Advanced Molecular Detection Clips Content (Published on 09/15/2022)
SARS-CoV-2 Sequence Analysis Points to Extensive Within-Host Viral Diversity
GenomeWeb, Sep 9, 2022.
Feds' Planned Move out of COVID-19 Testing Raises Public Health Worries
Cima G. 360dx, Sep 7, 2022.
China and India approve nasal COVID vaccines — are they a game changer?
Waltz E. Nature, Sep 7, 2022.
So you haven't caught COVID yet. Does that mean you're a superdodger?
Doucleff M. NPR, Sep 12, 2022.
The Mystery of Why Some People Don’t Get Covid
Brown G. Wired, Sep 12, 2022.
EVENTS / TRAINING / WEB RESOURCES
The SARS-CoV-2 Spike Protein Mutation Explorer: Using an Interactive Application to Improve the Public Understanding of SARS-CoV-2 Variants of Concern
Iannucci S, et al. bioRxiv, Sep 12, 2022.
A global dataset of microbial community in ticks from metagenome study.
Liu Mei-Chen et al. Scientific data 2022 9 (1) 560
CONCEPTS / COMMENTS
METHODS / TOOLS
Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea.
Lee Jingyeong et al. PLoS neglected tropical diseases 2022 9 (9) e0010763
Measuring the latent reservoir for HIV-1: Quantification bias in near full-length genome sequencing methods.
White Jennifer A et al. PLoS pathogens 2022 9 (9) e1010845
A Serotype-Specific and Multiplex PCR Method for Whole-Genome Sequencing of Dengue Virus Directly from Clinical Samples.
Su Wenzhe et al. Microbiology spectrum 2022 9 e0121022
EVOLUTION / ECOLOGY / POPULATIONS
COVID-19 infection and transmission includes complex sequence diversity.
Chan Ernest R et al. PLoS genetics 2022 9 (9) e1010200
Putative Host-Derived Insertions in the Genomes of Circulating SARS-CoV-2 Variants.
Yang Yiyan et al. mSystems 2022 5 (3) e0017922
Recurrent SARS-CoV-2 mutations in immunodeficient patients.
Wilkinson S A J et al. Virus evolution 2022 8 (2) veac050
Phylogeography and genomic analysis of SARS-CoV-2 delta variant in Morocco.
El Mazouri Safae et al. Journal of infection in developing countries 2022 9 (8) 1258-1268
A threat from both sides: Multiple introductions of genetically distinct H5 HPAI viruses into Canada via both East Asia-Australasia/Pacific and Atlantic flyways
Alkie TN, et al. Virus Evol. 2022 Aug 25;8(2):veac077.
Plasmodium falciparum Genetic Diversity in Coincident Human and Mosquito Hosts.
Lapp Zena et al. mBio 2022 9 e0227722
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
Large-scale genomic analysis reveals the pESI-like megaplasmid presence in Salmonella Agona, Muenchen, Schwarzengrund, and Senftenberg.
Dos Santos Anamaria M P et al. Food microbiology 2022 9 104112
Analysis and comprehensive lineage identification for SARS-CoV-2 genomes through scalable learning methods
Cahuantzi R, et al. bioRxiv, Sep 14, 2022.
Comparison of Monkeypox virus genomes from the 2017 Nigeria outbreak and the 2022 outbreak.
Wassenaar Trudy M et al. Journal of applied microbiology 2022 9
High Levels of Pretreatment HIV-1 Drug Resistance Mutations Among South African Women Who Acquired HIV During a Prospective Study
Beesham I, et al. J Acquir Immune Defic Syndr. 2022 Oct 1;91(2):130-137.
DETECTION / DIAGNOSIS
Wastewater surveillance of pathogens can inform public health responses.
Diamond Megan B et al. Nature medicine 2022 9
Real-time metagenomics-based diagnosis of community-acquired meningitis: A prospective series, southern France.
Morsli Madjid et al. EBioMedicine 2022 9 104247
Visual closed dumbbell-mediated isothermal amplification (CDA) for on-site detection of Rickettsia raoultii.
Gui Zheng et al. PLoS neglected tropical diseases 2022 9 (9) e0010747
Population Normalization in SARS-CoV-2 Wastewater-Based Epidemiology: Implications from Statewide Wastewater Monitoring in Missouri
Li C, et al. medRxiv, Sep 10, 2022.
Urban monitoring of antimicrobial resistance during a COVID-19 surge through wastewater surveillance.
Harrington Anthony et al. The Science of the total environment 2022 9 158577
Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study.
Stirrup Oliver et al. eLife 2022 9
Wastewater Surveillance for Monkeypox Virus in Nine California Communities
Wolfe MK, et al. medRxiv, Sep 9, 2022.
Development of a rapid and accurate CRISPR/Cas13-based diagnostic test for GII.4 norovirus infection.
Duan Lei et al. Frontiers in microbiology 2022 9 912315
Development and evaluation of a real-time PCR for genotyping of Cryptosporidium spp. from water monitoring slides.
Elwin Kristin et al. Experimental parasitology 2022 9 108366
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
Whole-Genome Sequencing and Epidemiological Investigation of Tuberculosis Outbreaks in High Schools in Hunan, China.
Xu Zuhui et al. Infection and drug resistance 2022 9 5149-5160
Genomic epidemiology of SARS-CoV-2 infections in The Gambia, March 2020 to Jan 2022
Kanteh A, et al. medRxiv, Sep 9, 2022.
The role of real-time, on-site, whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in guiding the management of hospital outbreaks of coronavirus disease 2019 (COVID-19).
Marinelli Tina M et al. Infection control and hospital epidemiology 2022 9 1-5
Nosocomial Outbreak of SARS-CoV-2 Delta Variant Amongst Vaccinated Healthcare Workers and Immunocompromised Patients on a Solid Organ Transplant Unit: Complexities of an Epidemiologic and Genomic Investigation.
Ryder Jonathan H et al. Infection control and hospital epidemiology 2022 9 1-21
Regional importation and asymmetric within-country spread of SARS-CoV-2 variants of concern in the Netherlands.
Han Alvin X et al. eLife 2022 9
Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants
Lamarca AP, et al. Microb Genom. 2022 Sep;8(9).
First Patient-to-Patient Intrahospital Transmission of Clade I Candida auris in France Revealed after a Two-Month Incubation Period.
Alanio Alexandre et al. Microbiology spectrum 2022 9 e0183322
Cryptosporidiosis outbreaks linked to the public water supply in a military camp, France.
Watier-Grillot Stéphanie et al. PLoS neglected tropical diseases 2022 9 (9) e0010776
Immune Imprinting Drives Human Norovirus Potential for Global Spread
Lindesmith LC, et al. mBio. 2022 Sep 14;e0186122
A blood-based circulating microbial metagenomic panel for early diagnosis and prognosis of oesophageal adenocarcinoma.
Zaidi Ali H et al. British journal of cancer 2022 9
Disclaimer: Articles listed in the Advanced Molecular Detection Clips are selected by the CDC Office of Genomics and Precision Public Health 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.