Prolonged SARS-CoV-2 Infection and Intra-Patient Viral Evolution in an Immunodeficient Child

Article Biochemistry & Molecular Biology

Emergence of unique SARS-CoV-2 ORF10 variants and their impact on protein structure and function

Sk. Sarif Hassan et al.

Summary: The article highlights the potential impact of single and co-occurring mutations in the emerging SARS-CoV-2 ORF10 variants on the severity of the virus and its associated consequences.

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2022)

Add to Collection

Letter Medicine, General & Internal

Characteristics and Outcomes of Hospitalized Patients in South Africa During the COVID-19 Omicron Wave Compared With Previous Waves

Caroline Maslo et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2022)

Add to Collection

Article Medicine, General & Internal

Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study

Nicole Wolter et al.

Summary: According to data analysis from South Africa, individuals infected with the omicron variant have a lower likelihood of hospitalization compared to those infected with non-omicron variants. Furthermore, individuals infected with the omicron variant have a lower odds of severe disease compared to individuals infected with the earlier delta variant.

LANCET (2022)

Add to Collection

Article Microbiology

Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil

Felipe Gomes Naveca et al.

Microbiology Spectrum (2022)

Add to Collection

Article Multidisciplinary Sciences

Whole genome sequencing of SARS-CoV2 strains circulating in Iran during five waves of pandemic

Jila Yavarian et al.

Summary: The whole genome sequencing of SARS-CoV2 in Iran revealed different viral lineages and variants, highlighting the importance of monitoring for timely detection and control of possible variants.

PLOS ONE (2022)

Add to Collection

Article Microbiology

Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication

Carolina Garcia-Vidal et al.

Summary: We report a case of a hematologic patient with prolonged SARS-CoV-2 viral replication, in whom viral mutations emerged after the consecutive use of antivirals and convalescent plasma. The virus accumulated multiple changes in amino acids and nucleotides, including mutations of concern defined by WHO. This finding poses a significant epidemiological threat and clinical challenge.

FRONTIERS IN MICROBIOLOGY (2022)

Add to Collection

Article Medicine, General & Internal

Clinical Characteristics of COVID-19 Patients Infected by the Omicron Variant of SARS-CoV-2

Jianguo Zhang et al.

Summary: This study reported the clinical characteristics and vaccine effectiveness of 169 COVID-19 patients infected with the Omicron variant. The results showed that the virulent effect of the Omicron variant was milder than previous circulating variants, and full vaccination or booster shots were effective in preventing clinical severity.

FRONTIERS IN MEDICINE (2022)

Add to Collection

Article Virology

Recurrent SARS-CoV-2 mutations in immunodeficient patients

Sam A. J. Wilkinson et al.

Summary: Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunodeficient patients are an important source of variation for the virus but are understudied. This study aims to rectify this and study the genomics of this patient group. Spike gene receptor-binding domain and N-terminal domain (NTD) were identified as mutation hotspots, and numerous mutations associated with variants of concern were observed to emerge recurrently. Additionally, a mutation in the envelope gene, T30I, was determined to be the second most frequent recurrently occurring mutation in persistent infections. Many recurrent mutations in immunodeficient individuals are associated with ACE2 affinity, immune escape, or viral packaging optimization.

VIRUS EVOLUTION (2022)

Add to Collection

Review Immunology

COVID-19 in Immunocompromised Hosts: What We Know So Far

Monica Fung et al.

Summary: The COVID-19 pandemic caused by SARS-CoV-2 has led to significant morbidity and mortality globally. The impact of the disease on immunosuppressed patients, such as cancer patients and transplant recipients, remains unclear. Further research is needed to determine the risk of COVID-19 severity and death in immunocompromised patients.

CLINICAL INFECTIOUS DISEASES (2021)

Add to Collection

Article Infectious Diseases

Neutralisation of SARS-CoV-2 lineage P.1 by antibodies elicited through natural SARS-CoV-2 infection or vaccination with an inactivated SARS-CoV-2 vaccine: an immunological study

William M. Souza et al.

Summary: The study aimed to investigate whether isolates of wild-type P.1 lineage SARS-CoV-2 can escape from neutralising antibodies generated by a polyclonal immune response. The results showed that the neutralising capacity against the P.1 isolates was significantly lower than against the lineage B isolate, especially in individuals previously infected with SARS-CoV-2.

LANCET MICROBE (2021)

Add to Collection

Review Biochemistry & Molecular Biology

Structural insights into SARS-CoV-2 proteins

Rimanshee Arya et al.

Summary: The unprecedented scale of the ongoing COVID-19 pandemic has led to an intensive global scientific effort to understand various aspects of the disease in a short period. More than three hundred experimental structures of SARS-CoV-2 proteins have been determined recently, revealing the intricate workings of the viral machinery and their potential as drug targets.

JOURNAL OF MOLECULAR BIOLOGY (2021)

Add to Collection

Article Infectious Diseases

Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation

Meriane Demoliner et al.

Summary: The highest wave of SARS-CoV-2 epidemic in Rio Grande do Sul, Southern Brazil, since the beginning of the pandemic was predominantly caused by the Gamma lineage, with the emergence of a new S:D614A mutation. Understanding immune protection and vigilance towards variants is essential for better management of the health crisis caused by SARS-CoV-2.

INFECTION GENETICS AND EVOLUTION (2021)

Add to Collection

Review Virology

Mutation Rates, Mutation Frequencies, and Proofreading-Repair Activities in RNA Virus Genetics

Esteban Domingo et al.

Summary: The error rate during template copying for viral RNA progeny production is a biologically relevant parameter for virus replication complexes, with implications for virus-host interactions and virus diversification. Mutation rates for RNA viruses range from 10(-3) to 10(-6) copying errors per nucleotide incorporated into the new RNA product. Some viruses possess error correction mechanisms, like the proofreading-repair 3' to 5' exonuclease in coronaviruses, to decrease error rates during replication and maintain genetic stability.

VIRUSES-BASEL (2021)

Add to Collection

Article Multidisciplinary Sciences

Clinical and molecular characteristics of COVID-19 patients with persistent SARS-CoV-2 infection

Bin Yang et al.

Summary: Persistent SARS-CoV-2 infection in COVID-19 patients is associated with immune suppression and reduced expression of ribosomal protein genes, as revealed by single-cell RNA sequencing and other data analysis.

NATURE COMMUNICATIONS (2021)

Add to Collection

Article Virology

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool

Aine O'Toole et al.

Summary: The global virus genomics community has responded unprecedentedly to the SARS-CoV-2 pandemic, leading to significant advances in 'real-time' generation and sharing of genomic data. The development of new analytical methods, such as pangolin, has been necessary to handle the rapid growth in virus genome data production. Pangolin has processed nearly two million virus genomes, aiding in SARS-CoV-2 genomic epidemiology and providing researchers with valuable information about the pandemic's transmission lineages.

VIRUS EVOLUTION (2021)

Add to Collection

Article Infectious Diseases