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1.
Curr Opin Gastroenterol ; 37(1): 4-8, 2021 01.
Article in English | MEDLINE | ID: covidwho-2318694

ABSTRACT

PURPOSE OF REVIEW: We discuss the potential role of the faecal chain in COVID-19 and highlight recent studies using waste water-based epidemiology (WBE) to track severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RECENT FINDINGS: WBE has been suggested as an adjunct to improve disease surveillance and aid early detection of circulating disease. SARS-CoV-2, the aetiological agent of COVID-19, is an enveloped virus, and as such, typically not associated with the waste water environment, given high susceptibility to degradation in aqueous conditions. A review of the current literature supports the ability to detect of SARS-CoV-2 in waste water and suggests methods to predict community prevalence based on viral quantification. SUMMARY: The summary of current practices shows that while the isolation of SARS-CoV-2 is possible from waste water, issues remain regarding the efficacy of virial concentration and subsequent quantification and alignment with epidemiological data.


Subject(s)
COVID-19/epidemiology , Public Health Surveillance/methods , SARS-CoV-2/isolation & purification , Sewage/virology , COVID-19/diagnosis , Feces/virology , Global Health , Humans
2.
Science ; 375(6585): 1100-1104, 2022 Mar 11.
Article in English | MEDLINE | ID: covidwho-2285693
3.
Epidemiol Prev ; 44(5-6): 330-332, 2020.
Article in Italian | MEDLINE | ID: covidwho-2240354

ABSTRACT

Systematic reviews have shown a prevalence close to 20% of gastrointestinal symptoms in COVID-19 positive patients, with nearly 40% of patients shedding viral RNA in their faeces, even if it may not be infectious, possibly because of inactivation by colonic fluid.According to current evidence, this virus is primarily transmitted by respiratory droplets and contact routes, including contaminated surfaces. The virus is quite stable on stainless steel, being detected up to 48-72 hours after application. Therefore, some individuals can be infected touching common contaminated surfaces, such as bathroom taps. Taps can be underestimated critical points in the transmission chain of the infection. Indeed, just by turning the knob, people leave germs on it, especially after coughing over their hands, sneezing, and/or blowing their nose. After handwashing with soap, user take back their germs when turning the knob. Paradoxically, the following user collects the germs back on his/her fingers by implementing a preventive measure, maybe before putting food into the mouth or wearing contact lenses.The Italian National Institute of Health recommends to clean and disinfect high-touched surfaces, but it is unrealistic and inefficient to do so after each tap use. As an alternative, new toilets should install long elbow-levers - or at least short levers - provided that people are educated to close them with the forearm or the side of the hand. This is already a standard measure in hospitals, but it is particularly important also in high-risk communities, such as retirement homes and prisons. It would be important also in schools, in workplaces, and even in families, contributing to the prevention both of orofaecal and respiratory infections.In the meantime, people should be educated to close existing knobs with disposable paper towel wipes or with toilet paper sheets.


Subject(s)
Bathroom Equipment/virology , COVID-19/prevention & control , Fomites/virology , Hand Hygiene , Health Education , SARS-CoV-2/physiology , COVID-19/transmission , Equipment Contamination , Equipment Design , Feces/virology , Female , Humans , Italy , Male , SARS-CoV-2/isolation & purification , Touch
4.
PLoS One ; 18(1): e0278675, 2023.
Article in English | MEDLINE | ID: covidwho-2197053

ABSTRACT

BACKGROUND: HIV may increase SARS-CoV-2 infection risk and COVID-19 severity generally, but data are limited about its impact on postpartum women and their infants. As such, we characterized SARS-CoV-2 infection among mother-infant pairs in Nairobi, Kenya. METHODS: We conducted a nested study of 62 HIV-uninfected and 64 healthy women living with HIV, as well as their HIV-exposed uninfected (N = 61) and HIV-unexposed (N = 64) infants, participating in a prospective cohort. SARS-CoV-2 serology was performed on plasma collected between May 1, 2020-February 1, 2022 to determine the incidence, risk factors, and symptoms of infection. SARS-CoV-2 RNA PCR and sequencing was also performed on available stool samples from seropositive participants. RESULTS: SARS-CoV-2 seropositivity was found in 66% of the 126 mothers and in 44% of the 125 infants. There was no significant association between SARS-CoV-2 infection and maternal HIV (Hazard Ratio [HR] = 0.810, 95% CI: 0.517-1.27) or infant HIV exposure (HR = 1.47, 95% CI: 0.859-2.53). Maternal SARS-CoV-2 was associated with a two-fold increased risk of infant infection (HR = 2.31, 95% CI: 1.08-4.94). Few participants (13% mothers, 33% infants) had symptoms; no participant experienced severe COVID-19 or death. Seroreversion occurred in about half of mothers and infants. SARS-CoV-2 sequences obtained from stool were related to contemporaneously circulating variants. CONCLUSIONS: These data indicate that postpartum Kenyan women and their infants were at high risk for SARS-CoV-2 infection and that antibody responses waned over an average of 8-10 months. However, most cases were asymptomatic and healthy women living with HIV did not have a substantially increased risk of infection or severe COVID-19.


Subject(s)
COVID-19 , HIV Infections , Female , Humans , Infant , COVID-19/epidemiology , COVID-19/complications , HIV Infections/epidemiology , HIV Infections/complications , Kenya/epidemiology , Postpartum Period , Prospective Studies , RNA, Viral/analysis , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Case-Control Studies , Feces/virology , Polymerase Chain Reaction
6.
Gastroenterol Hepatol ; 43(8): 464-471, 2020 Oct.
Article in English, Spanish | MEDLINE | ID: covidwho-2095369

ABSTRACT

The SARS-CoV-2 pandemic is leading to high mortality and a global health crisis. The primary involvement is respiratory; however, the virus can also affect other organs, such as the gastrointestinal tract and liver. The most common symptoms are anorexia and diarrhea. In about half of the cases, viral RNA could be detected in the stool, which is another line of transmission and diagnosis. covid19 has a worse prognosis in patients with comorbidities, although there is not enough evidence in case of previous digestive diseases. Digestive endoscopies may give rise to aerosols, which make them techniques with a high risk of infection. Experts and scientific organizations worldwide have developed guidelines for preventive measures. The available evidence on gastrointestinal and hepatic involvement, the impact on patients with previous digestive diseases and operating guidelines for Endoscopy Units during the pandemic are reviewed.


Subject(s)
Betacoronavirus/pathogenicity , Coronavirus Infections/complications , Digestive System Diseases/etiology , Digestive System/virology , Pandemics , Pneumonia, Viral/complications , Aerosols , Angiotensin-Converting Enzyme 2 , Anorexia/etiology , Antiviral Agents/adverse effects , Betacoronavirus/isolation & purification , Betacoronavirus/physiology , COVID-19 , Cohort Studies , Coronavirus Infections/drug therapy , Coronavirus Infections/prevention & control , Coronavirus Infections/transmission , Diarrhea/etiology , Digestive System Diseases/virology , Endoscopy, Digestive System/adverse effects , Feces/virology , Humans , Immunosuppressive Agents/adverse effects , Intestines/chemistry , Intestines/virology , Liver Diseases/etiology , Multicenter Studies as Topic , Pandemics/prevention & control , Peptidyl-Dipeptidase A/analysis , Peptidyl-Dipeptidase A/physiology , Personal Protective Equipment , Pneumonia, Viral/drug therapy , Pneumonia, Viral/prevention & control , Pneumonia, Viral/transmission , Receptors, Virus/analysis , Receptors, Virus/physiology , Risk , SARS-CoV-2 , Universal Precautions , COVID-19 Drug Treatment
7.
J Virol ; 96(18): e0103422, 2022 09 28.
Article in English | MEDLINE | ID: covidwho-2019727

ABSTRACT

The duration of SARS-CoV-2 genomic RNA shedding is much longer than that of infectious SARS-CoV-2 in most COVID-19 patients. It is very important to determine the relationship between test results and infectivity for efficient isolation, contact tracing, and post-isolation. We characterized the duration of viable SARS-CoV-2, viral genomic and subgenomic RNA (gRNA and sgRNA), and rapid antigen test positivity in nasal washes, oropharyngeal swabs, and feces of experimentally infected Syrian hamsters. The duration of viral genomic RNA shedding is longer than that of viral subgenomic RNA, and far longer than those of rapid antigen test (RAgT) and viral culture positivity. The rapid antigen test results were strongly correlated with the viral culture results. The trend of subgenomic RNA is similar to that of genomic RNA, and furthermore, the subgenomic RNA load is highly correlated with the genomic RNA load. IMPORTANCE Our findings highlight the high correlation between rapid antigen test and virus culture results. The rapid antigen test would be an important supplement to real-time reverse transcription-RCR (RT-PCR) in early COVID-19 screening and in shortening the isolation period of COVID-19 patients. Because the subgenomic RNA load can be predicted from the genomic RNA load, measuring sgRNA does not add more benefit to determining infectivity than a threshold determined for gRNA based on viral culture.


Subject(s)
COVID-19 , RNA, Viral , SARS-CoV-2 , Animals , COVID-19/diagnosis , COVID-19/virology , Cricetinae , Feces/virology , Genomics , Humans , Mesocricetus , RNA, Viral/analysis , RNA, Viral/genetics , SARS-CoV-2/genetics , Virus Shedding
9.
J Med Virol ; 93(2): 886-891, 2021 02.
Article in English | MEDLINE | ID: covidwho-1898895

ABSTRACT

Italy was one of the most affected nations by coronavirus disease 2019 outside China. The infections, initially limited to Northern Italy, spread to all other Italian regions. This study aims to provide a snapshot of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) epidemiology based on a single-center laboratory experience in Rome. The study retrospectively included 6565 subjects tested for SARS-CoV-2 at the Laboratory of Virology of Sapienza University Hospital in Rome from 6 March to 4 May. A total of 9995 clinical specimens were analyzed, including nasopharyngeal swabs, bronchoalveolar lavage fluids, gargle lavages, stools, pleural fluids, and cerebrospinal fluids. Positivity to SARS-CoV-2 was detected in 8% (527/6565) of individuals, increased with age, and was higher in male patients (P < .001). The number of new confirmed cases reached a peak on 18 March and then decreased. The virus was detected in respiratory samples, in stool and in pleural fluids, while none of gargle lavage or cerebrospinal fluid samples gave a positive result. This analysis allowed to gather comprehensive information on SARS-CoV-2 epidemiology in our area, highlighting positivity variations over time and in different sex and age group and the need for a continuous surveillance of the infection, mostly because the pandemic evolution remains unknown.


Subject(s)
COVID-19 , Pandemics , SARS-CoV-2/pathogenicity , Adolescent , Adult , Aged , Aged, 80 and over , Bronchoalveolar Lavage Fluid/virology , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19 Testing , Child , Child, Preschool , Feces/virology , Female , Hospitals, University , Humans , Infant , Infant, Newborn , Laboratories , Male , Middle Aged , Nasopharynx/virology , Pleural Effusion/virology , Retrospective Studies , Reverse Transcriptase Polymerase Chain Reaction , Rome/epidemiology , SARS-CoV-2/genetics , Severity of Illness Index
10.
PLoS One ; 17(3): e0265426, 2022.
Article in English | MEDLINE | ID: covidwho-1745308

ABSTRACT

BACKGROUND: Faecal microbiota transplantation (FMT) is an efficacious treatment for patients with recurrent Clostridioides difficile infections (rCDI). Stool banks facilitate FMT by providing screened faecal suspensions from highly selected healthy donors. Due to the ongoing coronavirus disease 2019 (COVID-19) pandemic and the potential risk of SARS coronavirus-2 (SARS-CoV-2) transmission via FMT, many stool banks were forced to temporarily halt and adjust donor activities. GOAL: The evaluation of a strategy to effectively continue stool banking activities during the ongoing COVID-19 pandemic. STUDY: To restart our stool banking activities after an initial halt, we implemented periodic SARS-CoV-2 screening in donor faeces and serum, and frequent donor assessment for COVID-19 related symptoms. FMT donor and recipient data obtained before (2016-2019) and during the COVID-19 pandemic (March 2020-August 2021) were compared to assess stool banking efficacy. RESULTS: Two out of ten donors developed COVID-19. No differences during versus before the COVID-19 pandemic were observed in the number of approved faeces donations (14 vs 22/month, p = 0.06), FMT requests for rCDI (3.9 vs 4.3/month, p = 0.6); rCDI patients eligible for FMT (80.6% vs 73.3%, p = 0.2); rCDI cure rate (90.3% vs 89.2%, p = 0.9); CDI-free survival (p = 0.7); the number of non-rCDI patients treated with FMT (0.5/month vs 0.4/month), and the number of possibly FMT related adverse events (9.5% vs 7.8%, p = 0.7). Two FMTs for rCDI were delayed due to COVID-19. CONCLUSIONS: There is a continued need for FMT treatment of rCDI during the COVID-19 pandemic. Appropriate donor screening and SARS-CoV-2 infection prevention measures can be implemented in existing protocols without increasing the burden for donors, and allow safe, effective and efficient FMT during the ongoing COVID-19 pandemic. Stool banks should evaluate their SARS-CoV-2 donor screening protocols for long-term sustainability and efficacy, and share their experiences to help the utilisation, standardisation and improvement of stool banks worldwide.


Subject(s)
COVID-19/prevention & control , Fecal Microbiota Transplantation/methods , Feces/virology , Tissue Banks , Aged , COVID-19/epidemiology , COVID-19/transmission , Clostridium Infections/therapy , Female , Humans , Male , Netherlands/epidemiology , Retrospective Studies , SARS-CoV-2
11.
J Med Virol ; 94(4): 1315-1329, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1718396

ABSTRACT

In December 2019, novel severe acute respiratory syndrome coronavirus 2 (nSARS-CoV-2) virus outbreaks emerged from Wuhan, China, and spread all over the world, including India. Molecular diagnosis of Coronavirus Disease 2019 (COVID) 19 for densely and highly populated countries like India is time-consuming. A few reports have described the successful diagnosis of nSARS-CoV-2 virus from sewage and wastewater samples contaminated with fecal matter, suggesting the diagnosis of COVID 19 from the same to raise an alarm about the community transmission of virus for implementation of evacuation and lockdown strategies. So far, the association between the detection of virus and its concentration in stool samples with severity of the disease and the presence or absence of gastrointestinal symptoms have been rarely reported. We led the search utilizing multiple databases, specifically PubMed (Medline), EMBASE, and Google Scholar. We conducted a literature survey on gastrointestinal infection and the spread of this virus through fecal-oral transmission. Reports suggested that the existence and persistence of nSARS-CoV-2 in anal/rectal swabs and stool specimens for a longer period of time than in nasopharyngeal swabs provides a strong tenable outcome of gastrointestinal contamination and dissemination of this infection via potential fecal-oral transmission. This review may be helpful to conduct further studies to address the enteric involvement and excretion of nSARS-CoV-2 RNA in feces and control the community spread in both COVID-19 patients ahead of the onset of symptoms and in asymptomatic individuals through wastewater and sewage surveillance as an early indication of infection. The existence of the viral genome and active viral particle actively participate in genomic variations. Hence, we comprehended the enteric spread of different viruses amongst communities with special reference to nSARS-CoV-2.


Subject(s)
COVID-19/virology , Disease Transmission, Infectious , Gastrointestinal Diseases/virology , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/transmission , Disease Transmission, Infectious/prevention & control , Feces/virology , Gastrointestinal Diseases/epidemiology , Gastrointestinal Diseases/prevention & control , Gastrointestinal Tract/virology , Humans , India/epidemiology , SARS-CoV-2/genetics , Sewage/virology , Water Purification
12.
Viruses ; 14(2)2022 02 17.
Article in English | MEDLINE | ID: covidwho-1704412

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have spilled over from humans to companion and wild animals since the inception of the global COVID-19 pandemic. However, whole genome sequencing data of the viral genomes that infect non-human animal species have been scant. Here, we detected and sequenced a SARS-CoV-2 delta variant (AY.3) in fecal samples from an 11-year-old domestic house cat previously exposed to an owner who tested positive for SARS-CoV-2. Molecular testing of two fecal samples collected 7 days apart yielded relatively high levels of viral RNA. Sequencing of the feline-derived viral genomes showed the two to be identical, and differing by between 4 and 14 single nucleotide polymorphisms in pairwise comparisons to human-derived lineage AY.3 sequences collected in the same geographic area and time period. However, several mutations unique to the feline samples reveal their divergence from this cohort on phylogenetic analysis. These results demonstrate continued spillover infections of emerging SARS-CoV-2 variants that threaten human and animal health, as well as highlight the importance of collecting fecal samples when testing for SARS-CoV-2 in animals. To the authors' knowledge, this is the first published case of a SARS-CoV-2 delta variant in a domestic cat in the United States.


Subject(s)
COVID-19/veterinary , Feces/virology , Pets/virology , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Animals , COVID-19/transmission , COVID-19/virology , Cats , Female , Genome, Viral/genetics , Humans , Phylogeny , RNA, Viral/genetics , SARS-CoV-2/classification , United States , Whole Genome Sequencing
13.
Viruses ; 14(1)2022 01 09.
Article in English | MEDLINE | ID: covidwho-1611142

ABSTRACT

We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the greater (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern regions of Russia. The viruses, named Khosta-1 and Khosta-2, together with related viruses from Bulgaria and Kenya, form a separate phylogenetic lineage. We found evidence of recombination events in the evolutionary history of Khosta-1, which involved the acquisition of the structural proteins S, E, and M, as well as the nonstructural genes ORF3, ORF6, ORF7a, and ORF7b, from a virus that is related to the Kenyan isolate BtKY72. The examination of bats by RT-PCR revealed that 62.5% of the greater horseshoe bats in one of the caves were positive for Khosta-1 virus, while its overall prevalence was 14%. The prevalence of Khosta-2 was 1.75%. Our results show that SARS-like coronaviruses circulate in horseshoe bats in the region, and we provide new data on their genetic diversity.


Subject(s)
Chiroptera/virology , Severe acute respiratory syndrome-related coronavirus/genetics , Animals , Base Sequence , Chiroptera/classification , Evolution, Molecular , Feces/virology , Metagenomics , Mouth/virology , Phylogeny , Prevalence , Recombination, Genetic , Russia , Severe acute respiratory syndrome-related coronavirus/classification , Species Specificity , Spike Glycoprotein, Coronavirus/genetics , Viral Proteins/genetics
14.
Arch Virol ; 166(6): 1599-1605, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1549420

ABSTRACT

Pigeon paramyxovirus-1 (PPMV-1) is a strain of Newcastle disease virus (NDV) that has adapted to infect pigeons and poses a constant threat to the commercial poultry industry. Early detection via rapid and sensitive methods, along with timely preventative and mitigating actions, is important for reducing the spread of PPMV-1. Here, we report the development of a TaqMan loop-mediated isothermal amplification assay (TaqMan-LAMP) for rapid and specific detection of PPMV-1 based on the F gene. This system makes use of six novel primers and a TaqMan probe that targets nine distinct regions of the F gene that are highly conserved among PPMV-1 isolates. The results showed that the limit of detection was 10 copies µL-1 for PPMV-1 cDNA and 0.1 ng for PPMV-1 RNA. The reaction was completed within 25 min and was thus faster than conventional RT-PCR. Moreover, no cross-reactions with similar viruses or with peste des petits ruminants virus (PPRV) or NDV LaSota vaccine strains were observed under the same conditions. To evaluate the applicability of the assay, the TaqMan-LAMP assay and a commercial RT-PCR assay were compared using 108 clinical samples, and the concordance rate between two methods was found to be 96.3%. The newly developed PPMV-1 TaqMan-LAMP assay can therefore be used for simple, efficient, rapid, specific, and sensitive diagnosis of PPMV-1 infections.


Subject(s)
Molecular Diagnostic Techniques/veterinary , Newcastle disease virus/genetics , Newcastle disease virus/isolation & purification , Nucleic Acid Amplification Techniques/veterinary , Animals , Columbidae , Feces/virology , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , RNA, Viral , Sensitivity and Specificity , Time Factors
16.
Eur Rev Med Pharmacol Sci ; 25(21): 6745-6766, 2021 11.
Article in English | MEDLINE | ID: covidwho-1524863

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has created the current pandemic, has caused a worldwide worry. Different countries have since enforced varying levels of lockdowns and guidelines for their populations to follow in a serious effort to mitigate the spread. Up until recently, the majority of these regulations and policies were established on the assumption that the dominant routes of transmission of this virus are through droplets and fomite contact. However, there is now a substantial amount of research pointing towards the strong possibility that SARS-CoV-2 can spread through airborne means. The World Health Organization (WHO) and the Center for Disease Control and Prevention (CDC) have recently recognized this, which poses the question of whether our collective methods of lessening transmission risk and keeping people safe have been sufficient. This paper is a comprehensive review of the evidence on SARS-CoV-2 being an airborne disease, through different epidemiological, experimental, and animal-model based published research. Studies opposing this evidence have also been discussed. The majority of these studies are favoring the high plausibility of SARS-CoV-2 aerosol transmission, and therefore the many implications of aerosol transmission have been discussed in this paper to suggest effective mitigation and control strategies.


Subject(s)
Aerosols , COVID-19/transmission , SARS-CoV-2/physiology , Animals , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/virology , Cricetinae , Disease Models, Animal , Equipment and Supplies, Hospital/virology , Feces/virology , Humans , Masks , Pandemics , Particulate Matter , RNA, Viral/metabolism , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Ventilation/standards , Virus Inactivation
17.
J Korean Med Sci ; 36(44): e301, 2021 Nov 15.
Article in English | MEDLINE | ID: covidwho-1526760

ABSTRACT

We used serial rectal swabs to investigate the amount and duration of virus secretion through the gastrointestinal tract and assessed the association between fecal shedding and gastrointestinal symptoms and to clarify the clinical usefulness testing rectal swabs. We enrolled ten adult patients hospitalized with symptomatic coronavirus disease 2019 (COVID-19). Respiratory and stool specimens were collected by physicians. The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed using real-time reverse-transcription polymerase chain reaction. All ten patients had respiratory symptoms, six had diarrhea, and seven were positive for SARS-CoV-2 on rectal swabs. The viral loads in the respiratory specimens was higher than those in the rectal specimens, and no rectal specimens were positive after the respiratory specimens became negative. There was no association between gastrointestinal symptoms, pneumonia, severity, and rectal viral load. Rectal swabs may play a role in detecting SARS-CoV-2 in individuals with suspected COVID-19, regardless of gastrointestinal symptoms.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/virology , Rectum/virology , SARS-CoV-2/isolation & purification , Virus Shedding , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/complications , COVID-19/transmission , Diarrhea/etiology , Diarrhea/virology , Feces/virology , Female , Humans , Male , Middle Aged , Nasopharynx/virology , Prospective Studies , Real-Time Polymerase Chain Reaction , Severity of Illness Index , Time Factors , Viral Load
18.
Viruses ; 12(8)2020 08 18.
Article in English | MEDLINE | ID: covidwho-1453290

ABSTRACT

Enteric viral co-infections, infections involving more than one virus, have been reported for a diverse group of etiological agents, including rotavirus, norovirus, astrovirus, adenovirus, and enteroviruses. These pathogens are causative agents for acute gastroenteritis and diarrheal disease in immunocompetent and immunocompromised individuals of all ages globally. Despite virus-virus co-infection events in the intestine being increasingly detected, little is known about their impact on disease outcomes or human health. Here, we review what is currently known about the clinical prevalence of virus-virus co-infections and how co-infections may influence vaccine responses. While experimental investigations into enteric virus co-infections have been limited, we highlight in vivo and in vitro models with exciting potential to investigate viral co-infections. Many features of virus-virus co-infection mechanisms in the intestine remain unclear, and further research will be critical.


Subject(s)
Coinfection/virology , Gastroenteritis/virology , Virus Diseases/physiopathology , Viruses/classification , Viruses/pathogenicity , Animals , Asymptomatic Infections , Disease Models, Animal , Feces/virology , Humans , Intestines/virology , Mice , Primates
19.
Am J Trop Med Hyg ; 106(1): 127-131, 2021 10 29.
Article in English | MEDLINE | ID: covidwho-1497592

ABSTRACT

This article aims to understand the changes in the detection rates of H5, H7, and H9 subtypes of avian influenza viruses (AIVs) in the live poultry markets (LPMs) in Nanchang City, Jiangxi Province, before and after the outbreak of the COVID-19. From 2019 to 2020, we monitored the LPM and collected specimens, using real-time reverse transcription polymerase chain reaction technology to detect the nucleic acid of type A AIV in the samples. The H5, H7, and H9 subtypes of influenza viruses were further classified for positive results. We analyzed 1,959 samples before and after the outbreak and found that the positive rates of avian influenza A virus (39.69%) and H9 subtype (30.66%) after the outbreak were significantly higher than before the outbreak (26.84% and 20.90%, respectively; P < 0.001). In various LPMs, the positive rate of H9 subtypes has increased significantly (P ≤ 0.001). Positive rates of the H9 subtype in duck, fecal, daub, and sewage samples, but not chicken samples, have increased to varying degrees. This study shows that additional measures are needed to strengthen the control of AIVs now that LPMs have reopened after the relaxing of COVID-19-related restrictions.


Subject(s)
COVID-19/prevention & control , Disease Outbreaks/prevention & control , Influenza A virus/isolation & purification , Influenza in Birds/epidemiology , Animals , COVID-19/epidemiology , China/epidemiology , Ducks/virology , Environmental Microbiology , Feces/virology , Humans , Influenza A Virus, H9N2 Subtype/isolation & purification , Influenza A virus/classification , Poultry , Sewage/virology
20.
Viruses ; 13(10)2021 10 06.
Article in English | MEDLINE | ID: covidwho-1460085

ABSTRACT

According to various estimates, only a small percentage of existing viruses have been discovered, naturally much less being represented in the genomic databases. High-throughput sequencing technologies develop rapidly, empowering large-scale screening of various biological samples for the presence of pathogen-associated nucleotide sequences, but many organisms are yet to be attributed specific loci for identification. This problem particularly impedes viral screening, due to vast heterogeneity in viral genomes. In this paper, we present a new bioinformatic pipeline, VirIdAl, for detecting and identifying viral pathogens in sequencing data. We also demonstrate the utility of the new software by applying it to viral screening of the feces of bats collected in the Moscow region, which revealed a significant variety of viruses associated with bats, insects, plants, and protozoa. The presence of alpha and beta coronavirus reads, including the MERS-like bat virus, deserves a special mention, as it once again indicates that bats are indeed reservoirs for many viral pathogens. In addition, it was shown that alignment-based methods were unable to identify the taxon for a large proportion of reads, and we additionally applied other approaches, showing that they can further reveal the presence of viral agents in sequencing data. However, the incompleteness of viral databases remains a significant problem in the studies of viral diversity, and therefore necessitates the use of combined approaches, including those based on machine learning methods.


Subject(s)
Alphacoronavirus/isolation & purification , Betacoronavirus/isolation & purification , Chiroptera/virology , Genome, Viral/genetics , Metagenome/genetics , Alphacoronavirus/classification , Alphacoronavirus/genetics , Animals , Betacoronavirus/classification , Betacoronavirus/genetics , Chiroptera/genetics , Computational Biology/methods , Feces/virology , High-Throughput Nucleotide Sequencing , Metagenomics/methods , Moscow , Phycodnaviridae/classification , Phycodnaviridae/genetics , Phycodnaviridae/isolation & purification , Sequence Analysis, DNA
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