individuals with mutations was sequenced using the Sanger protocol. RESULTS: Nine individuals from Talesh (0.86%; 95%CI: 0.45-1.64%) carried the p.Gly61Glu mutation, and 73 from the east of Guilan (2.41%; 95%CI: 1.91-3.04%) carried p.Arg368His. There was no significant difference in frequencies between urban and rural regions of the various cities, nor among four cities within the east of Guilan. CONCLUSION: The frequencies of p.Gly61Glu carriers in Talesh and of p.Arg368His carriers in the east of Guilan were within the 95% confidence interval of a previous study based on screenings of fewer individuals. The reliability of the recent estimates is higher, as the confidence interval for p.Gly61Glu decreased from 6.5% to 1.19% and the interval for p.Arg368His decreased from 4% to 1.13%. Based on the new findings, the maximum expected frequency of p.Gly61Glu carriers in Talesh is 1.64%, and of p.Arg368His carriers in the east of Guilan is 3%. The need for performing premarital screenings in the respective cities can be evaluated.

Prenatal diagnosis of primary congenital glaucoma and histopathological features in a fetal globe with cytochrome p4501B1 mutations.

BACKGROUND/OBJECTIVES: This study aims to report the developmental and histopathological features of ocular tissues from an electively aborted human fetus with mutations in cytochrome p4501B1, and thus predisposed to primary congenital glaucoma in comparison to an age-matched healthy fetal globe. SUBJECTS/METHODS: Both eyes of two 17-week gestational aged fetuses, the first with CYP1B1 mutations and the second as healthy control fetus, were studied. Hematoxylin and eosin, Periodic acid-Schiff, Gomori's trichrome, and Verhoeff-Van Gieson staining protocols in addition to immunohistochemistry staining using anti-cytochrome p4501B1, anti-fibrillin-1, and anti-4-hydroxy-2-nonenal antibodies, as primary antibodies, were performed to assess the effect of the mutations on tissue development, cytochrome p4501B1 protein expression, extracellular matrix structure, and oxidative stress in the developing fetus eye. Quantitative analyses were performed using ImageJ software. Student's t-test was used for statistical analysis and P-values <0.05 were considered as significant. RESULTS: Delayed development in ocular tissues, decreased expression of cytochrome p4501B1 protein, irregular extracellular matrix structure, and increased oxidative stress biomarker were evident in the ocular tissues of the fetus with cytochrome p4501B1 mutations as compared to a normal globe from an age-matched fetus. CONCLUSION: To the best of our knowledge, this is the first report of prenatal diagnosis of primary congenital glaucoma. We also describe histopathological changes in the primary congenital glaucoma-affected globes revealing the effect of cytochrome p4501B1 deficiency on ocular tissues during early fetal development contributing to the glaucoma phenotype.

Study on SARS-CoV-2 strains in Iran reveals potential contribution of co-infection with and recombination between different strains to the emergence of new strains.

We aimed to describe SARS-CoV-2 strains in Iranians from nine distributed cities infected during two months expanding late 2020 and early 2021 by genotyping known informative single nucleotide in five PCR amplicons. Two variants associated with haplotype H1 (clade G) and nine additional variants associated with other haplotypes were genotyped, respectively, in RNA isolates of 244 and 85 individuals. The variants associated with the H1a (GR) and H1b (GH) haplotypes were most prevalent, indicating a significant change in infection pattern with passage of time. The most important findings were that recombinant genomes and co-infection, respectively, were surmised in 44.7% and 12.9% of the samples extensively genotyped. Partners of many of the recombinations were relatively common strains. Co-existing viruses were among those currently circulating in Iran. In addition to random mutations, co-infection with different existing strains and recombination between their genomes may significantly contribute to the emergence of new SARS-CoV-2 strains.

A case of adult onset Sandhoff disease that mimics Brown-Vialetto-Van Laere syndrome.

Sandhoff disease is a rare fatal infantile neurologic disorder. Adult onset Sandhoff is even rarer. Variability of clinical features in adult onset Sandhoff patients and overlaps between these and features of other neurologic diseases have sometimes led to mis-diagnosis. We describe an adult onset Sandhoff disease affected individual whose clinical presentation were also consistent with the Brown-Vialetto-Van Laere syndrome (BVVL) diagnosis. Screening of BVVL-causing genes, SLC52A3 and SLC52A2, did not identify candidate disease-causing mutations, but exome sequencing revealed compound heterozygous mutations in the known Sandhoff disease-causing gene, HEXB. Decreased blood hexosaminidase activity and evidence of cerebellar atrophy confirmed Sandhoff disease diagnosis. To the best of our knowledge, this is the first report of a Sandhoff disease case that mimics BVVL and that presents with prominent cranial nerve involvement. For differential diagnosis, measurement of hexosaminidase activity and MRI should quickly be performed. Genetic analysis can be done for confirmation of diagnosis.

World-wide tracking of major SARS-CoV-2 genome haplotypes in sequences of June 1 to November 15, 2020 and discovery of rapid expansion of a new haplotype.

Earlier, 13 haplotype groups defined by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequence variations were identified in 2790 sequences available in March 2020. Also, 23403A>G that causes p. Asp614Gly in the spike protein and is one of the defining variations of the haplotype group H1, was becoming increasingly prevalent. As a follow-up, 74922 SARS-CoV-2 sequences retrieved from individuals infected in June 1 to November 15 were analyzed. Consistent with the reports on 23403A>G, H1 haplotype frequency increased world-wide; among August to November sequences, only 0.3% were associated with non-H1 haplotypes. This finding prompted assessment of H1 sub-haplotypes among the sequences of the later stage of the coronavirus disease 2019 pandemic. The distribution of the sub-haplotypes differed in different regions, but 98.4% of the sequences were associated with five H1 sub-haplotypes. One of these had not been previously observed and had emerged in Europe by June 2020. The most important finding of the present study is identification of this new sub-haplotype (H1r) and finding evidence that suggest it may have a high potential for expansion. Its frequency had reached 10%-90% in various countries/territories of Europe by the end of September. The new sub-haplotype is defined by seven sequence variations, one of which causes Ala222Val in the spike protein.

Putative founder effect in the Polish, Iranian and United States populations for the L144S SOD1 mutation associated with slowly uniform phenotype of amyotrophic lateral sclerosis.

Mutations in SOD1 cause approximately 12-25% of familial ALS and ≈2% of apparently sporadic ALS cases. Clinical phenotypes linked to SOD1 mutations are heterogeneous and intra-familial variability of the clinical phenotype is frequently observed. SOD1 L144S mutation, identified also in Brazil, Iran and United States, is the second most frequent mutation among ALS patients in Poland. So far, 10 FALS pedigrees with SOD1 L144S mutation have been reported worldwide. The aim of the study was to establish the origin of SOD1 L144S mutation in geographically distinct populations. The clinical presentation of the Polish patients was compared with those from the previously reported populations (26 ever-reported patients). Clinically, L144S mutation is associated with both sporadic and familial ALS of relatively slow uniform course, a prevalent onset in the lower limbs, either classic or PMA presentation and a long survival time. Like in the case of other previously described SOD1 mutations, there was an intra-familial heterogeneity and reduced penetrance for ALS was observed. We propose that the L144S SOD1 mutation in the three studied populations has a common founder most likely of Polish origin.

Deep geno- and phenotyping in two consanguineous families with CMT2 reveals HADHA as an unusual disease-causing gene and an intronic variant in GDAP1 as an unusual mutation.

BACKGROUND: Charcot-Marie-Tooth (CMT) disease is a prevalent and heterogeneous peripheral neuropathy. Most patients affected with the axonal form of CMT (CMT2) do not harbor mutations in the approximately 90 known CMT-associated genes. We aimed to identify causative genes in two CMT2 pedigrees. METHODS: Neurologic examination, laboratory tests and brain MRIs were performed. Genetic analysis included exome sequencing of four patients from the two pedigrees. The predicted effect of a deep intronic mutation on splicing was tested by regular and real-time PCR and sequencing. RESULTS: Clinical data were consistent with CMT2 diagnosis. Inheritance patterns were autosomal recessive. Exome data of CMT2-101 did not include mutations in known CMT-associated genes. Sequence data, segregation analysis, bioinformatics analysis, evolutionary conservation, and information in the literature strongly implicated HADHA as the causative gene. An intronic variation positioned 23 nucleotides away from following intron/exon border in GDAP1 was ultimately identified as cause of CMT in CMT2-102. It was shown to affect splicing. CONCLUSION: The finding of a HADHA mutation as a cause of CMT is of interest because its encoded protein is a subunit of the mitochondrial trifunctional protein (MTP) complex, a mitochondrial enzyme involved in long chain fatty acid oxidation. Long chain fatty acid oxidation is an important source of energy for skeletal muscles. The mutation found in CMT2-102 is only the second intronic mutation reported in GDAP1. The mutation in the CMT2-102 pedigree was outside the canonical splice site sequences, emphasizing the importance of careful examination of available intronic sequences in exome sequence data.

Evolution of SARS-CoV-2 genome from December 2019 to late March 2020: Emerged haplotypes and informative Tag nucleotide variations.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes serious disease in humans. First identified in November/December 2019 in China, it has rapidly spread worldwide. We analyzed 2790 SARS-CoV-2 genome sequences from 56 countries that were available on April 2, 2020, to assess the evolution of the virus during this early phase of its expansion. We aimed to assess sequence variations that had evolved in virus genomes, giving the greatest attention to the S gene. We also aimed to identify haplotypes that the variations may define and consider their geographic and chronologic distribution. Variations at 1930 positions that together cause 1203 amino acid changes were identified. The frequencies of changes normalized to the lengths of genes and encoded proteins were relatively high in ORF3a and relatively low in M. A variation that causes an Asp614Gly near the receptor-binding domain of S were found at a high frequency, and it was considered that this may contribute to the rapid spread of viruses with this variation. Our most important findings relate to haplotypes. Sixty-six haplotypes that constitute thirteen haplotype groups (H1-H13) were identified, and 84.6% of the 2790 sequences analyzed were associated with these haplotypes. The majority of the sequences (75.1%) were associated with haplotype groups H1-H3. The distribution pattern of the haplotype groups differed in various geographic regions. A few were country/territory specific. The location and time of emergence of some haplotypes are discussed. Importantly, nucleotide variations that define the various haplotypes and Tag/signature variations for most of the haplotypes are reported. The practical applications of these variations are discussed.

BVVL/ FL: features caused by SLC52A3 mutations; WDFY4 and TNFSF13B may be novel causative genes.

Brown-Vialetto-Van Laere (BVVL) and Fazio-Londe are disorders with amyotrophic lateral sclerosis-like features, usually with recessive inheritance. We aimed to identify causative mutations in 10 probands. Neurological examinations, genetic analysis, audiometry, magnetic resonance imaging, biochemical and immunological testings, and/or muscle histopathology were performed. Mutations in known causative gene SLC52A3 were found in 7 probands. More importantly, only 1 mutated allele was observed in several patients, and variable expressivity and incomplete penetrance were clearly noted. Environmental insults may contribute to variable presentations. Putative causative mutations in other genes were identified in 3 probands. Two of the genes, WDFY4 and TNFSF13B, have immune-related functions. Inflammatory responses were implicated in the patient with the WDFY4 mutation. Malfunction of the immune system and mitochondrial anomalies were shown in the patient with the TNFSF13B mutation. Prevalence of heterozygous SLC52A3 BVVL causative mutations and notable variability in expressivity of homozygous and heterozygous genotypes are being reported for the first time. Identification of WDFY4 and TNFSF13B as candidate causative genes supports conjectures on involvement of the immune system in BVVL and amyotrophic lateral sclerosis.