Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Publication Date: Aug 5, 2020

Advanced Molecular Detection Clips Content

• News
• Events / Training / Web Resources
• Concepts / Comments
• Methods / Tools
• Evolution / Ecology / Populations
• Pathogenicity / Antimicrobial Resistance
• Detection / Diagnosis
• Epidemiology / Outbreaks / Transmission
• Antimicrobials / Vaccines / Interventions
• Host-Microbe Interactions

NEWS

• National Labs Focused on Building PCR SARS-CoV-2 Test Capacity in Anticipation of Fall
  Bonislawski A. 360dx, Jul 31, 2020.
• SARS-Cov-2 E Gene SNP Raises Concerns About Test Accuracy, Transparency
  Johnson M. 360dx, Jul 31, 2020.
• California and Zuckerberg lab team up to map coronavirus genome, one of the largest efforts to discover how it spreads
  Ho C. San Francisco Chronicle, Jul 30, 2020.
• Coronavirus (COVID-19) Update: FDA Authorizes First Tests that Estimate a Patient's Antibodies from Past SARS-CoV-2 Infection
  (news release) FDA, July 31, 2020.
• Some scientists are taking a DIY coronavirus vaccine, and nobody knows if it's legal or if it works
  Regalado A/ Tech Rev, Jul 29, 2020.
• How an ancient microbial arms race remodeled human cells
  Gibbons A. Science, Jul 31, 2020.

EVENTS / TRAINING / WEB RESOURCES

• Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2: Modernizing Pandemic Response Strategies
  (report) NASEM, Aug 2020.
• Time to Amplify Our Voices Calling for Inexpensive Rapid Home Testing for COVID-19
  (blog post) Sax PE. NEJM Journal Watch, Jul 28, 2020.

CONCEPTS / COMMENTS

• Virus Surveillance and Diagnosis With a CRISPR-Based Platform.
  Hampton Tracy et al. JAMA 2020 Aug (5) 430
• Desperate Times: Protecting the Public From Research Without Consent or Oversight During Public Health Emergencies.
  Beach Mary Catherine et al. Annals of internal medicine 2020 Jul

METHODS / TOOLS

• Distance-based phylogenetic inference from typing data: a unifying view.
  Vaz Cátia et al. Briefings in bioinformatics 2020 Jul 
• A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics.
  Frentrup Martinique et al. Microbial genomics 2020 Jul
• Estimating the relative probability of direct transmission between infectious disease patients.
  Leavitt Sarah V et al. International journal of epidemiology 2020 Jun (3) 764-775
• Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences.
  Walter Katharine S et al. Microbial genomics 2020 Jul 
• Molecular Epidemiological Information System to Support Management of Multidrug-Resistant Tuberculosis in Thailand: Abstract.
  Disratthakit Areeya et al. Online journal of public health informatics 2020 (1) e5
• Determining the Suitability of MinION's Direct RNA and DNA Amplicon Sequencing for Viral Subtype Identification.
  Leigh Deborah M et al. Viruses 2020 Jul (8) 
• Large-scale Multi-omic Analysis of COVID-19 Severity.
  Overmyer Katherine A et al. medRxiv : the preprint server for health sciences 2020 Jul
• Evaluation of an ensemble-based distance statistic for clustering MLST datasets using epidemiologically defined clusters of cyclosporiasis.
  Nascimento Fernanda S et al. Epidemiology and infection 2020 Aug 1-30 
• Implementing parasite genotyping into national surveillance frameworks: feedback from control programmes and researchers in the Asia-Pacific region.
  Noviyanti Rintis et al. Malaria journal 2020 Jul (1) 271 

EVOLUTION / ECOLOGY / POPULATIONS

• Genotypic characterization and genome comparison reveal insights into potential vaccine coverage and genealogy of Neisseria meningitidis in military camps in Vietnam.
  Le Trang Thu et al. PeerJ 2020 e9502
• Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Reveals Mosaic Pattern of Phylogeographical Distribution.
  Kumar Roshan et al. mSystems 2020 Jul (4)
• Bats and humans during the SARS-CoV-2 outbreak: the case of bat-coronavirus from Mexico.
  Pablo Colunga-Salas et al. Transboundary and emerging diseases 2020 Jul
• Genomic heterogeneity and clinical characterization of SARS-CoV-2 in Oregon
  Dowdell AK, et al. medRxiv, Aug 4, 2020.
• Variant analysis of SARS-CoV-2 genomes.
  Koyama Takahiko et al. Bulletin of the World Health Organization 2020 Jul (7) 495-504
• Diversity of the hepatitis C virus NS5B gene during HIV co-infection.
  Ngwaga Tshegofatso et al. PloS one 2020 (8) e0237162 
• High prevalence of Hepatitis C Virus infection among people who use crack cocaine in an important international drug trafficking route in Central-West Region Brazil.
  Castro Vivianne Oliveira Landgraf et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 Jul 104488 
• Evolutionary history of endogenous Human Herpesvirus 6 reflects human migration out of Africa.
  Aswad Amr et al. Molecular biology and evolution 2020 Jul
• Population genomics identifies a distinct Plasmodium vivax population on the China-Myanmar border of Southeast Asia.
  Brashear Awtum M et al. PLoS neglected tropical diseases 2020 Aug (8) e0008506
• Circumpolar diversification of the Ixodes uriae tick virome.
  Pettersson John H-O et al. PLoS pathogens 2020 Aug (8) e1008759
• Genetic diversity and population structure of Aedes aegypti after massive vector control for dengue fever prevention in Yunnan border areas.
  Lv Rui-Chen et al. Scientific reports 2020 Jul (1) 12731 

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

• The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity.
  Li Qianqian et al. Cell 2020 Jul
• Drug resistance mutations among South African children living with HIV on WHO-recommended ART regimens.
  Hackett Stephanie et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jul 
• A Zika virus envelope mutation preceding the 2015 epidemic enhances virulence and fitness for transmission.
  Shan Chao et al. Proceedings of the National Academy of Sciences of the United States of America 2020 Aug

DETECTION / DIAGNOSIS

• Detection and characterization of diphtheria toxin gene-bearing Corynebacterium species through a new real-time PCR assay.
  Williams Margaret M et al. Journal of clinical microbiology 2020 Jul 
• Evaluation of MALDI Biotyper interpretation criteria for the accurate identification of nontuberculous mycobacteria.
  Rodriguez-Temporal David et al. Journal of clinical microbiology 2020 Jul
• Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia.
  Wallace Rhiannon L et al. PloS one 2020 (7) e0236889
• Use of a Whole Genome Sequencing-based approach for Mycobacterium tuberculosis surveillance in Europe in 2017-2019: an ECDC pilot study.
  Tagliani Elisa et al. The European respiratory journal 2020 Jul 
• Molecular Detection and Typing of Pathogenic Leptospira in Febrile Patients and Phylogenetic Comparison with Leptospira Detected among Animals in Tanzania.
  Allan Kathryn J et al. The American journal of tropical medicine and hygiene 2020 Aug 
• Utility of MALDI-TOF MS for differentiation of Neisseria gonorrhoeae isolates with dissimilar azithromycin susceptibility profiles.
  Pham Cau D et al. The Journal of antimicrobial chemotherapy 2020 Jul 
• A longitudinal survey for genome-based identification of SARS-CoV-2 in sewage water in selected lockdown areas of Lahore city, Pakistan; a potential approach for future smart lockdown strategy
  Yaqub T, et al., medRxiv, Aug 4, 2020.
• Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome.
  Khan Kashif Aziz et al. Royal Society open science 2020 Jun (6) 200636
• A recurrent mutation at position 26,340 of SARS-CoV-2 is associated with failure of the E-gene qRT-PCR utilized in a commercial dual-target diagnostic assay.
  Artesi Maria et al. Journal of clinical microbiology 2020 Jul 
• Age-Related Differences in Nasopharyngeal Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Levels in Patients With Mild to Moderate Coronavirus Disease 2019 (COVID-19)
  Heald-Sargent T, et al. JAMA Pediatr, Jul 30, 2020.
• Aerosol and surface contamination of SARS-CoV-2 observed in quarantine and isolation care.
  Santarpia Joshua L et al. Scientific reports 2020 07 (1) 12732
• Performance characteristics of a high throughput automated transcription mediated amplification test for SARS-CoV-2 detection.
  Pham Jimmykim et al. Journal of clinical microbiology 2020 Jul
• Detection of SARS-CoV-2 in nasal swabs using MALDI-MS.
  Nachtigall Fabiane M et al. Nature biotechnology 2020 Jul
• Epidemiology of SARS-CoV-2 Emergence Amidst Community-Acquired Respiratory Viruses.
  Leuzinger Karoline et al. The Journal of infectious diseases 2020 Jul
• Pooled RNA sample reverse transcriptase real time PCR assay for SARS CoV-2 infection: A reliable, faster and economical method.
  Gupta Ekta et al. PloS one 2020 (7) e0236859
• The genus Madurella: Molecular identification and epidemiology in Sudan.
  Ahmed Elhadi A et al. PLoS neglected tropical diseases 2020 Jul (7) e0008420
• A novel method for identifying and distinguishing Cryptococcus neoformans and Cryptococcus gattii by surface-enhanced Raman scattering using positively charged silver nanoparticles.
  Hu Shan et al. Scientific reports 2020 Jul (1) 12480
• Contribution of hospitals to the occurrence of enteric protists in urban wastewater.
  Jiang Wen et al. Parasitology research 2020 Aug 
• Duplex Real-Time PCR Assay for Clinical Differentiation of Onchocerca lupi and Onchocerca volvulus .
  de Almeida Marcos et al. The American journal of tropical medicine and hygiene 2020 Aug 

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

• INCREASED RISK OF SARS-CoV-2 INFECTION IN STAFF WORKING ACROSS DIFFERENT CARE HOMES ENCHANCED CoVID-19 OUTBREAK INVESTIGATIONS IN LONDON CARE HOMES.
  Ladhani Shamez N et al. The Journal of infection 2020 Jul
• The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing.
  Xavier Joilson et al. Emerging microbes & infections 2020 Jul 1-42
• Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak.
  Sekizuka Tsuyoshi et al. Proceedings of the National Academy of Sciences of the United States of America 2020 Jul
• Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic.
  Lai Alessia et al. Viruses 2020 07 (8)
• Lassa fever in Benin: description of the 2014 and 2016 epidemics and genetic characterization of a new Lassa virus.
  Yadouleton Anges et al. Emerging microbes & infections 2020 Dec (1) 1761-1770
• Evaluation of HIV Transmission Clusters among Natives and Foreigners Living in Italy.
  Fabeni Lavinia et al. Viruses 2020 Jul (8)
• HIV drug resistance, phylogenetic analysis, and superinfection among men who have sex with men and transgender women in sub-Saharan Africa: HPTN 075.
  Sivay Mariya V et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Aug
• Geographic distribution of HIV transmission networks in the United States.
  Board Amy R et al. Journal of acquired immune deficiency syndromes (1999) 2020 Jul 
• Genetic evidence for imported malaria and local transmission in Richard Toll, Senegal
  Daniels RF, et al. Malaria J, Aug 3, 2020.

ANTIMICROBIALS / VACCINES / INTERVENTIONS

• COVID-19 Coronavirus Vaccine Design Using Reverse Vaccinology and Machine Learning.
  Ong Edison et al. Frontiers in immunology 2020 1581
• Immunogenic SARS-CoV-2 Epitopes: In Silico Study Towards Better Understanding of COVID-19 Disease-Paving the Way for Vaccine Development.
  Ranga Vipin et al. Vaccines 2020 Jul (3)

HOST-MICROBE INTERACTIONS

• Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection
  Ramlall V, et al. Nat Med, Aug 3, 2020.
• Deciphering the Role of Host Genetics in Susceptibility to Severe COVID-19.
  Carter-Timofte Madalina Elena et al. Frontiers in immunology 2020 1606
• Establishing a Unified COVID-19 "Immunome": Integrating Coronavirus Pathogenesis and Host Immunopathology.
  Wauters Els et al. Frontiers in immunology 2020 1642
• Noroviruses are highly infectious but there is strong variation in host susceptibility and virus pathogenicity.
  Teunis Peter F M et al. Epidemics 2020 Jul 100401
• Global systematic review of primary immunodeficiency registries.
  Abolhassani Hassan et al. Expert review of clinical immunology 2020 Jul 

Note:  indicates that at least one CDC-affiliated author;  indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice.

Disclaimer: Articles listed in the Advanced Molecular Detection Clips are selected by the CDC Office of Public Health Genomics to provide current awareness of the scientific literature and news. Inclusion in the clips does not necessarily represent the views of the Centers for Disease Control and Prevention nor does it imply endorsement of the article's methods or findings. CDC and DHHS assume no responsibility for the factual accuracy of the items presented. The selection, omission, or content of items does not imply any endorsement or other position taken by CDC or DHHS. Opinion, findings and conclusions expressed by the original authors of items included in the Clips, or persons quoted therein, are strictly their own and are in no way meant to represent the opinion or views of CDC or DHHS. References to publications, news sources, and non-CDC Websites are provided solely for informational purposes and do not imply endorsement by CDC or DHHS.