A comparison of amplification methods to detect Avian Influenza viruses in California wetlands targeted via remote sensing of waterfowl

McCuen, Madeline M.; Pitesky, Maurice; Buler, Jeffrey J.; Acosta, Sarai; Wilcox, Alexander H.; Bond, Ronald F.; Díaz‐Muñoz, Samuel L.

doi:10.1111/tbed.13612

Cited by 6 publications

(7 citation statements)

References 33 publications

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“…This uncoupling of detection by qRT-PCR vs sequencing is likely due to the fact that qRT-PCR targets only a small portion of the genome and sequencing primers cover the entire genome (e.g. [ 35 ]). Furthemore, environmental samples in particular may have been degraded or diluted, affecting the genomic RNA available for reverse transcription, as observed in multiple studies of environmental samples [ 36 – 38 ].…”

Section: Resultsmentioning

confidence: 99%

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SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis

et al. 2021

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Rationale There is little doubt that aerosols play a major role in the transmission of SARS-CoV-2. The significance of the presence and infectivity of this virus on environmental surfaces, especially in a hospital setting, remains less clear. Objectives We aimed to analyze surface swabs for SARS-CoV-2 RNA and infectivity, and to determine their suitability for sequence analysis. Methods Samples were collected during two waves of COVID-19 at the University of California, Davis Medical Center, in COVID-19 patient serving and staff congregation areas. qRT-PCR positive samples were investigated in Vero cell cultures for cytopathic effects and phylogenetically assessed by whole genome sequencing. Measurements and main results Improved cleaning and patient management practices between April and August 2020 were associated with a substantial reduction of SARS-CoV-2 qRT-PCR positivity (from 11% to 2%) in hospital surface samples. Even though we recovered near-complete genome sequences in some, none of the positive samples (11 of 224 total) caused cytopathic effects in cultured cells suggesting this nucleic acid was either not associated with intact virions, or they were present in insufficient numbers for infectivity. Phylogenetic analysis suggested that the SARS-CoV-2 genomes of the positive samples were derived from hospitalized patients. Genomic sequences isolated from qRT-PCR negative samples indicate a superior sensitivity of viral detection by sequencing. Conclusions This study confirms the low likelihood that SARS-CoV-2 contamination on hospital surfaces contains infectious virus, disputing the importance of fomites in COVID-19 transmission. Ours is the first report on recovering near-complete SARS-CoV-2 genome sequences directly from environmental surface swabs.

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Section: Resultsmentioning

confidence: 99%

Section: Whole-genome Pcr and Sequencing Yields More Effective Detection Of Sars-cov-2 Than Qrt-pcrmentioning

confidence: 99%

SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis

et al. 2021

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show abstract

“…This uncoupling of detection by qRT-PCR vs sequencing is likely due to the fact that qRT-PCR targets only a small portion of the genome and sequencing primers cover the entire genome (e.g. (33)). Furthemore, environmental samples in particular may have been degraded or diluted, affecting the genomic RNA available for reverse transcription, as observed in multiple studies of environmental samples ((34–36).…”

Section: Resultsmentioning

confidence: 99%

SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis

Coil

Albertson

Banerjee

et al. 2021

Preprint

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RationaleThere is little doubt that aerosols play a major role in the transmission of SARS-CoV-2. The significance of the presence and infectivity of this virus on environmental surfaces, especially in a hospital setting, remains less clear.ObjectivesWe aimed to analyze surface swabs for SARS-CoV-2 RNA and infectivity, and to determine their suitability for sequence analysis.MethodsSamples were collected during two waves of COVID-19 at the University of California, Davis Medical Center, in COVID-19 patient serving and staff congregation areas. qRT-PCR positive samples were investigated in Vero cell cultures for cytopathic effects and phylogenetically assessed by whole genome sequencing.Measurements and Main ResultsImproved cleaning and patient management practices between April and August 2020 were associated with a substantial reduction of SARS-CoV-2 qRT-PCR positivity (from 11% to 2%) in hospital surface samples. Even though we recovered near-complete genome sequences in some, none of the positive samples (11 of 224 total) caused cytopathic effects in cultured cells suggesting this nucleic acid was either not associated with intact virions, or they were present in insufficient numbers for infectivity. Phylogenetic analysis suggested that the SARS-CoV-2 genomes of the positive samples were derived from hospitalized patients. Genomic sequences isolated from qRT-PCR negative samples indicate a superior sensitivity of viral detection by sequencing.ConclusionsThis study confirms the low likelihood that SARS-CoV-2 contamination on hospital surfaces contains infectious virus, disputing the importance of fomites in COVID-19 transmission. Ours is the first report on recovering near-complete SARS-CoV-2 genome sequences directly from environmental surface swabs.

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“…Dispersion of virus-contaminated fecal matter and oropharyngeal excretions in surface waters is expected to potentiate transmission efficacy: (1) Depending on the AI virus strain but also on various physico-chemical properties of the water body such as temperature, pH, salinity, sedimentation rates, presence of biologic compounds and so on, the infectivity of virus particles shed into such water is retained for astonishingly long periods of up to several months [ 26 ]. Conversely, higher water temperatures (22°C), alkaline or acid pH and high salinity inactivate viral infectivity within hours to days [ 26–30 , 31 ]. Furthermore, the presence of invertebrate animals (clams, snails, shrimps, insects) may modulate the retention time of infectious AIV in surface water and sediments [ 26 , 32–34 ].…”

Section: Introductionmentioning

confidence: 99%

Exploring surface water as a transmission medium of avian influenza viruses – systematic infection studies in mallards

Ahrens

Selinka

Mettenleiter

et al. 2022

Emerging Microbes & Infections

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Mallards ( Anas platyrhynchos ) are an abundant anseriform migratory wild bird species worldwide and an important reservoir for the maintenance of low pathogenicity (LP) avian influenza viruses (AIV). They have also been implicated in the spread of high pathogenicity (HP) AIV after spill-over events from HPAIV-infected poultry. The spread of HPAIV within wild water bird populations may lead to viral contamination of natural habitats. The role of small shallow water bodies as a transmission medium of AIV among mallards is investigated here in three experimental settings. (i) Delayed onset but rapid progression of infection seeded by two mallards inoculated with either LP or HP AIV to each eight sentinel mallards was observed in groups with access to a small 100 L water pool. In contrast, groups with a bell drinker as the sole source of drinking water showed a rapid onset but lengthened course of infection. (ii) HPAIV infection also set off when virus was dispersed in the water pool; titres as low as 10 2 TCID 50 L −1 (translating to 0.1 TCID 50 mL −1 ) proved to be sufficient. (iii) Substantial loads of viral RNA (and infectivity) were also found on the surface of the birds’ breast plumage. “Unloading” of virus infectivity from contaminated plumage into water bodies may be an efficient mechanism of virus spread by infected mallards. However, transposure of HPAIV via the plumage of an uninfected mallard failed. We conclude, surface water in small shallow water bodies may play an important role as a mediator of AIV infection of aquatic wild birds.

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A comparison of amplification methods to detect Avian Influenza viruses in California wetlands targeted via remote sensing of waterfowl

Cited by 6 publications

References 33 publications

SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis

SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis

SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis

Exploring surface water as a transmission medium of avian influenza viruses – systematic infection studies in mallards

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