Coronaviruses from the One Health Perspective

Editorial

01 December 2023

Editorial: Coronaviruses from the One Health perspective

Maged Gomaa Hemida

Dilfuza Egamberdieva

and

Yashpal S. Malik

1,140 views

1 citations

Editors

Maged Gomaa Hemida

Long Island University

Dilfuza Egamberdieva

Leibniz Center for Agricultural Landscape Research (ZALF)

Yashpal S. Malik

College of Animal Biotechnology, Guru Angad Dev Vety and Animal Sciences University, Ludhiana, Punjab, India

Impact

Original Research

28 April 2023

Decay of enveloped SARS-CoV-2 and non-enveloped PMMoV RNA in raw sewage from university dormitories

Ye Li

, 9 more and

Terry C. Hazen

Persistence of SARS-CoV-2 over time (days) in raw sewage from university dormitories. (A) High-concentration level of SARS-CoV-2 (CSARS-CoV-2 RNA > 104 copies/L), (B) Medium-concentration level of SARS-CoV-2 (104 copies/L > CSARS-CoV-2 RNA > 103 copies/L), (C) Low-concentration level of SARS-CoV-2 (103 copies/L > CSARS-CoV-2 RNA > 102 copies/L), (D) Long time decay of SARS-CoV-2 at 4°C. LQ means the limit of quantification in RT-qPCR. F4, D13-6, D13-1, D13-24-1, D3, S14, D13-2-1, D13-24-2, S12-1, F7, S12-2, D13-2-2, F2, D14-1, D14-2, NC, and CL correspond to different campus samples.

Introduction: Although severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA has been frequently detected in sewage from many university dormitories to inform public health decisions during the COVID-19 pandemic, a clear understanding of SARS-CoV-2 RNA persistence in site-specific raw sewage is still lacking. To investigate the SARS-CoV-2 RNA persistence, a field trial was conducted in the University of Tennessee dormitories raw sewage, similar to municipal wastewater.

Methods: The decay of enveloped SARS-CoV-2 RNA and non-enveloped Pepper mild mottle virus (PMMoV) RNA was investigated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in raw sewage at 4°C and 20°C.

Results: Temperature, followed by the concentration level of SARS-CoV-2 RNA, was the most significant factors that influenced the first-order decay rate constants (k) of SARS-CoV-2 RNA. The mean k values of SARS-CoV-2 RNA were 0.094 day⁻¹ at 4°C and 0.261 day⁻¹ at 20°C. At high-, medium-, and low-concentration levels of SARS-CoV-2 RNA, the mean k values were 0.367, 0.169, and 0.091 day⁻¹, respectively. Furthermore, there was a statistical difference between the decay of enveloped SARS-CoV-2 and non-enveloped PMMoV RNA at different temperature conditions.

Discussion: The first decay rates for both temperatures were statistically comparable for SARS-CoV-2 RNA, which showed sensitivity to elevated temperatures but not for PMMoV RNA. This study provides evidence for the persistence of viral RNA in site-specific raw sewage at different temperature conditions and concentration levels.

3,135 views

17 citations

Rates of bacterial co-infection of COVID-19 patients in different subgroups (*p < 0.05). (A) Rates of bacterial co-infection in different clinical subgroups. (B) Rate of bacterial co-infection in different PII subgroups.

Original Research

29 June 2023

Bacterial co-infection raises in-hospital mortality of COVID-19 patients: a retrospective study

Kaican Zong

, 4 more and

Shiying Li

1,678 views

2 citations

Review

13 October 2022

The relation between avian coronaviruses and SARS-CoV-2 coronavirus

Hanan Al-Khalaifah

, 1 more and

Afaf Al-Nasser

The coronaviruses (CoVs) are a family of ribonucleic acid viruses that are present in both mammals and birds. SARS-CoV and MERS-CoV originated in bats, and there is a possibility that this could be the case for SARS-CoV-2 as well. There is already evidence that a probable intermediary host is responsible for the emergence of viruses in humans as was the case for SARS-CoVs and MERS-CoV. As the SARS-CoV-2 originated from a live animal market, there is always the question if domestic animals are susceptible to these viruses and the possible risk of zoonotic transmission with mammals, including humans. This uncertainty of the transmission of the COVID-19 virus between humans and animals is of great significance worldwide. Hence, this paper focuses on the avian CoVs and their possible relation and interaction with SARS-CoV-2.

7,150 views

4 citations

Study enrollment and data analysis flowcharts. (A) Patients at UMass Medical center were enrolled for our study according to the following flow chart. Fifty patients with acute COVID-19 were ultimately selected for our study cohort and followed for a clinical outcome of whether they needed respiratory support and what level of respiratory support was required, ranging from supplemental oxygen via simple nasal cannula escalating through intubation and mechanical ventilation. The number of patients requiring each level of respiratory support is shown in the final chart on the right. (B) Data from clinical covariates and microbiome sequencing results are combined in a random forest classifier to determine features predicting the need for respiratory support. We then applied the Stable and Interpretable RUle Set (SIRUS) to these results to generate easily interpretable rules predicting which clinical covariates and microbiome features are predictive of the need for respiratory support.

Original Research

30 September 2022

Oropharyngeal microbiome profiled at admission is predictive of the need for respiratory support among COVID-19 patients

Evan S. Bradley

, 11 more and

John P. Haran

The oropharyngeal microbiome, the collective genomes of the community of microorganisms that colonizes the upper respiratory tract, is thought to influence the clinical course of infection by respiratory viruses, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Infectious Disease 2019 (COVID-19). In this study, we examined the oropharyngeal microbiome of suspected COVID-19 patients presenting to the Emergency Department and an inpatient COVID-19 unit with symptoms of acute COVID-19. Of 115 initially enrolled patients, 50 had positive molecular testing for COVID-19+ and had symptom duration of 14 days or less. These patients were analyzed further as progression of disease could most likely be attributed to acute COVID-19 and less likely a secondary process. Of these, 38 (76%) went on to require some form of supplemental oxygen support. To identify functional patterns associated with respiratory illness requiring respiratory support, we applied an interpretable random forest classification machine learning pipeline to shotgun metagenomic sequencing data and select clinical covariates. When combined with clinical factors, both species and metabolic pathways abundance-based models were found to be highly predictive of the need for respiratory support (F1-score 0.857 for microbes and 0.821 for functional pathways). To determine biologically meaningful and highly predictive signals in the microbiome, we applied the Stable and Interpretable RUle Set to the output of the models. This analysis revealed that low abundance of two commensal organisms, Prevotella salivae or Veillonella infantium (< 4.2 and 1.7% respectively), and a low abundance of a pathway associated with LPS biosynthesis (< 0.1%) were highly predictive of developing the need for acute respiratory support (82 and 91.4% respectively). These findings suggest that the composition of the oropharyngeal microbiome in COVID-19 patients may play a role in determining who will suffer from severe disease manifestations.

4,612 views

14 citations

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