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Article ; Online: Comparative subgenomic mRNA profiles of SARS-CoV-2 Alpha, Delta and Omicron BA.1, BA.2 and BA.5 sub-lineages using Danish COVID-19 genomic surveillance data.

Tang, Man-Hung Eric / Ng, Kim Lee / Edslev, Sofie Marie / Ellegaard, Kirsten / Stegger, Marc / Alexandersen, Soren

2023 Volume 93, Page(s) 104669

Abstract: Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly spread worldwide in the population since it was first detected in late 2019. The transcription and replication of coronaviruses, although not fully understood, is ... ...

Abstract	Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly spread worldwide in the population since it was first detected in late 2019. The transcription and replication of coronaviruses, although not fully understood, is characterised by the production of genomic length RNA and shorter subgenomic RNAs to make viral proteins and ultimately progeny virions. Observed levels of subgenomic RNAs differ between sub-lineages and open reading frames but their biological significance is presently unclear. Methods: Using a large and diverse panel of virus sequencing data produced as part of the Danish COVID-19 routine surveillance together with information in electronic health registries, we assessed the association of subgenomic RNA levels with demographic and clinical variables of the infected individuals. Findings: Our findings suggest no significant statistical relationship between levels of subgenomic RNAs and host-related factors. Interpretation: Differences between lineages and subgenomic ORFs may be related to differences in target cell tropism, early virus replication/transcription kinetics or sequence features. Funding: The author(s) received no specific funding for this work.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19 ; Subgenomic RNA ; Genomics ; Denmark/epidemiology
Chemical Substances	Subgenomic RNA
Language	English
Publishing date	2023-06-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2851331-9
ISSN	2352-3964
ISSN (online)	2352-3964
DOI	10.1016/j.ebiom.2023.104669
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Exploring the Cause of Diarrhoea and Poor Growth in 8-11-Week-Old Pigs from an Australian Pig Herd Using Metagenomic Sequencing.

Bhatta, Tarka Raj / Chamings, Anthony / Alexandersen, Soren

Viruses

2021 Volume 13, Issue 8

Abstract: Diarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and ... ...

Abstract	Diarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and characterisation of diverse groups of viruses and bacteria and can thereby provide a better understanding of complex interactions among microorganisms potentially causing clinical disease. Here, we used a metagenomics approach to identify and characterise the possible pathogens in colon and lung samples from pigs with diarrhoea and poor growth in an Australian pig herd. We identified and characterized a wide diversity of porcine viruses including RNA viruses, in particular several picornaviruses-porcine sapelovirus (PSV), enterovirus G (EV-G), and porcine teschovirus (PTV), and a porcine astrovirus (PAstV). Single stranded DNA viruses were also detected and included parvoviruses like porcine bocavirus (PBoV) and porcine parvovirus 2 (PPV2), porcine parvovirus 7 (PPV7), porcine bufa virus (PBuV), and porcine adeno-associated virus (AAV). We also detected single stranded circular DNA viruses such as porcine circovirus type 2 (PCV2) at very low abundance and torque teno sus viruses (TTSuVk2a and TTSuVk2b). Some of the viruses detected here may have had an evolutionary past including recombination events, which may be of importance and potential involvement in clinical disease in the pigs. In addition, our metagenomics data found evidence of the presence of the bacteria
MeSH term(s)	Animals ; Bacteria/classification ; Bacteria/genetics ; Bacteria/isolation & purification ; Bacterial Infections/diagnosis ; Bacterial Infections/veterinary ; Coinfection/microbiology ; Coinfection/veterinary ; Coinfection/virology ; DNA Viruses/classification ; DNA Viruses/genetics ; DNA Viruses/isolation & purification ; Diarrhea/veterinary ; Diarrhea/virology ; Metagenome ; Metagenomics/methods ; Phylogeny ; RNA Viruses/classification ; RNA Viruses/genetics ; RNA Viruses/isolation & purification ; Swine/growth & development ; Swine/virology ; Swine Diseases/diagnosis ; Swine Diseases/virology ; Virus Diseases/diagnosis ; Virus Diseases/veterinary
Language	English
Publishing date	2021-08-13
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13081608
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Diverse Bacterial Resistance Genes Detected in Fecal Samples From Clinically Healthy Women and Infants in Australia-A Descriptive Pilot Study.

Guernier-Cambert, Vanina / Chamings, Anthony / Collier, Fiona / Alexandersen, Soren

Frontiers in microbiology

2021 Volume 12, Page(s) 596984

Abstract: The gut microbiota is an immense reservoir of antimicrobial resistance genes (ARGs), the so-called "resistome." In Australia, where antibiotic use is high and resistance rates in some common pathogens are increasing, very little is known about the human ... ...

Abstract	The gut microbiota is an immense reservoir of antimicrobial resistance genes (ARGs), the so-called "resistome." In Australia, where antibiotic use is high and resistance rates in some common pathogens are increasing, very little is known about the human resistome. To assess the presence and diversity of ARGs in the gut of Australians from south-eastern Victoria, we investigated fecal samples from clinically healthy infants and pregnant women using non-targeted (shotgun metagenomics sequencing or SMS) and targeted sequencing (two Ion Ampliseq
Language	English
Publishing date	2021-09-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2021.596984
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Metagenomic characterisation of additional and novel avian viruses from Australian wild ducks.

Vibin, Jessy / Chamings, Anthony / Klaassen, Marcel / Alexandersen, Soren

Scientific reports

2020 Volume 10, Issue 1, Page(s) 22284

Abstract: Birds, notably wild ducks, are reservoirs of pathogenic and zoonotic viruses such as influenza viruses and coronaviruses. In the current study, we used metagenomics to detect and characterise avian DNA and RNA viruses from wild Pacific black ducks, ... ...

Abstract	Birds, notably wild ducks, are reservoirs of pathogenic and zoonotic viruses such as influenza viruses and coronaviruses. In the current study, we used metagenomics to detect and characterise avian DNA and RNA viruses from wild Pacific black ducks, Chestnut teals and Grey teals collected at different time points from a single location. We characterised a likely new species of duck aviadenovirus and a novel duck gyrovirus. We also report what, to the best of our knowledge, is the first finding of an avian orthoreovirus from Pacific black ducks and a rotavirus F from Chestnut teals. Other viruses characterised from the samples from these wild ducks belong to the virus families Astroviridae, Caliciviridae and Coronaviridae. Some of the viruses may have potential cross-species transmissibility, while others indicated a wide genetic diversity of duck viruses within a genus. The study also showed evidence of potential transmission of viruses along the East Asian-Australasian Flyway; potentially facilitated by migrating shorebirds. The detection and characterisation of several avian viruses not previously described, and causing asymptomatic but potentially also symptomatic infections suggest the need for more virus surveillance studies for pathogenic and potential zoonotic viruses in wildlife reservoirs.
MeSH term(s)	Animals ; Animals, Wild/virology ; Birds/virology ; Ducks/genetics ; Ducks/virology ; Gyrovirus/genetics ; Gyrovirus/isolation & purification ; Influenza A virus/genetics ; Influenza A virus/isolation & purification ; Influenza in Birds/genetics ; Influenza in Birds/virology ; Metagenome/genetics ; Metagenomics ; Phylogeny
Language	English
Publishing date	2020-12-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-79413-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication.

Alexandersen, Soren / Chamings, Anthony / Bhatta, Tarka Raj

Nature communications

2020 Volume 11, Issue 1, Page(s) 6059

Abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was first detected in late December 2019 and has spread worldwide. Coronaviruses are enveloped, positive sense, single-stranded RNA viruses and employ a complicated pattern of virus genome ... ...

Abstract	Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was first detected in late December 2019 and has spread worldwide. Coronaviruses are enveloped, positive sense, single-stranded RNA viruses and employ a complicated pattern of virus genome length RNA replication as well as transcription of genome length and leader containing subgenomic RNAs. Although not fully understood, both replication and transcription are thought to take place in so-called double-membrane vesicles in the cytoplasm of infected cells. Here we show detection of SARS-CoV-2 subgenomic RNAs in diagnostic samples up to 17 days after initial detection of infection and provide evidence for their nuclease resistance and protection by cellular membranes suggesting that detection of subgenomic RNAs in such samples may not be a suitable indicator of active coronavirus replication/infection.
MeSH term(s)	Adult ; COVID-19/diagnosis ; COVID-19/virology ; COVID-19 Testing/methods ; Cytoplasm/virology ; Female ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/genetics ; Humans ; Male ; Middle Aged ; Nasopharynx/cytology ; Nasopharynx/virology ; Oropharynx/cytology ; Oropharynx/virology ; Polymerase Chain Reaction ; RNA, Viral/isolation & purification ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/pathogenicity ; Time Factors ; Virus Replication ; Young Adult
Chemical Substances	RNA, Viral
Language	English
Publishing date	2020-11-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-19883-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Neonatal parechovirus infection: Possibility of in-utero transmission.

Hilbig, Adelene / Liew, Kwee C / Foster, Claire / Fuller, David G / Chamings, Anthony / Alexandersen, Soren

Journal of paediatrics and child health

2021 Volume 58, Issue 6, Page(s) 1088–1090

MeSH term(s)	Communicable Diseases ; Humans ; Infant, Newborn ; Parechovirus ; Picornaviridae Infections/diagnosis
Language	English
Publishing date	2021-10-04
Publishing country	Australia
Document type	Case Reports
ZDB-ID	1024476-1
ISSN	1440-1754 ; 1034-4810
ISSN (online)	1440-1754
ISSN	1034-4810
DOI	10.1111/jpc.15763
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Variations in the persistence of 5'-end genomic and subgenomic SARS-CoV-2 RNAs in wastewater from aircraft, airports and wastewater treatment plants.

Tang, Man-Hung Eric / Bennedbaek, Marc / Gunalan, Vithiagaran / Qvesel, Amanda Gammelby / Thorsen, Theis Hass / Larsen, Nicolai Balle / Rasmussen, Lasse Dam / Krogsgaard, Lene Wulff / Rasmussen, Morten / Stegger, Marc / Alexandersen, Soren

Heliyon

2024 Volume 10, Issue 9, Page(s) e29703

Abstract: Wastewater sequencing has become a powerful supplement to clinical testing in monitoring SARS-CoV-2 infections in the post-COVID-19 pandemic era. While its applications in measuring the viral burden and main circulating lineages in the community have ... ...

Abstract	Wastewater sequencing has become a powerful supplement to clinical testing in monitoring SARS-CoV-2 infections in the post-COVID-19 pandemic era. While its applications in measuring the viral burden and main circulating lineages in the community have proved their efficacy, the variations in sequencing quality and coverage across the different regions of the SARS-CoV-2 genome are not well understood. Furthermore, it is unclear how different sample origins, viral extraction and concentration methods and environmental factors impact the reads sequenced from wastewater. Using high-coverage, amplicon-based, paired-end read sequencing of viral RNA extracted from wastewater collected directly from aircraft, pooled from different aircraft and airport buildings or from regular wastewater plants, we assessed the genome coverage across the sample groups with a focus on the 5'-end region covering the leader sequence and investigated whether it was possible to detect subgenomic RNA from viral material recovered from wastewater. We identified distinct patterns in the persistence of the different genomic regions across the different types of wastewaters and the existence of chimeric reads mapping to non-amplified regions. Our findings suggest that preservation of the 5'-end of the genome and the ability to detect subgenomic RNA reads, though highly susceptible to environment and sample processing conditions, may be indicative of the quality and amount of the viral RNA present in wastewater.
Language	English
Publishing date	2024-04-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2024.e29703
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication

Soren Alexandersen / Anthony Chamings / Tarka Raj Bhatta

Nature Communications, Vol 11, Iss 1, Pp 1-

2020 Volume 13

Abstract: ... into viral proteins. Here, Alexandersen et al. provide evidence that sgRNA is not necessarily an indicator ...

Abstract	During SARS-CoV-2 replication subgenomic RNAs (sgRNA) are transcribed and subsequently translated into viral proteins. Here, Alexandersen et al. provide evidence that sgRNA is not necessarily an indicator for active viral replication, but can be detected up to 17 days after symptom onset in clinical samples.
Keywords	Science ; Q
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Metagenomic characterisation of additional and novel avian viruses from Australian wild ducks

Jessy Vibin / Anthony Chamings / Marcel Klaassen / Soren Alexandersen

Scientific Reports, Vol 10, Iss 1, Pp 1-

2020 Volume 14

Abstract: Abstract Birds, notably wild ducks, are reservoirs of pathogenic and zoonotic viruses such as influenza viruses and coronaviruses. In the current study, we used metagenomics to detect and characterise avian DNA and RNA viruses from wild Pacific black ... ...

Abstract	Abstract Birds, notably wild ducks, are reservoirs of pathogenic and zoonotic viruses such as influenza viruses and coronaviruses. In the current study, we used metagenomics to detect and characterise avian DNA and RNA viruses from wild Pacific black ducks, Chestnut teals and Grey teals collected at different time points from a single location. We characterised a likely new species of duck aviadenovirus and a novel duck gyrovirus. We also report what, to the best of our knowledge, is the first finding of an avian orthoreovirus from Pacific black ducks and a rotavirus F from Chestnut teals. Other viruses characterised from the samples from these wild ducks belong to the virus families Astroviridae, Caliciviridae and Coronaviridae. Some of the viruses may have potential cross-species transmissibility, while others indicated a wide genetic diversity of duck viruses within a genus. The study also showed evidence of potential transmission of viruses along the East Asian—Australasian Flyway; potentially facilitated by migrating shorebirds. The detection and characterisation of several avian viruses not previously described, and causing asymptomatic but potentially also symptomatic infections suggest the need for more virus surveillance studies for pathogenic and potential zoonotic viruses in wildlife reservoirs.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Exploring the Cause of Diarrhoea and Poor Growth in 8–11-Week-Old Pigs from an Australian Pig Herd Using Metagenomic Sequencing

Bhatta, Tarka Raj / Chamings, Anthony / Alexandersen, Soren

Viruses. 2021 Aug. 13, v. 13, no. 8

2021

Abstract	Diarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and characterisation of diverse groups of viruses and bacteria and can thereby provide a better understanding of complex interactions among microorganisms potentially causing clinical disease. Here, we used a metagenomics approach to identify and characterise the possible pathogens in colon and lung samples from pigs with diarrhoea and poor growth in an Australian pig herd. We identified and characterized a wide diversity of porcine viruses including RNA viruses, in particular several picornaviruses—porcine sapelovirus (PSV), enterovirus G (EV-G), and porcine teschovirus (PTV), and a porcine astrovirus (PAstV). Single stranded DNA viruses were also detected and included parvoviruses like porcine bocavirus (PBoV) and porcine parvovirus 2 (PPV2), porcine parvovirus 7 (PPV7), porcine bufa virus (PBuV), and porcine adeno-associated virus (AAV). We also detected single stranded circular DNA viruses such as porcine circovirus type 2 (PCV2) at very low abundance and torque teno sus viruses (TTSuVk2a and TTSuVk2b). Some of the viruses detected here may have had an evolutionary past including recombination events, which may be of importance and potential involvement in clinical disease in the pigs. In addition, our metagenomics data found evidence of the presence of the bacteria Lawsonia intracellularis, Brachyspira spp., and Campylobacter spp. that may, together with these viruses, have contributed to the development of clinical disease and poor growth.
Keywords	Anelloviridae ; Bocaparvovirus ; Brachyspira ; Campylobacter ; Dependoparvovirus ; Enterovirus G ; Lawsonia intracellularis ; Mamastrovirus 3 ; Porcine circovirus-2 ; RNA ; Sapelovirus ; Teschovirus A ; Ungulate tetraparvovirus 3 ; circular DNA ; colon ; diarrhea ; herds ; lungs ; metagenomics ; single-stranded DNA ; swine ; viruses
Language	English
Dates of publication	2021-0813
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13081608
Database	NAL-Catalogue (AGRICOLA)

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