Use of whole genome sequencing to investigate a cluster of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections in emergency department personnel

Abstract Several recent reports have raised concern that infected co-workers may be an important source of SARS-CoV-2 acquisition by healthcare personnel. In a suspected outbreak among emergency department personnel, sequencing of SARS-CoV-2 confirmed transmission among co-workers. The suspected 6-person outbreak included 2 distinct transmission clusters and 1 unrelated infection.

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The Emergence and Spread of Novel SARS-CoV-2 Variants

Frontiers in Public Health ◽

10.3389/fpubh.2021.696664 ◽

2021 ◽

Vol 9 ◽

Author(s):

Huaimin Yi ◽

Jin Wang ◽

Jiong Wang ◽

Yuying Lu ◽

Yali Zhang ◽

...

Keyword(s):

Immune Response ◽

Severe Acute Respiratory Syndrome ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Neutralizing Antibodies ◽

Whole Genome ◽

Distribution Characteristics ◽

S Protein ◽

The World ◽

Viral Genes

Since severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) began to spread in late 2019, laboratories around the world have widely used whole genome sequencing (WGS) to continuously monitor the changes in the viral genes and discovered multiple subtypes or branches evolved from SARS-CoV-2. Recently, several novel SARS-CoV-2 variants have been found to be more transmissible. They may affect the immune response caused by vaccines and natural infections and reduce the sensitivity to neutralizing antibodies. We analyze the distribution characteristics of prevalent SARS-CoV-2 variants and the frequency of mutant sites based on the data available from GISAID and PANGO by R 4.0.2 and ArcGIS 10.2. Our analysis suggests that B.1.1.7, B.1.351, and P.1 are more easily spreading than other variants, and the key mutations of S protein, including N501Y, E484K, and K417N/T, have high mutant frequencies, which may have become the main genotypes for the spread of SARS-CoV-2.

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Genomic investigation of a suspected multi-drug resistant Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa

10.1101/2020.08.06.236117 ◽

2020 ◽

Author(s):

Jennifer Cornick ◽

Patrick Musicha ◽

Chikondi Peno ◽

Ezgi Saeger ◽

Pui-ying Iroh Toh ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Resistance Genes ◽

Sub Saharan Africa ◽

Whole Genome ◽

Drug Resistant ◽

Sub Saharan ◽

Neonatal Care Unit ◽

Suspected Outbreak

ABSTRACTA suspected outbreak of multi-drug resistant (MDR) Klebsiella pneumoniae in a Malawian neonatal unit was investigated using whole-genome sequencing. Strain-types, virulence and resistance genes of K. pneumoniae isolated from patients from the hospital over a four-year period were identified. A MDR ST340 clone was implicated as the likely outbreak cause.

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Flight-Associated Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Corroborated by Whole-Genome Sequencing

Emerging Infectious Diseases ◽

10.3201/eid2612.203910 ◽

2020 ◽

Vol 26 (12) ◽

pp. 2872-2880 ◽

Cited By ~ 8

Author(s):

Hollie Speake ◽

Anastasia Phillips ◽

Tracie Chong ◽

Chisha Sikazwe ◽

Avram Levy ◽

...

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome

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SARS-CoV-2 B.1.1.7 lineage rapidly spreads and overwhelms R.1 lineage in Japan: serial and stationary observation in a community

10.1101/2021.06.30.21259820 ◽

2021 ◽

Author(s):

Yosuke Hirotsu ◽

Masao Omata

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Analysis ◽

Whole Genome ◽

Community Based ◽

The World ◽

Viral Lineage

Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulates in the world and acquires mutations during evolution. To identify the new emergent variants, the surveillance of the variants of concern (VOC) and variants of interest (VOI) is ongoing. This study aimed to determine how the transition of viral lineage occurred by stationary genome analysis in Yamanashi, Japan. Methods We performed the whole genome sequencing using SARS-CoV-2 positive samples (n=325) collected from February 2020 to the end of June 2021. The number of analyzed samples accounted for 15.4% of the total 2,109 samples identified in our community. Viral lineage was defined by the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineages. Results We identified 13 types of viral lineages including R.1, P.1, B.1.1.7 (Alpha) and B.1.617.2 (Delta) These virus lineages had distinct periods of expansion and decline. After the emerging of the R.1 lineage harboring E484K variant (designated VOI in Japan), the prevalent B.1.1.214 lineage were no longer identified. The R.1 lineages were temporarily prevalent afterwards, but the influx of B.1.1.7 lineage (designated VOC) led to a decline in R.1. Currently, B.1.1.7 has become dominant after mid-April, 2021. Conclusion We clearly elucidated the transition and replacement of viral lineage by the community-based analysis. The virus completely replaced by more infectious lineages, therefore, it will be necessary to continue to monitor the VOC and VOI.

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Coronavirus Disease 2019 (COVID-19) Re-infection by a Phylogenetically Distinct Severe Acute Respiratory Syndrome Coronavirus 2 Strain Confirmed by Whole Genome Sequencing

Clinical Infectious Diseases ◽

10.1093/cid/ciaa1275 ◽

2020 ◽

Cited By ~ 90

Author(s):

Kelvin Kai-Wang To ◽

Ivan Fan-Ngai Hung ◽

Jonathan Daniel Ip ◽

Allen Wing-Ho Chu ◽

Wan-Mui Chan ◽

...

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Natural Infection ◽

Acute Infection ◽

Virus Genome ◽

First Episode ◽

Whole Genome ◽

Viral Genomes ◽

Viral Shedding

Abstract Background Waning immunity occurs in patients who have recovered from Coronavirus Disease 2019 (COVID-19). However, it remains unclear whether true re-infection occurs. Methods Whole genome sequencing was performed directly on respiratory specimens collected during 2 episodes of COVID-19 in a patient. Comparative genome analysis was conducted to differentiate re-infection from persistent viral shedding. Laboratory results, including RT-PCR Ct values and serum Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) IgG, were analyzed. Results The second episode of asymptomatic infection occurred 142 days after the first symptomatic episode in an apparently immunocompetent patient. During the second episode, there was evidence of acute infection including elevated C-reactive protein and SARS-CoV-2 IgG seroconversion. Viral genomes from first and second episodes belong to different clades/lineages. The virus genome from the first episode contained a a stop codon at position 64 of ORF8, leading to a truncation of 58 amino acids. Another 23 nucleotide and 13 amino acid differences located in 9 different proteins, including positions of B and T cell epitopes, were found between viruses from the first and second episodes. Compared to viral genomes in GISAID, the first virus genome was phylogenetically closely related to strains collected in March/April 2020, while the second virus genome was closely related to strains collected in July/August 2020. Conclusions Epidemiological, clinical, serological, and genomic analyses confirmed that the patient had re-infection instead of persistent viral shedding from first infection. Our results suggest SARS-CoV-2 may continue to circulate among humans despite herd immunity due to natural infection. Further studies of patients with re-infection will shed light on protective immunological correlates for guiding vaccine design.

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