Different Circulation Pattern of Multiple Respiratory Viruses in Southern China During the COVID-19 Pandemic.

China implemented stringent non-pharmaceutical interventions (NPIs) in spring 2020, which has effectively suppressed SARS-CoV-2. In this study, we utilized data from routine respiratory virus testing requests from physicians and examined circulation of 11 other respiratory viruses in Southern China, from January 1, 2018 to December 31, 2020. A total of 58,169 throat swabs from patients with acute respiratory tract infections (ARTIs) were collected and tested. We found that while the overall activity of respiratory viruses was lower during the period with stringent NPIs, virus activity rebounded shortly after the NPIs were relaxed and social activities resumed. Only influenza was effectively suppressed with very low circulation which extended to the end of 2020. Circulation of other respiratory viruses in the community was maintained even during the period of stringent interventions, especially for rhinovirus. Our study shows that NPIs against COVID-19 have different impacts on respiratory viruses.

A targeted gene capture next-generation sequencing panel for genetic screening of newborns.

OBJECTIVE: The application of next-generation sequencing (NGS) will greatly promote the screening and diagnosis of genetic diseases. This study aimed to implement and validate a targeted NGS panel for genetic screening of over fifty types of genetic disorders in newborns. METHODS: A targeted gene panel consisting of 104 known genes related to genetic diseases with a target size of 347.8 kb was designed. Genes were selected through reference to databases including HGMD, OMIM, GeneReviews®, and Genetic Home Reference, and the latest peer-reviewed publications associated with the genetics of hereditary diseases. RESULTS: The average coverage for all targeted exons was 596X, and the mean targeted region coverage of 1X, 10X, 20X and 50X reads for each sample were 99.8%, 99.2%, 98.8%, and 95.3%, respectively. The panel showed 100% consistency in detecting 8 pathogenic insertion/deletion (indels) variants ranging from 1 to 16 bp in size and 20 pathogenic single-nucleotide variations (SNVs) across 32 samples previously confirmed by Sanger sequencing. CONCLUSIONS: A dried blood spot (DBS)-based targeted NGS panel for efficient genetic screening of a wide variety of genetic diseases in newborns was developed and evaluated. Furthermore, our panel will contribute to providing accurate diagnosis for genetic disorders and will be helpful for gene therapy for specific diseases.

Genetic screening involving 101 hot spots for neonates not passing newborn hearing screening and those random recruited in Dongguan.

In order to investigate essential molecular causes for hearing loss and mutation frequency of deafness-related genes, 1315 newborns who did not pass the Newborn Hearing Screening (NHS) (audio-no-pass) and 1000 random-selected infants were subjected to detection for 101 hotspot mutations in 18 common deafness-related genes. Totally, 23 alleles of 7 deafness genes were detected out. Significant difference (χ2 = 25.320, p = 0.000) existed in causative mutation frequency between audio-no-pass group (81/1315, 6.160%) and random-selected cohort (18/1000, 1.80%). Of the genes detected out, GJB2 gene mutation was with significant difference (χ2 = 75.132, p = 0.000) between audio-no-pass group (417/1315, 31.711%) and random-selected cohort (159/1000, 15.900%); c.109G > A was the most common allele, as well as the only one with significantly different allele frequency (χ2 = 79.327, p = 0.000) between audio-no-pass group (392/1315, 16.84%) and random-selected cohort (140/1000, 7.55%), which suggested c.109G > A mutation was critical for newborns' hearing loss. This study performed detection for such a large scale of deafness-associated genes and for the first time compared mutations between audio-no-pass and random-recruited neonates, which not only provided more reliable DNA diagnosis result for medical practioners and enhanced clinical care for the newborns, but gave more accurate estimation for mutation frequency.

A novel mutation in the SLC26A4 gene in a Chinese family with non-syndromic hearing loss and enlarged vestibular aqueduct.

OBJECTIVES: To identity the genetic causes of hearing loss in a Han Chinese family with enlarged vestibular aqueduct syndrome. METHODS: Multiplex PCR technology combined with Ion Torrent™ next-generation sequencing technology was used to search for pathogenic mutations. A group of 1500 ethnically-matched normal hearing subjects screened for mutations in deafness-related genes using the same method in previously studied were included as a control. RESULTS: The proband and his little sister suffered from typical features of sensorineural hearing loss with enlarged vestibular aqueduct (EVA). Both subjects harbored two compound heterozygous mutations in the SLC26A4 gene. A novel mutation named c.2110 G > C (p.Glu704Gln) in exon 19 and another previously reported mutation c.1673 A > T (p.Asn558Ile) were identified. These mutations were carried in the heterozygous state by the parents and therefore co-segregated with the genetic disease. The c.2110 G > C (p.Glu704Gln) mutation was absent in 1500 healthy newborns. Protein alignment indicated high evolutionary conservation of the p.E704 residue, and this mutation was predicted by online tools to be damaging and deleterious. CONCLUSION: This study demonstrates that the novel mutation c.2110 G > C (p.Glu704Gln) in compound heterozygosity with c.1673 A > T (p.Asn558Ile) in the SLC26A4 gene corresponds to the EVA in this family. Our study will provide a foundation for elucidating the SLC26A4-related mechanisms of hearing loss.

A novel variant in the CDH23 gene is associated with non-syndromic hearing loss in a Chinese family.

OBJECTIVES: To explore the pathogenic causes of a proband who was diagnosed with non-syndromic hearing loss. METHODS: We performed targeted capture of 159 known deafness-related genes and next-generation sequencing in the proband who was tested negative for the twenty hotspot variants in four common deafness-related genes(GJB2, GJB3, SLC26A4 and MTRNR1); Clinical reassessments, including detailed audiological and ocular examinations were performed in the proband and his normal parents. RESULTS: We identified a novel heterozygous variant of CDH23:c.4567A > G (p.Asn1523Asp) in exon 37 (NM_022124), in conjunction with a reported mutation of CDH23:c.5101G > A (p.Glu1701Lys) in exon 40, to be a potentially pathogenic compound heterozygosity in the proband. The unaffected father has a heterozygous variant of CDH23:c.4567A > G, and the normal mother has another heterozygous variant, CDH23:c.5101G > A. The novel variant was absent in the 1000 Genomes Project. The clinical reassessments revealed binaural profound sensorineural hearing loss (DFNB12) without retinitis pigmentosa in the proband. CONCLUSIONS: This study demonstrates that the novel variant c.4567A > G (p.Asn1523Asp) in compound heterozygosity with c.5101G > A (p. Glu1701Lys) in the CDH23 gene is the main cause of DFNB12 in the proband. Simultaneously, this study provides a foundation to further elucidate the CDH23-related mechanisms of DFNB12.

A novel mutation in the MYO7A gene is associated with Usher syndrome type 1 in a Chinese family.

OBJECTIVES: We aimed to investigate the genetic causes of hearing loss in a Chinese proband with autosomal recessive congenital deafness. METHODS: The targeted capture of 159 known deafness genes and next-generation sequencing were performed to study the genetic causes of hearing loss in the Chinese family. Sanger sequencing was employed to verify the variant mutations in members of this family. RESULTS: The proband harbored two mutations in the MYO7A gene in the form of compound heterozygosity. She was found to be heterozygous for a novel insertion mutation c.3847_3848 ins TCTG (p.N1285LfsX24) in exon 30 and for the known mutation c.2239_2240delAG (p.R747S fsX16)in exon 19. The novel mutation was absent in the 1000 Genomes Project. These variants were carried in the heterozygous state by the parents and were therefore co-segregated with the genetic disease. Clinical re-assessment, including detailed audiologic and ocular examinations, revealed congenital deafness and retinitis pigmentosa in the proband. Collectively, the combination of audiometric, ophthalmologic and genetic examinations successfully confirmed the phenotype of Usher syndrome type 1 (USH1). CONCLUSION: This study demonstrates that the novel mutation c.3847_3848insTCTG (p. N1285LfsX24) in compound heterozygosity with c.2239_2240delAG in the MYO7A gene is the main cause of USH1 in the proband. Our study expands the mutational spectrum of MYO7A and provides a foundation for further investigations elucidating the MYO7A-related mechanisms of USH1.

A novel missense mutation in the SLC26A4 gene causes nonsyndromic hearing loss and enlarged vestibular aqueduct.

OBJECTIVES: We aimed to investigate the genetic causes of hearing loss in a Chinese proband with nonsyndromic hearing loss and enlarged vestibular aqueduct syndrome. METHODS: We conducted clinical and genetic evaluations in a deaf proband and his normal-hearing parents. Multiplex PCR technology combined with Ion Torrent™ next-generation sequencing technology was used to detect the pathogenic mutations. As a control, a group of 1500 previously studied healthy newborns from the same ethnic background were subjected to deafness gene screening using the same method as in our previous study. RESULTS: The proband harbored two mutations in the SLC26A4 gene in the form of compound heterozygosity. He was found to be heterozygous for a novel mutation named c.1742 G > T (p.Arg581Met) in exon 13 and for the known mutation c.589 G > A (p.Gly197Arg). These variants were carried in the heterozygous state by the parents and therefore co-segregated with the genetic disease. The c.1742 G > T (p.Arg581Met) mutation was absent in 1500 healthy newborns. Protein alignment indicated high evolutionary conservation of the p.R581 residue, and this mutation was predicted by PolyPhen-2 and other online tools to be damaging. CONCLUSION: This study demonstrates that the novel mutation c.1742 G > T (p.Arg581Met) in compound heterozygosity with c.589 G > A in the SLC26A4 gene is the main cause of deafness in a family clinically diagnosed with enlarged vestibular aqueduct (EVA). Our study will provide a basic foundation for further investigations to elucidate the SLC26A4-related mechanisms of hearing loss.