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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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.


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