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

Authors: Soren Alexandersen, Anthony Chamings &Tarka Raj Bhatta 


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.

Source: Nature Communications, 11, 2020

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Infection Dynamics of Swine Influenza Virus in a Danish Pig Herd Reveals Recurrent Infections with Different Variants of the H1N2 Swine Influenza A Virus Subtype

Authors: Bhatta, T.R., Ryt-Hansen, P., Nielsen, J.P., Larsen, L.E., Larsen, I., Chamings, A., Goecke, N.B., Alexandersen, S. 


Influenza A virus (IAV) in swine, so-called swine influenza A virus (swIAV), causes respiratory illness in pigs around the globe. In Danish pig herds, a H1N2 subtype named H1N2dk is one of the main circulating swIAV. In this cohort study, the infection dynamic of swIAV was evaluated in a Danish pig herd by sampling and PCR testing of pigs from two weeks of age until slaughter at 22 weeks of age. In addition, next generation sequencing (NGS) was used to identify and characterize the complete genome of swIAV circulating in the herd, and to examine the antigenic variability in the antigenic sites of the virus hemagglutinin (HA) and neuraminidase (NA) proteins. Overall, 76.6% of the pigs became PCR positive for swIAV during the study, with the highest prevalence at four weeks of age. Detailed analysis of the virus sequences obtained showed that the majority of mutations occurred at antigenic sites in the HA and NA proteins of the virus. At least two different H1N2 variants were found to be circulating in the herd; one H1N2 variant was circulating at the sow and nursery sites, while another H1N2 variant was circulating at the finisher site. Furthermore, it was demonstrated that individual pigs had recurrent swIAV infections with the two different H1N2 variants, but re-infection with the same H1N2 variant was also observed. Better understandings of the epidemiology, genetic and antigenic diversity of swIAV may help to design better health interventions for the prevention and control of swIAV infections in the herds.

SOURCE: Viruses 2020, 12, 1013. 

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Metagenomic characterisation of avian parvoviruses and picornaviruses from Australia wild ducks

Authors: Jessy Vibin, Anthony Chamings, Marcel Klassen, Tarka Raj Bhatta and Soren Alexandersen.


Ducks can shed and disseminate viruses and thus play a role in cross-species transmission. In the current study, we detected and characterised various avian parvoviruses and picornaviruses from wild Pacific black ducks, Chestnut teals, Grey teals and Wood ducks sampled at multiple time points from a single location using metagenomics. We characterised 46 different avian parvoviruses belonging to three different genera Dependoparvovirus, Aveparvovirus and Chaphamaparvovirus, and 11 different avian picornaviruses tentatively belonging to four different genera SicinivirusAnativirusMegrivirus and Aalivirus. Most of these viruses were genetically different from other currently known viruses from the NCBI dataset. The study showed that the abundance and number of avian picornaviruses and parvoviruses varied considerably throughout the year, with the high number of virus reads in some of the duck samples highly suggestive of an active infection at the time of sampling. The detection and characterisation of several parvoviruses and picornaviruses from the individual duck samples also suggests co-infection, which may lead to the emergence of novel viruses through possible recombination. Therefore, as new and emerging diseases evolve, it is relevant to explore and monitor potential animal reservoirs in their natural habitat.


SOURCE: Scientific Reports  2020; 10, 12800.

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An Emerging Human Parechovirus Type 5 Causing Sepsis-Like Illness in Infants in Australia

Authors: Anthony Chamings 1,2 , Kwee Chin Liew 3,4, Emily Reid 3, Eugene Athan 1,2,3, Amy Raditsis 2,3, Peter Vuillermin 2,3, Yano Yoga 5, Leon Caly 5, Julian Druce 5 and Soren Alexandersen 1,2,3,*

1.  Geelong Center for Emerging Infectious Diseases, Geelong, VI 3220, Australia
2 . Deakin University, School of Medicine, Geelong, VI 3220, Australia
3.  Barwon Health, University Hospital Geelong, Geelong, VI 3220, Australia
4.  Australian Clinical Labs, Geelong Laboratory, Geelong, VI 3220, Australia
5.  Victorian Infectious Diseases Reference Laboratory (VIDRL), Doherty Institute,
Melbourne, VI 3000, Australia
* Correspondence:; Tel.: +61-(0)-342159635
Received: 20 September 2019; Accepted: 1 October 2019; Published: 3 October 2019

Abstract: Human parechovirus (HPeV), particularly type 3 (HPeV3), is an important cause of sepsis-/meningitis-like illness in young infants. Laboratory records identified a total of ten HPeV-positive cases in Southeastern Australia between January and July 2019.

The HPeV present in these cases were typed by Sanger sequencing of the partial viral capsid protein 1 (VP1) region and selected cases were further characterised by additional Sanger or Ion Torrent near-full length virus sequencing.

In seven of the ten cases, an HPeV type 5 (HPeV5) was identified, and in the remaining
three cases, an HPeV type 1 was identified. The HPeV5-positive cases were infants under the age of 3 months admitted to hospital with fever, rash, lethargy and/or sepsis-like clinical signs. Near full-length virus sequencing revealed that the HPeV5 was most likely a recombinant virus, with structural genes most similar to an HPeV5 from Belarus in 2018, and a polymerase gene most similar to an HPeV3 from Australia in 2013/14.

While HPeV5 is not typically associated with severe clinical signs, the HPeV5 identified here may have been able to cause more severe disease in young infants through the acquisition of genes from a more virulent HPeV.

Keywords: parechovirus; picornaviral epidemiology; recombination; genome sequencing

SOURCE Viruses 201911(10), 913;

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Evolutionary analysis of human parechovirus type 3 and clinical outcomes of infection during the 2017-18 Australian epidemic

AuthorsAnthony Chamings, Julian  Druce, Leon Caly, Yano Yoga, Philip N. Britton, Kristine K. Macartney & Soren Alexandersen

Source: Scientific Reports 9, Article number: 8906 (2019)

Abstract: Human parechovirus type 3 (HPeV3) can cause severe sepsis-like illness in young infants and may be associated with long term neurodevelopmental delay later in childhood.

We investigated the molecular epidemiology of HPeV infection in thirty three infants requiring hospitalization before, during and after the peak of the 2017/18 HPeV epidemic wave in Australia.

During the peak of the epidemic, all cases were infected with an HPeV3, while before and after the peak, HPeV1 was the predominant type detected. The predominant HPeV3 was the recombinant HPeV3 also detected in the 2013/14 and 2015/16 Australian epidemics. Sepsis-like or meningitis-like symptoms were only reported in cases infected with the recombinant HPeV3. Phylogenetic analysis of the recombinant HPeV3 revealed that the virus continued to evolve, also between the Australian outbreaks, thus indicating continued circulation, despite not being detected and reported in Australia or elsewhere in between epidemic waves. The recombinant HPeV3 continued to show a remarkable stability in its capsid amino acid sequence, further strengthening our previous argument for development of a vaccine or immunotherapeutics to reduce the severity of HPeV3 outbreaks due to this virus.


Detection and characterisation of canine astrovirus, canine parvovirus and canine papillomavirus in puppies using next generation sequencing

Authors: Tarka Raj BhattaAnthony ChamingsJessy Vibin & Soren Alexandersen

Source: Scientific Reports 9, Article number: 4602 (2019)

Brief summary of the paper: Gastroenteritis in young animals is a clinical presentation with many infectious and non- infectious aetiologies. We used next generation sequencing (NGS) to investigate the possible infectious causes of gastroenteritis in puppies from a dog kennel in Victoria, Australia.

The near complete genome of a canine astrovirus was obtained from pooled faecal samples, and was found to be 94.7% identical with a canine astrovirus detected in the United Kingdom in 2012. The phylogenetic analysis of the capsid gene found similarities to those of canine astroviruses identified in Italy in 2005 and in UK and Hungary in 2012, but distant from that of a canine astrovirus previously identified in Australia in 2012.

Thus, different serotypes of canine astrovirus are likely circulating in Australia. The close relationship to European astroviruses also suggested that there had been recent movements of ancestor canine astroviruses between Australia and Europe.

NGS also detected other infections in the puppies including several canine papillomaviruses and a canine parvovirus (vaccine strain) as well as a very low level of campylobacter. Canine astrovirus was the probable cause of diarrhoea in these puppies, with the possible involvement of campylobacter bacteria. NGS was effective as a non-targeted method to determine the likely infectious cause of gastroenteritis.

APPRISE Q & A with Dr Chamings

The APPRISE Centre of Research Excellence is developing research to inform Australia’s emergency response to infectious diseases.  APPRISE is an Australia-wide network of experts in medical, scientific, public health and ethics research from many different institutions, including GCEID.  In their latest new article they held a question and answer session with GCEID researcher Dr Anthony Chamings.

The article can be read here


World “One Health” Day 2018

Join GCEID and the partner organisations in celebrating World One Health day.  “One Health” is a multidisciplinary approach to managing infectious diseases in people, animals and the environment. This event will showcase how researchers in Geelong are undertaking collaborative research to protect people, animals and the environment from infectious diseases.
When: Thursday 15 November 2018 between 10am and 3pm
This is an open house event, please feel free to drop in at any point throughout the day

Where: St Mary’s Building, 190 Myers Street, Geelong, 3220

All welcome at this free event.

  • Morning session: Research Talks (10-11:45am)
  • Lunch Session: Meet the researchers (noon-1:15pm)
  • Afternoon session: Showcasing the work of AAHL and Barwon Health in infectious disease control (1:30-3pm)

Please click here for Program details

Please feel free to drop in to one, two or all three sessions!  To ensure adequate catering you can register at eventbrite


Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds

Authors: Jessy Vibin, Anthony Chamings, Fiona Collier, Marcel Klaassen, Tiffanie M. Nelson & Soren Alexandersen

SourceScientific Reportsvolume 8, Article number: 8686 (2018)

Brief summary of the paper: We present an optimised metagenomics method for detection and characterisation of all virus types including single and double stranded DNA/RNA and enveloped and non-enveloped viruses.

Initial evaluation included both spiked and non-spiked bird faecal samples as well as non-spiked human faecal samples. From the non-spiked bird samples (Australian Muscovy duck and Pacific black ducks) we detected 21 viruses, and we also present a summary of a few viruses detected in human faecal samples.

We then present a detailed analysis of selected virus sequences in the avian samples that were somewhat similar to known viruses, and had good quality (Q20 or higher) and quantity of next-generation sequencing reads, and was of interest from a virological point of view, for example, avian coronavirus and avian paramyxovirus 6. Some of these viruses were closely related to known viruses while others were more distantly related with 70% or less identity to currently known/sequenced viruses.

Besides detecting viruses, the technique also allowed the characterisation of host mitochondrial DNA present and thus identifying host species, while ribosomal RNA sequences provided insight into the “ribosomal activity microbiome”; of gut parasites; and of food eaten such as plants or insects, which we correlated to non-avian host associated viruses.