Clinical course and molecular characterization of human Bocavirus associated with acute lower respiratory tract infections in tertiary care hospital of north India.

Respiratory samples from 139 hospitalized children were screened for the Human Bocavirus (HBoV) genome. Positive samples were sequenced for partial VP1/VP2 gene followed by molecular and phylogenetic analyses. HBoV positivity was noted in 7.2% (10/139) patients. All HBoV positive children presented with fever followed by cough and respiratory distress (90%; 9/10). Three children developed multisystemic viral illness with one fatality. Eight children required intensive care management and mechanical ventilation required for 5 children. Nucleotide percent identity of partial VP1/VP2 gene of HBoV study strains were ranging from 97.52% to 99.67%. Non-synonymous amino acid mutations in VP1 protein revealed T591S (n=8) and Y517S (n=1) mutations in comparison to HBoVSt1 strain where N475S (n=8) and S591T (n=2) mutations in comparison to HBoVSt2 strain. One study strain showed A556P, H556P, I561S and M562R non-synonymous mutations. All the study strains belong to HBoV1 type. Seven HBoV strains belong to same lineage and three belong to another lineage. For evolutionary dynamics, GTR+I substitution model with uncorrelated relaxed lognormal clock and Bayesian Skyline tree prior showed 9.0 x 10-4 [95% HPD interval: 3.1 x10-6, 2.1 x 10-3] nucleotide substitutions/site/year. The clinical suspicion and virological screening is necessary for identification HBoV in children.

Cycle threshold values of SARS-CoV-2 RNA in conjunctival swabs and nasopharyngeal secretions: a comparative study from a tertiary care center in India.

PURPOSE: To detect the viral RNA load of SARS-CoV-2 in conjunctival swabs of COVID-19 patients, and compare with nasopharyngeal swabs. METHODS: Conjunctival swabs of COVID-19 patients (with PCR positive nasopharyngeal swabs) were subjected to quantitative reverse transcription-polymerase chain reaction (RT-PCR) for detection of SARS-CoV-2 RNA. The cycle threshold (Ct) values of Open Reading Frame 1 (ORF 1 Ab gene) and nucleoprotein (N gene) PCRs were used to assess the viral RNA load, and compare them with the baseline values of nasopharyngeal swabs. RESULTS: Of 93 patients, 17 (18.27%) demonstrated SARS-CoV-2 RNA in conjunctival swabs. Baseline nasopharyngeal swabs were collected at a median of 2 days; while, the conjunctival swabs were collected at median 7 days, from onset of illness (p < 0.001). Despite a significant delay in conjunctival swab collection than nasopharyngeal swabs, the Ct values (ORF or N gene PCRs) were comparable between nasopharyngeal swab and conjunctival swab samples. Subsequently, during the recovery period, in four of these 17 patients (with conjunctival swab positivity), when the second nasopharyngeal swab was 'negative', the conjunctival swab was 'positive'. CONCLUSION: The conjunctival swabs demonstrated SARS-CoV-2 RNA in 17 (18.27%) of 93 COVID-19 patients. Our results may suggest a delayed or a prolonged shedding of the virus/viral RNA on the ocular surface than in nasopharyngeal mucosa.

The continuum of liver injury with severity of dengue fever: A retrospective observational study.

BACKGROUND: Dengue is a major international health concern prevalent in tropical and sub-tropical countries. There are a paucity of studies on the relationship of hepatic complications with inflammatory parameters in dengue infection. METHODS: Single-centre observational study was conducted at the tertiary care centre in North India. Patients (>12 years) diagnosed with dengue infection between August and November 2021 were enrolled in the study. The frequency of hepatic derangements and their associations with inflammatory severity was analysed. RESULTS: Based on the clinical symptoms, 170 patients were classified into three categories, namely, dengue fever, warning dengue and severe dengue. Higher incidence of liver dysfunction was observed in severe dengue patients with median values of aspartate aminotransferase (AST) (3051 U/L, p < 0.001), alanine aminotransferase (ALT) (1792 U/L, p = 0.009), alkaline phosphatase (172 U/L, p = 0.001), T.Bil (34.2 µmol/L, p < 0.001), albumin (30 g/L, <0.001), and gamma-glutamyl transferase (152 U/L, p < 0.001) along with inflammatory marker C-reactive protein (CRP) (43 mg/dL, p < 0.001) highly deranged, in comparison to patients with/without warning signs. Median levels of CRP were found to be positively and significantly correlated with the median levels of AST and ALT (p < 0.05, r = 0.99) in all three categories of dengue patients. Liver injury was noted in 107 (63%) of the cohort, and mixed type of liver injury involving both hepatocellular and cholestatic patterns was observed as the most common type of injury (n = 50, 29.4%). Liver injury correlated with the severity of dengue illness as about 85% of severe dengue patients had significant liver injury (p = 0.014). CONCLUSION: In dengue patients, the association of the liver injury with inflammatory severity suggests that the mechanism of liver injury may be related to inflammatory response apart from the hepatotropic nature of the virus.

Outbreak investigation of acute febrile illness from the Himalayan foothills: Solving the puzzle of fever.

In September 2022, Panchkula Civil Hospital reported an outbreak of acute febrile illness (AFI) in Pinjore, located in the Himalayan foothills, Haryana, North India. There was an upsurge of fever cases. Blood samples were taken from suspected patients (n = 58) with AFI and subjected to serology of dengue, chikungunya, Japanese encephalitis, leptospira and scrub typhus. The samples were also screened for West Nile & Zika virus RNA using real-time PCR. Viral strains were characterized by sequencing. Of the 58 cases of AFI, Dengue could be identified in 45 (77.58%) followed by JE and Chikungunya in 2 cases each (3.44%), respectively. Among Dengue positive cases, 44 had monoinfection (97.77%) and 1 patient had dengue and JE. None were positive for Zika, West Nile, Scrub typhus, and Leptospira with the testing protocol. Four patients developed dengue with warning signs, such as abdominal pain in one patient and recurrent vomiting in the remaining three. The dengue serotype could be determined in 17 samples and revealed serotype 2. Molecular evolution analysis based on the complete envelope gene revealed that all DENV-2 strains (n = 13) circulated in the outbreak area belonged to the DENV-2 cosmopoliton genotype. In the early stages of infection, relying only on clinical manifestations is ineffective, so both molecular and serological assays along with clinical diagnosis are noteworthy for determining the aetiology of AFI.

Utility of CDC DENV1-4 real time PCR assay and trioplex assay for the diagnosis of dengue in patients with acute febrile illness.

Nucleic acid amplification tests (NAATs) have revolutionized reliable detection of dengue virus (DENV) during acute phase of infection. The study evaluated performance of CDC DENV-1-4 real-time assay, trioplex RT-PCR and heminested conventional RT-PCR assay in the diagnosis of DENV. The three NAATs were performed on 107 consecutive samples collected from patients suspected of DENV infection during acute phase of illness. Their performance was compared against composite reference standard, consisting of DENV NS1 antigen ELISA and DENV IgM ELISA. 88/107 study samples were positive by DENV ELISA, either NS1Ag (80), IgM (3) or both (5). The overall sensitivity of CDC DENV-1-4 RT-PCR assay, trioplex RT-PCR assay and conventional multiplex RT-PCR was 68.18%, 54.55% and 38.64%, respectively in diagnosing dengue during acute phase, with an area under the curve of 0.841, 0.773 and 0.693 respectively when compared against composite reference standard. The sensitivity was 82.93%, 73.17% and 51.22%, respectively within three days of illness and 60%, 42.86% and 28.57%, respectively between 4 and 5th day of illness. All the three molecular assays had 100% specificity. Maximum concordance values of 86.9% were recorded among CDC DENV-1-4 rRT-PCR assay and trioplex assay with kappa value of 0.74, suggestive of substantial agreement. CDC DENV-1-4 rRT-PCR assay can be used as a reliable and accurate test for diagnosis of DENV during acute phase of illness.

Paradigm shift of respiratory viruses causing lower respiratory tract infection in children during COVID-19 pandemic in India.

INTRODUCTION: Acute lower respiratory tract infections (ALRTIs) are the commonest cause of mortality in children mostly attributed to respiratory viruses. During the coronavirus disease 2019 (COVID-19) pandemic, the dynamics and transmission of infections changed worldwide due to widespread public health measures. This study aimed to understand the pattern of respiratory viruses associated with ALRTIs in children pre and during COVID-19 pandemic in India. METHODOLOGY: Respiratory samples were collected from ALRTI patients during pre-pandemic period (October 2019 to February 2020; n = 166), Delta (July 2021 to December 2021; n = 78) and Omicron wave (January 2022 to July 2022; n = 111). Samples were screened for Influenza (Inf) A pdmH1N1, InfA H3N2, InfB, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), human bocavirus (hBoV), human rhinovirus (hRV), and parainfluenza virus (PIV-2 and PIV-3) by nucleic acid amplification techniques (NAATs). RESULTS: Significantly higher proportion of children with ALRTIs had virus/es isolated during pre-pandemic period than during mid-pandemic period [78.9% (131/166) vs. 52.9% (100/189); p < 0.001). RSV positivity was significantly higher (51.2%) in pre-pandemic period than 10.3% and 0.9% during the Delta and Omicron waves respectively. No significant difference in positivity rate of Inf A pdmH1N1, Inf A H3N2 and Inf B was seen. The increase in positivity of hRV (39.2% vs 42.3% vs 56.8%) and hBOV (1.2% vs 5.1% vs 9%) was documented in pre-pandemic, delta wave and omicron wave respectively. CONCLUSIONS: The COVID-19 pandemic significantly impacted the frequency and pattern of respiratory viruses among hospitalized children with ALRTIs in India.

Avian influenza revisited: concerns and constraints.

Avian influenza (AVI) is being known for its pandemic potential and devastating effects on poultry and birds. The AVI outbreaks in domesticated birds are of concern because the Low pathogenic avian influenza virus (LPAI) tends to evolve into a High pathogenic avian influenza virus (HPAI) resulting in the rapid spread and significant outbreak in poultries. The containment should be rapid and stringent precautions should be taken in handling the infected poultry cases or infected materials. In general, AVI viruses do not replicate efficiently in humans, indicating that transmitting these viruses to humans directly is a very rare preference. However, the HPAI ability to the cross-species barrier and infect humans has been known for H5N1 and H7N9. Recently, the world's first human case of transmission of the H5N8 strain from the avian species to humans has been documented. In this recent scenario, it is worth discussing the strain variations, disease severity, economic loss, and effective controlling strategies for controlling avian influenza.

Hydroxychloroquine in Treatment of Asymptomatic and Mildly Symptomatic COVID-19: A Multi-Centre Cohort Study.

BACKGROUND: Although hydroxychloroquine (HCQ) lacks benefit in patients with moderate-to-severe COVID-19, its role in asymptomatic and mildly symptomatic disease needs better elucidation. METHODS: This multi-centre cohort study included asymptomatic and mildly symptomatic, RT-PCR confirmed COVID-19 cases between 30 March and 20 May, 2020. Patients were categorized into two groups (HCQ-treated and untreated) based on exposure to HCQ. Dose of HCQ used was 400 mg twice daily (day one) followed by once daily for seven days. HCQ-untreated patients were managed supportively without any active antiviral or immunomodulatory therapy. Nasopharyngeal SARS-CoV-2 clearance by RT-PCR (primary outcome) was compared between HCQ-treated and untreated patients using Kaplan-Meier analysis and Cox proportional-hazards regression. Clinical efficacy and safety profile of HCQ were assessed (secondary outcomes). RESULTS: 162 patients [84 (51·9%) males; mean age 38·2 (15·2) years] were included. Forty-four (27·2%) patients had mild disease, rest 118 (72·8%) were asymptomatic. Seventy-five (46·3%) patients received HCQ. Median time to virological negativity was lesser in HCQ-treated (13 days) versus untreated patients (15 days) (logrank<0·001) in both asymptomatic and mildly symptomatic patients. Treatment with HCQ was the only independent predictor of virological negativity (hazardratio=2·24; adjusted p-value<0·001). Two (5·4%) mildly symptomatic patients progressed to severe disease within 24 hours (two doses) of HCQ initiation, compared to none in the HCQ-untreated group. Five HCQ-treated patients developed minor gastrointestinal side effects, not requiring drug discontinuation. CONCLUSION: HCQ reduced the time to virologic negativity (by 2 days) in asymptomatic and mildly symptomatic COVID-19, without any serious adverse events. However, no obvious clinical benefit was noted.

Clinico-virological Profile, Intensive Care Needs, and Outcome of Infants with Acute Viral Bronchiolitis: A Prospective Observational Study.

OBJECTIVES: The objective of the study was to describe the clinico-virological profile, treatment details, intensive care needs, and outcome of infants with acute viral bronchiolitis (AVB). METHODOLOGY: In this prospective observational study, 173 infants with AVB admitted to the pediatric emergency room and pediatric intensive care unit (PICU) of a tertiary care teaching hospital in North India during November 2019 to February 2020 were enrolled. The data collection included clinical features, viruses detected [respiratory syncytial virus (RSV), rhinovirus, influenza A virus, parainfluenza virus (PIV) 2 and 3, and human metapneumovirus (hMPV)], complications, intensive care needs, treatment, and outcomes. Multivariate analysis was performed to determine independent predictors for PICU admission. RESULTS: Most common symptoms were rapid breathing (98.8%), cough (98.3%), and fever (74%). On examination, tachypnea (98.8%), chest retractions (93.6%), respiratory failure (84.4%), wheezing (49.7%), and crepitations (23.1%) were observed. RSV and rhinovirus were the predominant isolates. Complications were noted in 25% of cases as encephalopathy (17.3%), transaminitis (14.3%), shock (13.9%), acute kidney injury (AKI) (7.5%), myocarditis (6.4%), multiple organ dysfunction syndrome (MODS) (5.8%), and acute respiratory distress syndrome (ARDS) (4.6%). More than one-third of cases required PICU admission. The treatment details included nasal cannula oxygen (11%), continuous positive airway pressure (51.4%), high-flow nasal cannula (14.5%), mechanical ventilation (23.1%), nebulization (74%), antibiotics (35.9%), and vasoactive drugs (13.9%). The mortality was 8.1%. Underlying comorbidity, chest retractions, respiratory failure at admission, presence of shock, and need for mechanical ventilation were independent predictors of PICU admission. Isolation of virus or coinfection was not associated with disease severity, intensive care needs, and outcomes. CONCLUSION: Among infants with AVB, RSV and rhinovirus were predominant. One-third infants with AVB needed PICU admission. The presence of comorbidity, chest retractions, respiratory failure, shock, and need for mechanical ventilation independently predicted PICU admission. HOW TO CITE THIS ARTICLE: Angurana SK, Takia L, Sarkar S, Jangra I, Bora I, Ratho RK, et al. Clinico-virological Profile, Intensive Care Needs, and Outcome of Infants with Acute Viral Bronchiolitis: A Prospective Observational Study. Indian J Crit Care Med 2021;25(11):1301-1307.

Clinico demographic profiling of the Respiratory syncytial virus (RSV) infected children admitted in tertiary care hospital in North India.

BACKGROUND: Acute bronchiolitis is fatal disease involving lower respiratory tract of infants and children of paediatric age group. Respiratory Syncytial Virus (RSV) is responsible for causing more than 70% hospital admissions of children aged less than 2 years thus making a necessity for accurate and timely diagnosis. AIMS: The main aim of study was clinicodemographic correlation of RSV positive children presenting to our tertiary care hospital. SETTING AND DESIGN: It is a retrospective study done between December to January 2018. MATERIALS AND METHODS: Detection of RSV antigen from nasophyrangeal aspirates using Mouse Monoclonal anti RSV Antibody (by Novatetra) and Goat Anti Mouse Antibody conjugated with FITC as secondary antibody. RESULTS: A total of 147 samples were received in the laboratory and 20 were tested as positive for RSV Antigen. Totally, 19/20 children were aged less than 1 year and with a male predominance. The most common symptom was cough and respiratory distress. Eight percent of the children showed wheezing and 18/20 required assisted ventilation. The clinical course in one child deteriorated leading to death of that patient. CONCLUSIONS: The timely diagnosis and management of RSV infected children is utmost needed to prevent morbidity and mortality. The premorbid conditions can assist to differentiate the viral from bacterial pneumonia and thus enable speedy recovery of the child.

Rapid antigen detection kit for the diagnosis of SARS-CoV-2 - are we missing asymptomatic patients?

PURPOSE: To determine the utility, diagnostic accuracy, sensitivity, specificity, and negative predictive value of the laboratory based Covid-19 antigen detection test (Coris Bio- Concept, Gembloux, Belgium) for the diagnosis of SARS-CoV-2 in a tertiary care hospital among symptomatic and asymptomatic patients. METHODS: The nasopharyngeal swab samples were collected from the symptomatic patients and their contacts. The diagnostic accuracy of this antigen kit was determined in comparison to SARS-CoV-2 real-time reverse transcriptase (RT-PCR). RESULTS: A total of 825 patients fulfilling the inclusion criteria were included in the study; RT-PCR and antigen detection was performed simultaneously for 484 samples to determine the sensitivity and specificity of the test. The overall specificity and sensitivity was 99.32% and 71.96% respectively. Also, 3.7% of the asymptomatic patients who were negative by RAT were detected positive by RT-PCR. CONCLUSION: This rapid antigen test (RAT) was sensitive in the symptomatic patients presenting during the initial phase of the illness. Since, majority of the SARS-CoV-2 patients are asymptomatic and considering the huge population, the testing strategy formulated by Indian Council of Medical Research (ICMR) at the national level was cost effective. Thus, Ag-RDTs could play a pivotal role in early diagnosis, policy making and surveillance of the SARS-CoV-2.

Perplexity vs Clarity in choosing the right molecular diagnostic techniques for SARS-COV2 detection in Indian setup.

After the havoc created by Spanish flu a century ago, the world is witnessing exactly a similar pandemic situation since the beginning of the year 2020. The unexplained respiratory illness with high morbidity & mortality which started in Wuhan, China and spread across the world was finally termed as COVID-19 disease caused by SARS-CoV-2 and later announced as pandemic by WHO. This novel virus SARS-CoV-2 is a new variant of SARS corona virus with high infectivity and mysterious pathophysiology. The major step towards containment of this pandemic is to scale up the testing for SARS-CoV-2 and thereby isolating and managing the patients at the earliest. Molecular amplification based methods such a Real time Polymerase chain reaction (RT-PCR), CBNAAT and TrueNAT are the most commonly used techniques for detection of SARS-CoV2. To utilize these diagnostic facilities optimally in the management of the suspected COVID 19 patients, it is of utmost importance for the healthcare providers to understand the intricacies related to these technologies. Thus, the technical details along with the pros & cons of these three amplification-based technologies for proper understanding of these diagnostic modalities for SARS COV-2 diagnosis are discussed herewith.

Clinical Profile, Hospital Course and Outcome of Children with COVID-19.

OBJECTIVES: To describe the epidemiological and clinical characteristics and outcome of hospitalized children with COVID-19 during the initial phase of the pandemic. METHODS: This was a cross-sectional descriptive study conducted at the dedicated COVID-19 hospital of a tertiary care referral center in North India. Consecutive children aged 14 y or younger who tested positive for SARS-CoV-2 by RT-PCR from nasopharyngeal swab between 1 April 2020 and 15 July 2020 were included. RESULTS: Of 31 children with median (IQR) age of 33 (9-96) mo, 9 (29%) were infants. About 74% (n = 23) had history of household contact. Comorbidities were noted in 6 (19%) children. More than half (58%) were asymptomatic. Of 13 symptomatic children, median (IQR) duration of symptoms was 2 (1-5.5) d. Fever (32%) was most common followed by cough (19%), rapid breathing (13%), diarrhea (10%) and vomiting (10%). Severe [n = 4, 13%] and critical [n = 1, 3%] illnesses were noted more commonly in infants with comorbidities. Three (10%) children required PICU admission and invasive ventilation; one died. Median (IQR) length of hospital stay was 15 (11-20) d. Follow up RT-PCR before discharge was performed in 17 children and the median (IQR) duration to RT-PCR negativity was 16 (12-19) d. CONCLUSIONS: In the early pandemic, most children with COVID-19 had a household contact and presented with asymptomatic or mild illness. Severe and critical illness were observed in young infants and those with comorbidities.

Multi-Organ Involvement in COVID-19: Beyond Pulmonary Manifestations.

Coronavirus Disease 19 (COVID-19), due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become an on-going global health emergency affecting over 94 million cases with more than 2 million deaths globally. Primarily identified as atypical pneumonia, it has developed into severe acute respiratory distress syndrome (ARDS), a multi-organ dysfunction with associated fatality. Ever since its emergence, COVID-19 with its plethora of clinical presentations has signalled its dynamic nature and versatility of the disease process. Being a disease with droplet transmission has now assumed the proportion of a suspected airborne nature which, once proved, poses a Herculean task to control. Because of the wide distribution of the human angiotensin-converting enzyme-2 (hACE2) receptors, known for its transmission, we envisage its multiorgan spread and extensive disease distribution. Thus, an extensive review of the extrapulmonary organotropism of SARS-CoV-2 with organ-specific pathophysiology and associated manifestations like dermatological complications, myocardial dysfunction, gastrointestinal symptoms, neurologic illnesses, hepatic and renal injury is needed urgently. The plausible mechanism of site-specific viral invasion is also discussed to give a comprehensive understanding of disease complexity, to help us to focus on research priorities and therapeutic strategies to counter the disease progression. A note on the latest advancements in vaccine research will enlighten the scientific world and equip it for better preparedness.

Viral Hepatitis E and Chronicity: A Growing Public Health Concern.

Hepatitis E viral infection recently emerges as a global health concern. Over the last decade, the understanding of hepatitis E virus (HEV) had changed with the discovery of new genotypes like genotype-7 and genotype-8 with associated host and mode of infection. Diversification in the mode of hepatitis E infection transmission through blood transfusion, and organ transplants in contrast to classical feco-oral and zoonotic mode is the recent medical concern. The wide spectrum of infection ranging from self-limiting to acute liver failure is now overpowered by HEV genotype-specific chronic infection especially in transplant patients. This concern is further escalated by the extra-hepatic manifestations of HEV targeting the central nervous system (CNS), kidney, heart, and pancreas. However, with the development of advanced efficient cell culture systems and animal models simulating the infection, much clarity toward understanding the pathogenetic mechanism of HEV has been developed. Also this facilitates the development of vaccines research or therapeutics. In this review, we highlight all the novel findings in every aspect of HEV with special emphasis on recently emerging chronic mode of infection with specific diagnosis and treatment regime with an optimistic hope to help virologists and/or liver specialists working in the field of viral hepatitis.

Persistence of SARS-COV-2 in body fluids: a bystander or whistle blower.

The novel Coronavirus COVID-19 is wrecking a havoc across the globe and has been declared as a pandemic by WHO. Apart from transmission and shedding of the virus through respiratory secretions in the form of droplets (mainly), several studies have shown the presence of the virus in various samples such as stool, urine and occasionally in blood, semen, tears and breastmilk. Whereas government authority guidelines consider a person as cured from COVID-19 when along with clinical improvement no more virus can be detected primarily on respiratory samples along with clinical improvement; the persistence of the virus in these body fluids even after clinical recovery and negative RT-PCR test results on respiratory samples, has raised many questions about the elusive nature of this novel virus along with the possibility of other routes of transmission of this virus in the community. Although studies performed till now across the globe on persistence of SARSCOV-2 in various body fluids are sparse, in this review we would like to present and analyse the results of those studies performed globally on the aforesaid topic to get a better insight of this side of the COVID-19 story.