Evaluation of Simplified HCV Diagnostics in HIV/HCV Co-Infected Patients in Myanmar.

To evaluate a decentralised testing model and simplified treatment protocol of hepatitis C virus (HCV) infection to facilitate treatment scale-up in Myanmar, this prospective, observational study recruited HIV-HCV co-infected outpatients receiving sofosbuvir/daclatasvir in Yangon, Myanmar. The study examined the outcomes and factors associated with a sustained virological response (SVR). A decentralised "hub-and-spoke" testing model was evaluated where fingerstick capillary specimens were transported by taxi and processed centrally. The performance of the Xpert HCV VL Fingerstick Assay in detecting HCV RNA was compared to the local standard of care ( plasma HCV RNA collected by venepuncture). Between January 2019 and February 2020, 162 HCV RNA-positive individuals were identified; 154/162 (95%) initiated treatment, and 128/154 (84%) returned for their SVR12 visit. A SVR was achieved in 119/154 (77%) participants in the intent-to-treat population and 119/128 (93%) participants in the modified-intent-to-treat population. Individuals receiving an antiretroviral therapy were more likely to achieve a SVR (with an odds ratio (OR) of 7.16, 95% CI 1.03-49.50), while those with cirrhosis were less likely (OR: 0.26, 95% CI 0.07-0.88). The sensitivity of the Xpert HCV VL Fingerstick Assay was 99.4% (95% CI 96.7-100.0), and the specificity was 99.2% (95% CI 95.9-99.9). A simplified treatment protocol using a hub-and-spoke testing model of fingerstick capillary specimens can achieve an SVR rate in LMIC comparable to well-resourced high-income settings.

TBC and COVID: an interplay between two infections.

INTRODUCTION: In a historical era dominated by the SARS-CoV-2 pandemic, a fact of growing interest emerges regarding co-infection with Mycobacterium tuberculosis (M. tuberculosis). This represents today an important clinical and diagnostic challenge, as the two pathogens are capable, through specific immunopathological mechanisms, of interacting with each other, determining a severe respiratory condition with a severe prognosis. AREAS COVERED: With this review, we wanted to collect and analyze the latest scientific evidence concerning the main immunopathogenetic mechanisms shared by these two respiratory pathogens, with particular interest in the possible iatrogenic factors favoring coinfection and the need to define multidisciplinary and standardized screening tools aimed to identify coinfection early, ensuring the best clinical and therapeutic management. EXPERT OPINION: The existence of a direct immunopathogenetic link between COVID-19 and TB indirectly contributes to mutual morbidity and mortality. The identification and application of early and standardized screening tools aimed at the identification of this condition is essential, in addition to vaccine prevention.

Back to the future of viruses: a case of triple coinfection caused by respiratory syncytial virus, human coronavirus OC43, and rhinovirus.

We present the case of an 81-year-old man, who was immunocompetent, who was admitted to the hospital with symptoms of fever and dyspnea suspected to be caused by COVID-19. Further examination revealed a triple coinfection, as determined by multiplex polymerase chain reaction testing, caused by the respiratory syncytial virus, human coronavirus OC43, and rhinovirus. Upon auscultation, diffuse wheezing without crackles was detected. After ruling out the possibility of acute heart failure with pulmonary edema, the patient was treated with nebulization of terbutaline for a period of 72 hours. This case serves to demonstrate the potential dangers of lifting barrier measures, such as mandatory face masks in high-risk areas, during the fall-winter season. In addition, it highlights the challenges that may arise in the post-COVID-19 era because reliance on flu vaccinations alone may not be sufficient.

Clinical Presentation and Severity of SARS-CoV-2 Infection Compared to Respiratory Syncytial Virus and Other Viral Respiratory Infections in Children Less than Two Years of Age.

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the implementation of restrictive measures led to a dramatic reduction in respiratory syncytial virus (RSV) occurrence together with rare and mild bronchiolitis induced by SARS-CoV-2. We described the respiratory picture of SARS-CoV-2 infection and evaluated the frequency and the severity of SARS-CoV-2 bronchiolitis comparing it with other respiratory viral infections in children less than two years of age. The severity of respiratory involvement was evaluated based on the need for oxygen therapy, intravenous hydration, and the length of hospital stay. A total of 138 children hospitalized for respiratory symptoms were enrolled: 60 with SARS-CoV-2 and 78 with RSV. In the group of SARS-CoV-2-infected children, 13/60 (21%) received a diagnosis of co-infection. Among the enrolled children, 87/138 (63%) received a diagnosis of bronchiolitis. The comparative evaluation showed a higher risk of the need for oxygen therapy and intravenous hydration in children with RSV infection and co-infection compared to children with SARS-CoV-2 infection. In the children with a diagnosis of bronchiolitis, no differences in the main outcomes among the groups were observed. Although children with SARS-CoV-2 infection have less severe respiratory effects than adults, the pediatrician should pay attention to bronchiolitis due to SARS-CoV-2, which could have a severe clinical course in younger children.

A tale of three in symbiosis: TB-COVID-19-Bordetella coinfection.

Coinfections/mixed infections are common in the respiratory tract. Many times existing organisms have similar risk factors and clinical features that make the diagnosis difficult. Coronavirus diagnosed in 2019 (COVID-19) and tuberculosis (TB) are two such diseases. Patients with TB have lower cellular immunity and impaired pulmonary function. In such environment, atypical organisms, can infect and make the outcome unfavorable. A 21-year-old malnourished (body mass index- 15 kg/m2) girl presented with fever and cough for 10 days. Sputum for Cartridge Based Nucleic Acid Amplification Test demonstrated Mycobacterium tuberculosis with no rifampin resistance. Fever persisted (100-101°F) and saturation was dropping even after 10 days of antitubercular treatment. A repeat reverse transcription-polymerase chain reaction was done and was positive. In view of persistent symptoms after 20 days, bronchoscopy was done, and cultures showed Bordetella bronchiseptica. Fever and symptoms resolved completely after initiation of the sensitive drug. Diagnostic delay in coinfections can lead to increased morbidity and mortality.

Coinfection and cross-reaction of dengue and COVID-19: a case series analysis.

BACKGROUND: The risk of possible cross-reactions between serological tests, together with the clinical similarities between dengue fever and COVID-19, can delay diagnosis and increase the risk of both COVID-19 transmission and worsening. The present study aimed to determine the possibility of cross-reactions among rapid serological tests based on clinical symptoms. METHODS: Patients with COVID-19, confirmed by RT-PCR and clinical criteria for diagnosing dengue, were recruited consecutively between September 2020 and August 2021 and underwent rapid immunochromatographic diagnostic (RID) tests for AgNS1, IgM, and IgG. Patients who tested positive for acute-phase dengue IgM and AgNS1 underwent a follow-up test after 12-30 days for diagnostic confirmation. RESULTS: A total of 43 patients were included, 38 of whom required hospital admission, and 8 received intensive care. Seven patients tested positive on the RID tests, comprising 2 NS1 positive (coinfection), one reactive for IgM and IgG (coinfection), three reactive for IgM not confirmed (false-positive), and one reactive for IgG due to previous infection. Two of the 3 patients with coinfection died. Fever, myalgia, headache, and cough were the most common clinical symptoms, while lymphopenia was the most prevalent laboratory finding. CONCLUSIONS: Cross-reactivity was found in only three patients and coinfection in another three patients, two of whom died of severe COVID-19 manifestations.

A multiplex-NGS approach to identifying respiratory RNA viruses during the COVID-19 pandemic.

A methodological approach based on reverse transcription (RT)-multiplex PCR followed by next-generation sequencing (NGS) was implemented to identify multiple respiratory RNA viruses simultaneously. A convenience sampling from respiratory surveillance and SARS-CoV-2 diagnosis in 2020 and 2021 in Montevideo, Uruguay, was analyzed. The results revealed the cocirculation of SARS-CoV-2 with human rhinovirus (hRV) A, B and C, human respiratory syncytial virus (hRSV) B, influenza A virus, and metapneumovirus B1. SARS-CoV-2 coinfections with hRV or hRSV B and influenza A virus coinfections with hRV C were identified in adults and/or children. This methodology combines the benefits of multiplex genomic amplification with the sensitivity and information provided by NGS. An advantage is that additional viral targets can be incorporated, making it a helpful tool to investigate the cocirculation and coinfections of respiratory viruses in pandemic and post-pandemic contexts.

Rapid differential diagnosis of SARS-CoV-2, influenza A/B and respiratory syncytial viruses: Validation of a novel RT-PCR assay.

BACKGROUND: Influenza and respiratory syncytial (RSV) viruses are expected to co-circulate with SARS-CoV-2 in the upcoming seasons and clinical differential diagnosis between them is difficult. Laboratory-based RT-PCR is a gold standard diagnostic method for influenza, RSV and SARS-CoV-2. The objective of this study was to estimate the diagnostic performance of a novel point-of-care RT-PCR assay STANDARD M10 Flu/RSV/SARS-CoV-2 (SD Biosensor) in a large number of clinical specimens with diversified (co)-infection patterns and viral loads. METHODS: This was a retrospective study, in which all samples were tested in both STANDARD M10 Flu/RSV/SARS-CoV-2 index and Allplex SARS-CoV-2/Respiratory Panel 1 (Seegene) reference kits. Samples with discordant results were further processed in a third resolver test (Resp-4-Plex, Abbott). RESULTS: A total of 1,019 naso-/oropharyngeal samples (50.3% positive for at least one virus) were processed in both STANDARD M10 Flu/RSV/SARS-CoV-2 and Allplex assays and the overall between-assay agreement was as high as 94.6%. Positive percent agreement of the STANDARD M10 Flu/RSV/SARS-CoV-2 was 100%, 96.6%, 97.3% and 99.4% for influenza A, B, RSV and SARS-CoV-2, respectively. The corresponding negative percent agreement was 99.7%. 100%, 100% and 98.4%, respectively. The expected positive and negative predictive values for all viruses were constantly above 96% in a reasonable range of disease prevalence. CONCLUSIONS: STANDARD M10 Flu/RSV/SARS-CoV-2 is a reliable RT-PCR assay able to detect influenza A, influenza B, RSV and SARS-CoV-2 in one hour or less, fostering a rapid differential diagnosis of common respiratory viruses.

SARS-CoV-2 and Plasmodium falciparum coinfection: a case report.

BACKGROUND: A rare case of coinfection of Plasmodium falciparum and SARS-CoV-2 disease in Croatia is presented in this report. METHODS: We tracked epidemiological and laboratory findings in a patient with SARS-CoV-2 and Plasmodium falciparum coinfection. A complete blood count was performed using the Sysmex XN-2000 analyser (Sysmex Corporation, Kobe, Japan), coagulation analyses were performed using the BCS XP coagulometer (Siemens Healthineers AG, Erlangen, Germany). Procalcitonin (PCT) and Interleukin-6 (IL-6) were measured by electrochemiluminescence immunoassay (ECLIA) using the Cobas e411 (Roche Diagnostics GmbH, Mannheim, Germany) analyser and high sensitivity troponin I (hsTnI) was measured using the Dimension EXL with LM analyser (Siemens Healthcare Diagnostics, Newark, USA). All other biochemistry analyses were performed using the Olympus AU680 (Beckman Coulter, Brea, California, USA) analyser. White blood cell differential analysis has been performed by examining the blood smear using the CellaVision DM1200 (CellaVision AB, Lund, Sweden) automatic analyser. RESULTS: Even though the patient's initial health condition was disturbed, as a result of the physician's comprehensive anamnesis accompanied by laboratory findings, prompt diagnosis and appropriate therapy were assured, and consequently, the patient recovered. CONCLUSION: In a pandemic, testing each febrile patient for the SARS-CoV-2 virus is of essential importance. However, the possibility of coinfection with another infectious disease agent cannot be disregarded.

Development of multiplex RT-ddPCR assays for detection of SARS-CoV-2 and other common respiratory virus infections.

BACKGROUND: Measures for mitigation of Coronavirus Disease 2019 (COVID-19) were set to reduce the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 and other respiratory viruses share similar transmission routes and some common clinical manifestations. Co-circulation of SARS-CoV-2 and other common respiratory viruses is imminent. Therefore, development of multiplex assays for detecting these respiratory viruses is essential for being prepared for future outbreaks of respiratory viruses. METHODS: A panel of three reverse transcription droplet digital PCR (RT-ddPCR) assays were developed to detect 15 different human respiratory viruses. Evaluations of its performance were demonstrated. A total of 100 local and 98 imported COVID-19 cases in Hong Kong were screened for co-infection with other common respiratory viruses. RESULTS: All detected viral targets showed distinct signal clusters using the multiplex RT-ddPCR assays. These assays have a broad range of linearity and good intra-/inter-assay reproducibility for each target. The lower limits of quantification for all targets were ≤46 copies per reaction. Six imported cases of COVID-19 were found to be co-infected with other respiratory viruses, whereas no local case of co-infection was observed. CONCLUSIONS: The multiplex RT-ddPCR assays were demonstrated to be useful for screening of respiratory virus co-infections. The strict preventive measures applied in Hong Kong may be effective in limiting the circulation of other human respiratory viruses. The multiplex assays developed in this study can achieve a robust detection method for clinical and research purposes.

Plasmodium vivax and SARS-CoV-2 co-infection in Venezuelan pregnant women: a case series.

BACKGROUND: Malaria-endemic areas are not spared from the impact of coronavirus disease 2019 (COVID-19), leading to co-infection scenarios where overlapping symptoms impose serious diagnostic challenges. Current knowledge on Plasmodium spp. and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infection in pregnant women remains limited, especially in Latin America, where Plasmodium vivax infection is highly prevalent. METHODS: This is a case series of five pregnant women with P. vivax and SARS-CoV-2 co-infection hospitalized in two main malaria referral centers of the Capital District and Bolivar state, Venezuela between March 13, 2020 and December 31, 2021. RESULTS: Clinical and laboratory data from five pregnant women with a mean age of 22 years were analyzed; three of them were in the third trimester of pregnancy. Comorbidities included obesity in two cases, hypertension in one, and asthma in one. Three out of five patients had severe to critical COVID-19 disease. Dry cough, fever, chills, and headache were the most frequent symptoms reported. Laboratory analyses showed elevated aspartate/alanine aminotransferase and creatinine levels, thrombocytopenia, and severe anemia as the most relevant abnormalities. The mean period between symptom onset and a positive molecular test for SARS-CoV-2 infection or positive microscopy for Plasmodium spp. was 4.8 ± 2.5 days and 2.8 ± 1.6 days, respectively. The mean hospital stay was 5.4 ± 7 days. Three women recovered and were discharged from the hospital. Two women died, one from cerebral malaria and one from respiratory failure. Three adverse fetal outcomes were registered, two miscarriages and one stillbirth. CONCLUSION: This study documented a predominance of severe/critical COVID-19 disease and a high proportion of adverse maternal-fetal outcomes among pregnant women with malaria and COVID-19 co-infection. More comprehensive prospective cohort studies are warranted to explore the risk factors, management challenges, and clinical outcomes of pregnant women with this co-infection.

A Multiplex PCR and DNA-Sequencing Workflow on Serum for the Diagnosis and Species Identification for Invasive Aspergillosis and Mucormycosis.

There has been significant increase in the use of molecular tools for the diagnosis of invasive aspergillosis (IA) and mucormycosis. However, their range of detection may be too limited as species diversity and coinfections are increasing. Here, we aimed to evaluate a molecular workflow based on a new multiplex PCR assay detecting the whole Aspergillus genus and the Mucorales order followed by a species-specific PCR or a DNA-sequencing approach for IA and/or mucormycosis diagnosis and species identification on serum. Performances of the MycoGENIE Aspergillus spp./Mucorales spp. duplex PCR kit were analyzed on a broad range of fungal strains and on sera from high-risk patients prospectively over a 12-month period. The kit allowed the detection of nine Aspergillus species and 10 Mucorales (eight genera) strains assessed. No cross-reactions between the two targets were observed. Sera from 744 patients were prospectively analyzed, including 35 IA, 16 mucormycosis, and four coinfections. Sensitivity varies from 85.7% (18/21) in probable/proven IA to 28.6% (4/14) in COVID-19-associated pulmonary aspergillosis. PCR-positive samples corresponded to 21 A. fumigatus, one A. flavus, and one A. nidulans infections. All the disseminated mucormycosis were positive in serum (14/14), including the four Aspergillus coinfections, but sensitivity fell to 33.3% (2/6) in localized forms. DNA sequencing allowed Mucorales identification in serum in 15 patients. Remarkably, the most frequent species identified was Rhizomucor pusillus (eight cases), whereas it is barely found in fungal culture. This molecular workflow is a promising approach to improve IA and mucormycosis diagnosis and epidemiology.

Severe Anemia Observed in a Chinese Patient with COVID-19 and Plasmodium Falciparum Malaria Co-Infection.

BACKGROUND: COVID-19 and malaria share some similar symptoms such as fever, difficulty in breathing, fatigue, and headaches of acute onset. With overlapping symptoms and travel history significant for COVID-19 and malaria, healthcare systems and professionals will face a great challenge in the case of COVID-19 and malaria co-infection. METHODS: Here we presented a patient with COVID-19 infection and refractory anemia of unknown reason. A diagnostic test for malaria was later performed. RESULTS: The patient was ultimately diagnosed with COVID-19 and plasmodium falciparum malaria co-infection. He recovered gradually after receiving anti-malaria treatment. CONCLUSIONS: The present case highlights the danger of focusing only on a diagnosis of COVID-19, reminding clinicians to be vigilant about the possibility of co-infections.

Decoding the double trouble: A mathematical modelling of co-infection dynamics of SARS-CoV-2 and influenza-like illness.

After the detection of coronavirus disease 2019 (Covid-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, Hubei Province, China in late December, the cases of Covid-19 have spiralled out around the globe. Due to the clinical similarity of Covid-19 with other flulike syndromes, patients are assayed for other pathogens of influenza like illness. There have been reported cases of co-infection amongst patients with Covid-19. Bacteria for example Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Mycoplasma pneumoniae, Chlamydia pneumonia, Legionella pneumophila etc and viruses such as influenza, coronavirus, rhinovirus/enterovirus, parainfluenza, metapneumovirus, influenza B virus etc are identified as co-pathogens. In our current effort, we develop and analysed a compartmental based Ordinary Differential Equation (ODE) type mathematical model to understand the co-infection dynamics of Covid-19 and other influenza type illness. In this work we have incorporated the saturated treatment rate to take account of the impact of limited treatment resources to control the possible Covid-19 cases. As results, we formulate the basic reproduction number of the model system. Finally, we have performed numerical simulations of the co-infection model to examine the solutions in different zones of parameter space.

Mycoplasma pneumoniae COVID-19 Delta Variant Co-Infection Mimicking COVID-19 ARDS.

The Delta variant of COVID-19 has been associated with severe disease causing a surge in the second half of 2021. Atypical pathogens can be present in those in particular with severe ARDS and can contribute to excess morbidity and mortality. We must maintain a high level of suspicion for these pathogens as this can present an opportunity to dramatically improve the prognosis of a patient with COVID-19 ARDS. However, lend caution to Mycoplasma IgM serology as this can be a false-positive. If suspicion remains high for Mycoplasma pneumoniae infection, sputum polymerase chain reaction (PCR) for M pneumoniae is the gold standard for diagnosis. We present the case of a 42-year-old female with COVID-19 Delta variant presumed ARDS who had co-infection with M pneumoniae confirmed by endotracheal sputum aspirate PCR with rapidly improving oxygenation and extubation within 4 days of effective antibiotic therapy.

RNA sequence analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic patients with COVID-19.

OBJECTIVES: The characterization of asymptomatic and mildly symptomatic patients with COVID-19 by observing changes in gene expression profile and possible bacterial coinfection is relevant to be investigated. We aimed to identify transcriptomic and coinfection profiles in both groups of patients. METHODS: A ribonucleic acid (RNA) sequence analysis on nasopharyngeal swabs were performed using a shotgun sequencing pipeline. Differential gene analysis, viral genome assembly, and metagenomics analysis were further performed using the retrieved data. RESULTS: Both groups of patients underwent a cilia modification and mRNA splicing. Modulations in macroautophagy, epigenetics, and cell cycle processes were observed specifically in the asymptomatic group. Modulation in the RNA transport was found specifically in the mildly symptomatic group. The mildly symptomatic group showed modulation in the RNA transport and upregulation of autophagy regulator genes and genes in the complement system. No link between viral variants and disease severity was found. Microbiome analysis revealed the elevation of Streptococcus pneumoniae and Veillonella parvula proportion in symptomatic patients. CONCLUSION: A reduction in the autophagy influx and modification in the epigenetic profile might be involved in halting the disease progression. A global dysregulation of RNA processing and translation might cause more severe outcomes in symptomatic individuals. Coinfection by opportunistic microflora should be taken into account when assessing the possible outcome of SARS-CoV-2 infection.

COVID-19 and Burkholderia cepacia co-infection in pregnancy associated with fetal demise: a case report.

Since the global pandemic of the 2019 coronavirus disease (COVID-19), few studies have reported on the relevance of bacteria co-infection on outcome of COVID-19 patients. Little is known about the clinical presentation among pregnant women, mother-to-child transmission, and fetal outcomes. This report shows a 24-year-old nulliparous woman who was 32 weeks pregnant and was admitted to the University Hospital, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi Ghana with symptoms of fever (40.3°C), cough and breathlessness of two weeks duration. Her nasopharyngeal sample tested positive for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) and blood culture isolated Burkholderia cepacia. She was given medications but went into pre-term labour and delivered a stillborn baby. This rare case of COVID-19 and Burkholderia cepacia co-infection emphasizes the need for a thorough assessment and appropriate treatment of patients presenting with fever and respiratory symptoms in order to mitigate poor outcome.

A 9-gene biomarker panel identifies bacterial coinfections in culture-negative COVID-19 cases.

Confirmatory diagnosis of bacterial coinfections with COVID-19 is challenging due to the limited specificity of the widely used gold-standard culture sensitivity test despite clinical presentations. A misdiagnosis can either lead to increased health complications or overuse of antibiotics in COVID-19 patients. With a multi-step systems biology pipeline, we have identified a 9-gene biomarker panel from host blood that can identify bacterial coinfection in COVID-19 patients, even in culture-negative cases. We have also formulated a qPCR-based score that diagnoses bacterial coinfection with COVID-19 with the accuracy, specificity, and sensitivity of 0.93, 0.96, and 0.89, respectively. This gene signature and score can assist in the clinical decision-making process of necessary and timely prescription of antibiotics in suspected bacterial coinfection cases with COVID-19 and thereby help to reduce the associated morbidity and mortality.