Persistent SARS-CoV-2 replication in severe COVID-19

BackgroundThe diagnosis of SARS-CoV-2 infection is based on viral RNA detection by real-time RT-PCR (rRT-PCR) in respiratory samples. This detection can remain positive for weeks without implying virus viability.MethodsWe have performed cell culture to assess viral replication in 106 respiratory samples rRT-PCR positive for SARS-CoV-2 from 105 patients with COVID-19. Fifty were samples from 50 patients with mild forms of COVID-19 who did not require hospital admission. Fifty-six samples were obtained from 55 hospitalized patients with severe pneumonia. Samples were obtained at different time points covering the time from clinical diagnosis to the follow up during hospital care.ResultsIn 49 samples (49/106, 46.2%) a cytopathic effect (CPE) was detected in cell culture. Our study demonstrates that while in patients with mild COVID-19, viral viability is maintained in fact up to 10 days in patients with severe COVID-19 the virus can remain viable for up to 32 days after the onset of symptoms. Patients with severe COVID-19 as compared with mild cases, presented infective virus in a significantly higher proportion in samples with moderate or low viral load (Ct value > 26): 22/46 (47.8%) versus 7/38 (18.4%), (p <0.01), respectively.ConclusionsPersistent SARS-CoV-2 replication could be demonstrated in severe COVID-19 cases for periods up to 32 days after the onset of symptoms and even at high Ct values. COVID-19 severity is a more determining factor for viral viability than the time elapsed since the onset of symptoms or the Ct value obtained in the RT-PCR assay.

Evolutionary origins of epidemic potential among human RNA viruses

To have epidemic potential, a pathogen must be able to spread in human populations, but of human-infective RNA viruses only a minority can do so. We investigated the evolution of human transmissibility through parallel analyses of 1755 virus genome sequences from 39 RNA virus genera. We identified 57 lineages containing human-transmissible species and estimated that at least 74% of these lineages have evolved directly from non-human viruses in other mammals or birds, a public health threat recently designated “Disease X”. Human-transmissible viruses rarely evolve from virus lineages that can infect but not transmit between humans. This result cautions against focussing surveillance and mitigation efforts narrowly on currently known human-infective virus lineages and supports calls for a better understanding of RNA virus diversity in non-human hosts.

Detection of Murine Norovirus-1 by Using TAT Peptide-Delivered Molecular Beacons

ABSTRACTA TAT peptide-delivered molecular beacon was developed and utilized to enumerate murine norovirus 1, a human norovirus (NoV) surrogate, in RAW 264.7 cells. This allowed the detection of a single infective virus within 6 h, a 12-fold improvement in time required for viral detection and quantification compared to that required by the conventional plaque assay.

Investigation on the transmission of some Tobamoviruses by pollen and seed in pepper (Capsicum annuum L.)

Five pepper cultivars were mechanically inoculated with isolates of three Tobamovirus species, viz. the "Gelb" strain of tobacco mosaic virus (TMV-G), the XM-isolate of dulcamara yellow fleck virus (DYFV-XM) and the Nov/H isolate of pepper mild mottle virus (PMMV-Nov/H), respectively. Symptoms caused by the viruses were characterised. The viruses were sucessfully re-isolated from different organs (roots, leaves, fruit parts) of susceptible peppers to test plants. It was estabilished, that the pollen of diseased peppers carried infective virions at least on their surface. Washes of seeds were highly infective, but no infectivity was found after treatment of the seeds with 2% NaOH or 10% Na3PO4. No infectivity of inocula prepared from seed-coats of alkaline treated seeds was established. Infection of young seedlings grown from untreated seeds was demonstrated, while the seedlings came from alkaline treated seeds remained free of infective virus. The possible role of pollen and seed in the epidemiology of Tobamoviruses pathogenic to pepper as well as the importance of seed treatment is discussed.

Experimental infection of ostriches with Crimean–Congo haemorrhagic fever virus

Following the occurrence of an outbreak of Crimean–Congo haemorrhagic fever (CCHF) among workers at an ostrich abattoir in South Africa in 1996, 9 susceptible young ostriches were infected subcutaneously with the virus in order to study the nature of the infection which they undergo. The ostriches developed viraemia which was demonstrable on days 1–4 following infection, with a maximum intensity of 4·0 log10 mouse intracerebral LD50/ml being recorded on day 2 in 1 of the birds. Virus was detectable in visceral organs such as spleen, liver and kidney up to day 5 post-inoculation, 1 day after it could no longer be found in blood. No infective virus was detected in samples of muscle, but viral nucleic acid was detected by reverse transcription-polymerase chain reaction in muscle from a bird sacrificed on day 3 following infection. It was concluded that the occurrence of infection in ostriches at abattoirs could be prevented by keeping the birds free of ticks for 14 days before slaughter.