scholarly journals Case report: change of dominant strain during dual SARS-CoV-2 infection

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Andrei E. Samoilov ◽  
Valeriia V. Kaptelova ◽  
Anna Y. Bukharina ◽  
Olga Y. Shipulina ◽  
Elena V. Korneenko ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Strain Ratio ◽  
Dual Infection ◽  
Swab Sample ◽  
Disease Manifestation ◽  
Case Presentation ◽  
Oropharyngeal Swab ◽  
Coronavirus Infection ◽  
Hospital Acquired ◽  
Icu Treatment

Abstract Background The dual infection with SARS-CoV-2 is poorly described and is currently under discussion. We present a study of two strains of SARS-CoV-2 detected in the same patient during the same disease presentation. Case presentation A patient in their 90 s was hospitalised with fever. Oropharyngeal swab obtained on the next day (sample 1) tested positive for SARS-CoV-2. Five days later, the patient was transferred to the ICU (intensive care unit) of the hospital specialising in the treatment of COVID-19 patients, where the patient's condition progressively worsened and continuous oxygen insufflation was required. Repeated oropharyngeal swab (sample 2), which was taken eight days after the first one, also tested positive for SARS-CoV-2. After 5 days of ICU treatment, the patient died. The cause of death was a coronavirus infection, which progressed unfavourably due to premorbid status. We have performed sequencing of full SARS-CoV-2 genomes from oropharyngeal swabs obtained eight days apart. Genomic analysis revealed the presence of two genetically distant SARS-CoV-2 strains in both swabs. Detected strains belong to different phylogenetic clades (GH and GR) and differ in seven nucleotide positions. The relative abundance of strains was 70% (GH) and 30% (GR) in the first swab, and 3% (GH) and 97% (GR) in the second swab. Conclusions Our findings suggest that the patient was infected by two genetically distinct SARS-CoV-2 strains at the same time. One of the possible explanations is that the second infection was hospital-acquired. Change of the dominant strain ratio during disease manifestation could be explained by the advantage or higher virulence of the GR clade strain.

scholarly journals Change of dominant strain during dual SARS-CoV-2 infection

2020 ◽  
Author(s):  
AE Samoilov ◽  
VV Kaptelova ◽  
AY Bukharina ◽  
OY Shipulina ◽  
EV Korneenko ◽  
...  
Keyword(s):  
Viral Load ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Genomic Analysis ◽  
Strain Ratio ◽  
High Viral Load ◽  
Dual Infection ◽  
Disease Manifestation ◽  
Lobar Pneumonia

SummaryBackgroundThe effect of SARS-CoV-2 mutations and viral load on the severity of COVID-19 is not well understood. The possibility of reinfection with SARS-CoV-2 has already been reported, but dual infection with SARS-CoV-2 is poorly described and is currently under discussion. We describe a study of two strains of SARS-CoV-2 detected in the same patient during the same disease presentation.MethodsTwo nasopharyngeal swabs were obtained eight days apart from the patient in their 90s, diagnosed with lobar pneumonia (J18.1). Both tests were positive for SARS-CoV-2 with high viral load (Ct = 13). We have performed high-throughput sequencing of SARS-CoV-2 genomes from both swabs.FindingsGenomic analysis of SARS-CoV-2 revealed the presence of two genetically distant strains in both swabs. Detected strains belong to different phylogenetic clades (GH and GR) and differ in the seven nucleotide positions. The relative abundance of strains was 70% (GH) and 30% (GR) in the first swab, and 3% (GH) and 97% (GR).InterpretationOur findings suggest that the patient was infected by two genetically distinct SARS-CoV-2 strains at the same time. One of the possible explanations is that the second infection occurred in the hospital. Change of the dominant strain ratio during disease manifestation could be explained by the advantage or higher virulence of the strain belonging to the clade GR.

Fever in the returning traveller: Dual infection with SARS-CoV-2 and Plasmodium falciparum malaria

2020 ◽  
pp. 105-108
Author(s):  
MA Parker ◽  
E Nell ◽  
A Mowlana ◽  
MS Moolla ◽  
S Karamchand ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Falciparum Malaria ◽  
Clinical Course ◽  
Febrile Illness ◽  
Plasmodium Falciparum Malaria ◽  
Dual Infection ◽  
Pneumocystis Pneumonia ◽  
Case Presentation ◽  
Presenting Symptoms ◽  
Uncomplicated Plasmodium Falciparum Malaria

Background: More than 90% of the global 400 000 annual malaria deaths occur in Africa. The current SARS-CoV-2 pandemic has resulted in more than 830 000 deaths in its first 10 months. Case presentation: This case describes a patient who had travelled from Mozambique to Cape Town, presented with a mild febrile illness, and was diagnosed with both COVID-19 and uncomplicated Plasmodium falciparum malaria infection. She responded well to malaria treatment and had an uneventful COVID-19 admission. Her blood smear showed a low malaria parasitaemia and a relatively high gametocyte load. Conclusion: We postulate that her clinical course and abnormal smear could well be due to reciprocal disease-modifying effects of the infections. The presenting symptoms of COVID-19 may mimic endemic infectious diseases including malaria, tuberculosis, pneumocystis pneumonia and influenza thus there is a need for clinical vigilance to identify and treat such co-infections.

scholarly journals An Update on Animal Models for Severe Acute Respiratory Syndrome Coronavirus 2 Infection and Countermeasure Development

2021 ◽  
Vol 12 ◽  
Author(s):  
Liang Zhang ◽  
Shuaiyin Chen ◽  
Weiguo Zhang ◽  
Haiyan Yang ◽  
Yuefei Jin ◽  
...  
Keyword(s):  
Animal Models ◽  
Severe Acute Respiratory Syndrome ◽  
Research Progress ◽  
Laboratory Mice ◽  
Disease Manifestation ◽  
Highly Pathogenic ◽  
The World ◽  
Coronavirus Infection ◽  
Different Levels ◽  
Critical Aspects

Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic since March 2020 and led to significant challenges to over 200 countries and regions all over the world. The establishment of highly pathogenic coronavirus animal model is beneficial for the study of vaccines and pathogenic mechanism of the virus. Laboratory mice, Syrian hamsters, Non-human primates and Ferrets have been used to establish animal models of emerging coronavirus infection. Different animal models can reproduce clinical infection symptoms at different levels. Appropriate animal models are of great significance for the pathogenesis of COVID-19 and the research progress related to vaccines. This review aims to introduce the current progress about experimental animal models for SARS-CoV-2, and collectively generalize critical aspects of disease manifestation in humans and increase their usefulness in research into COVID-19 pathogenesis and developing new preventions and treatments.

scholarly journals A Case of Cholangiolocellular Carcinoma Preoperatively Diagnosed With Typical Imaging Findings

2019 ◽  
Vol 103 (1-2) ◽  
pp. 72-79
Author(s):  
Yoshihiro Mochizuki ◽  
Yuji Iimuro ◽  
Osamu Suzuki ◽  
Yoji Nagashima
Keyword(s):  
Preoperative Diagnosis ◽  
Imaging Finding ◽  
Genomic Analysis ◽  
Liver Neoplasm ◽  
Preoperative Imaging ◽  
Molecular Entity ◽  
Imaging Findings ◽  
Cholangiolocellular Carcinoma ◽  
Case Presentation ◽  
Contrast Enhanced

Introduction: Cholangiolocellular carcinoma (CoCC) is a rare primary liver neoplasm. A recent integrative genomic analysis has revealed that CoCC represents a distinct biliary-derived molecular entity. Several cases of CoCC have been reported so far, but accurate preoperative diagnosis was difficult in most cases. Case presentation: We report a case of 70-year-old woman with CoCC. Preoperative imaging findings revealed several typical signs of CoCC (i.e., thick early ring enhancement in the peripheral area of the tumor and its prolongation, vessel penetration through the tumor, no dilatation of the peripheral bile ducts, and dot-/band-like internal enhancement or a target appearance on contrast-enhanced magnetic resonance imaging). We strongly suspected CoCC from these preoperative imaging findings of the tumor and performed extended left hepatectomy. Pathologic diagnosis was CoCC, and the histologic findings such as peripheral highly cellular areas, central abundant hyalinized/edematous fibrotic stroma, and retained Glisson's sheath structures in the tumor, corresponded closely to each preoperative imaging finding. Immunohistochemical study revealed the tumor cells were positive for cytokeratin 7 and epithelial membrane antigen. The postoperative course was uneventful, and the patient is alive without recurrence for 15 months. The prognosis of CoCC is known to be better than that of cholangiocellular carcinoma, indicating the importance of preoperative differential diagnosis of these tumors. Conclusion: Even though preoperative diagnosis of CoCC is difficult because of its rarity, cautious investigation of preoperative typical imaging findings can possibly lead to accurate diagnosis of CoCC.

The Use of Moxisaxin for Treatment of a Decompensated Cirrhosis Patient with Severe Pulmonary Infection

2020 ◽  
Vol 13 (9) ◽  
Author(s):  
Junfei Jiang ◽  
Jing Wang ◽  
Zhiwen Yang
Keyword(s):  
Pulmonary Infection ◽  
Clinical Symptoms ◽  
Safety Data ◽  
Poor Response ◽  
Decompensated Cirrhosis ◽  
Clinical Safety ◽  
Case Presentation ◽  
Linezolid Therapy ◽  
Hospital Acquired Pneumonia ◽  
Hospital Acquired

Introduction: Moxifloxacin is recommended for empirical antibiotic treatment of patients with cirrhosis. However, due to a lack of clinical safety data on moxifloxacin in Child-Pugh C patients, it is unknown how to use moxifloxacin in clinical practice. Case Presentation: A 76-year-old female with decompensated cirrhosis developed pneumonia during hospitalization. She had an initial failure to respond to imipenem/cilastatin + linezolid therapy. After three-day therapy with imipenem/cilastatin + moxisaxin, her infection symptoms rapidly improved. At this time, she presented a poor response with suspected hepatic encephalopathy. Given the worsening clinical symptoms caused by drug hepatotoxicity, moxisaxin was discontinued. Then, her body temperature rapidly raised. Conclusions: Moxisaxin may be a potentially useful antibiotic for hospital-acquired pneumonia in patients with decompensated cirrhosis, but further studies are needed to validate its hepatotoxicity.

scholarly journals Severe Acute Respiratory Syndrome Coronavirus-2 and Pulmonary Tuberculosis Coinfection: Double Trouble

2020 ◽  
Author(s):  
Abhijeet Singh ◽  
Ayush Gupta ◽  
Kamanashish Das
Keyword(s):  
Throat Swab ◽  
Mycobacterium Tuberculosis Complex ◽  
Swab Sample ◽  
Rt Pcr ◽  
Tuberculosis Complex ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Case Presentation ◽  
Polymerase Chain ◽  
Novel Coronavirus

Abstract Background: The ongoing pandemic of novel coronavirus disease 2019 (COVID-19) has received worldwide attention by becoming a major global health threat. We encountered one case with COVID-19 and tuberculosis (TB) coinfection which has not been frequently reported. Case presentation: A 76 year old female presented with acute respiratory symptoms superimposed on chronic symptoms, suggestive to have pneumonia. Oropharyngeal throat swab sample for COVID-19 was positive as detected by real-time reverse-transcriptase–polymerase-chain-reaction (RT-PCR) assay. GeneXpert Ultra detected Mycobacterium tuberculosis complex with Rifampicin resistance indeterminate. Patient was treated with appropriate management. Conclusion: Clinicians should suspect coinfection with TB during ongoing pandemic of COVID-19 as therapeutic strategies need to be determined timely to improve outcome and prevent transmission in community.

An unusual Staphylococcus saccharolyticus spondylodiscitis post vertebroplasty, a case report

2020 ◽  
Author(s):  
Marie Charlotte Trojani ◽  
brigitte Lamy ◽  
Raymond Ruimy ◽  
nicolas Amoretti ◽  
Karine Risso ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Control Procedure ◽  
Strictly Anaerobic ◽  
Pathogenic Potential ◽  
Case Presentation ◽  
Poor Condition ◽  
Microbiological Characteristics ◽  
Health Care Associated Infection ◽  
Timely Treatment ◽  
Infection Control Procedure

Abstract Background: Staphylococcus saccharolyticus is a rarely encountered coagulase-negative slowly grower and strictly anaerobic staphylococcus from the skin. It is usually considered as a contaminant, but some rare reports describe deep-seated infections. Virulence factors remain poorly known although genomic analysis highlight pathogenic potential.Case presentation: we report a case of Staphylococcus saccharolyticus spondylodiscitis that followed kyphoplasty, a procedure associated with a low rate of sometimes severe infectious complication (0.46%) and we reviewed the literature. This case specifically stresses the risk of S. saccharolyticus health-care associated infection in patients of poor condition.Conclusion: infection to S. saccharolyticus is difficult to diagnose due to microbiological characteristics of this bacterium, requires timely treatment and improved infection control procedure should be encouraged for patients with poor condition.

scholarly journals Genomic Characterization of MDR Escherichia coli Harboring blaOXA-48 on the IncL/M-type Plasmid Isolated from Blood Stream Infection

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
S. Alousi ◽  
T. Salloum ◽  
H. Arabaghian ◽  
G. M. Matar ◽  
G. F. Araj ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Blood Stream Infection ◽  
Genomic Analysis ◽  
Blood Stream ◽  
Population Movements ◽  
E Coli ◽  
Resistance Determinants ◽  
Genomic Characterization ◽  
Hospital Acquired

Escherichia coli is responsible for a wide variety of community and hospital acquired extraintestinal infections, and the emergence of ESBL resistant isolates is a major clinical concern. In this study, we characterized the genomic attributes of an OXA-48 and CTX-M-3 producing E. coli EC-IMP153. Whole-genome initial assembly produced 146 contigs with a combined 5,504,170 bp in size and a G+C content of 50.5%. wgSNPs-based phylogenetic comparison with 36 publically available genomes was also performed. Comprehensive genomic analysis showed that EC-IMP153 belonged to sequence type ST-405 and harbored several resistance determinants including the β-lactam resistance genes blaOXA-48, blaCTX-M-3, blaTEM-1B, blaOXA-1, and blaCMY-70, aminoglycoside fyuA and aac(3)IId, tetracycline tet(A) and tet(R), and fluoroquinolone gyrA, parC, and mfd resistance determinants. Plasmids with the following incompatibility groups were detected in silico and confirmed using PBRT: IncI1-α, IncL, IncW, Col (BS512), and IncF. To our knowledge this is the first in-depth genomic analysis of an OXA-48 producing E. coli ST-405 isolated from a patient in Lebanon and linked to a blood stream infection. Continuous monitoring is necessary to better understand the continued diffusion of such pathogens, especially in view of the population movements triggered by unrest in the Middle East.

scholarly journals Post SARS-CoV-2 infection reactive arthritis: a brief report of two pediatric cases

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Reza Sinaei ◽  
Sara Pezeshki ◽  
Saeedeh Parvaresh ◽  
Roya Sinaei ◽  
Reza Shiari ◽  
...  
Keyword(s):  
Tract Infection ◽  
Severe Acute Respiratory Syndrome ◽  
Reactive Arthritis ◽  
Pediatric Rheumatology ◽  
Joint Effusion ◽  
Severe Illness ◽  
Medical Problems ◽  
Case Presentation ◽  
Inflammatory Drugs ◽  
Coronavirus Infection

Abstract Background Although, preliminary reports of Severe Acute Respiratory Syndrome (SARS)-CoV-2 infection suggest that the infection causes a less severe illness in children, there is now growing evidence of other rare or even serious complications of disease. Case presentation During the recent COVID-19 pandemic in Kerman, Iran, two children (an 8 year-old boy and a 6 year-old girl) were referred to outpatient Clinic of Pediatric Rheumatology with complaints of limping. Both children had experienced fever and mild respiratory tract infection. At the beginning of the second week of infection, they developed joint effusion. They both tested positive for coronavirus infection and were therefore diagnosed with post Coronavirus reactive arthritis. Both children were treated successfully with rest and Non-Steroidal Anti-Inflammatory Drugs (NSAID). They did not have any medical problems in the two months fallow up. Conclusions These two cases suggest that COVID-19 may be rheumatogenic. Highlighting the need for awareness of physicians, especially pediatricians, regarding the pathogenesis margins of this virus, as late presentations are of great importance.

scholarly journals Acute Ischemic Stroke in COVID-19 Patient with Lung Collapse: A Case Report

2021 ◽  
pp. 1-5
Author(s):  
Mahpara Nawazish ◽  
Sana Iqbal ◽  
Mujeeb Ur Rehman Abid Butt
Keyword(s):  
Ischemic Stroke ◽  
Acute Ischemic Stroke ◽  
Rna Virus ◽  
Altered State ◽  
Lung Collapse ◽  
Case Presentation ◽  
Uncommon Presentation ◽  
Altered State Of Consciousness ◽  
Coronavirus Infection

Novel corona virus 2019 also known as severe acute respiratory syndrome coronavirus 2 [SARS COV2] is enveloped non segmented ribonucleic acid (RNA) virus. Acute ischemic stroke remains emergency during covid19 pandemic [1] Here we present a case of a woman with COVID 19 who presented to us with symptoms of altered state of consciousness (ASOC), cough, fever, dysarthria, right sided body weakness and massive bilateral middle cerebral artery (MCA)/ anterior. Our case was unique in the sense that it showed drastic central nervous system (CNS) damage in the presence of coronavirus infection. There are a few cases of patients who develop stroke after COVID 19 infection. Aims: Clinicians need to be aware of possible causes of unconsciousness in coronavirus disease (COVID 19) patients, particularly as delirium appears to be common complications to find out the association between stroke and COVID 19 and its impact and mortality. Case Presentation: A 70 years old lady presented to us with symptoms of stroke like ASOC, right sided body weakness, dysarthria, and symptoms of pneumonia like mild cough and fever later which turned out to be COVID 19. Clinicians need to be aware of possible causes of unconsciousness in coronavirus disease (COVID 19) patients, particularly as delirium appears to be common complications to find out the association between stroke and COVID 19 and its impact and mortality. Discussion: Bilateral ischemic stroke is relatively uncommon presentation in general population and is usually the result of cardio embolic cause such as atrial fibrillation and recent myocardial infarction. While this patient had pre existing risk factors for stroke such as type 2 diabetes mellitus, hypertension and old age and her electrocardiography showed sinus rhythm. Conclusion: COVID-19 may be a risk factor or aggravating factor for stroke.

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