Effect of COVID-19 pandemic on influenza; observation of a tertiary level virology laboratory.

The lockdown enforced amid the COVID-19 pandemic has affected the occurrence and trends of various respiratory virus infections, with a particular focus on influenza. Our study seeks to analyze the repercussions of the COVID-19 pandemic on the positivity of the influenza virus throughout a 4-year span, encompassing both the pre-COVID-19 era (2018 and 2019) and the COVID-19 period (2020 and 2021). Data collected from patients clinically diagnosed with Influenza-like Illness and Severe Acute Respiratory Illness (SARI) from January 2018 to December 2021 for influenza virus detection were acquired and analyzed through multiplex RT-qPCR. The statistical analysis was conducted using SPSS (Statistical Package for Social Sciences) Version 21.0 Software. A total of 4464 samples were tested over 4 years (2018-2021), with 3201 samples from the pre-COVID era and 1263 samples from the COVID era. Influenza A positivity dropped from 17.7 to 9.57% and Influenza B positivity decreased from 3.74 to 2.61%. Subtyping revealed changes in prevalence for both viruses. Seasonal variations showed more pronounced peaks in the pre-COVID-19 era with reduced activity during lockdown. Influenza A saw a resurgence in August 2021. Throughout the COVID-19 pandemic (2020-2021) SARI cases did not decrease. The positivity rate for Influenza A slightly rose to 7.79% from 4.23% in the COVID period (2020-2021). This increase correlates with heightened hospitalization rates during the pandemic, sparking concerns of potential coinfection with coronavirus and Influenza A. The notable drop in influenza cases in 2020-2021 is likely due to stringent precautions, lockdowns, drug repurposing, and prioritized testing, indicating no reduction in influenza transmission. Increased influenza positivity in SARI patients during COVID-19 highlights a heightened risk of coinfection. Emphasizing solely on COVID-19 may lead to underreporting of other respiratory pathogens, including influenza viruses.

Effect of siRNA targeting dengue virus genes on replication of dengue virus: an in vitro experimental study.

Dengue is a notorious viral infection, which affects a large segment of world populations in absence of vaccines and anti-viral treatment. The current study evaluates role of effective siRNA in dengue virus replication. Eight siRNA were synthesized against five different genes (Capsid, CprM, NS1, NS3 and NS5) of all serotypes of dengue virus. All serotype of DV were transfected with all synthesized siRNA in vitro, using BHK-21 cell lines. Culture fluid from test and control was tested by Real time PCR for CT value comparison in siRNA treated cell line (test) and untreated cell line (controls). Percent knockdown (%KD) was calculated by ∆∆CT methods to know the difference in test and control CT value. It was found that siRNA targeted against capsid gene worked best and showed inhibition of all four DV serotypes. DV-1, DV-2, DV-3 and DV-4 showed 93.8%, 99.3%, 87.5% and 93.8% knock down (%KD) respectively by siRNA targeted against capsid gene. Additionally, Si2 (target CprM gene 60-899) and Si 6 (target NS1 gene 3007-3025) were also showing inhibition of replication. Most serotypes of DV (with few exceptions) were not inhibited by siRNA targeted against NS-1, NS-3, and NS-5 genes. Animal studies using siRNAs are warranted to establish their therapeutic role.

Feasibility, efficiency & effectiveness of pooled sample testing strategy (pooled NAAT) for molecular testing of COVID-19.

BACKGROUND & OBJECTIVES: During the current COVID-19 pandemic, a large number of clinical samples were tested by real-time PCR. Pooling the clinical samples before testing can be a good cost-saving and rapid alternative for screening large populations. The aim of this study was to compare the performance characteristics, feasibility and effectiveness of pooling nasal swab and throat swab samples for screening and diagnosis of SARS-CoV-2. METHODS: The pool testing was applied on a set of samples coming from low COVID-19 positivity areas. A total of 2410 samples were tested in pools of five samples each. A total of five pools of five samples each were generated and tested for E gene. RESULTS: Of the total of 482 pools (2410 samples) 24 pools flagged positive. Later on pool de-convolution, a total of 26 samples were detected as positive for COVID-19, leading to positivity of about one per cent in the test population. For the diagnosis of individual samples, the pooling strategies resulted in cost savings of 75 per cent (5 samples per pool). INTERPRETATION & CONCLUSIONS: It was observed that testing samples for COVID-19 by reverse transcription (RT)- PCR after pooling could be a cost-effective method which would save both in manpower and cost especially for resource-poor countries and at a time when test kits were short in supply.

SARS-CoV-2 -RNA persists longer in faecal sample as compared to nasal and throat swab samples of COVID-19 patients'; an observational study.

The route of transmission of Novel SARS-CoV-2 virus is ambiguous. In this regard we planned a study to find out SARS-CoV-RNA shedding in various clinical samples of 9 COVID-19 positive patients. SARS-CoV-RNA was detected in nasal swab (NS), throat swab (TS) and faecal sample but was not detected in serum and urine samples. We also report that SARS-CoV-2-RNA persisted in faeces for >20 days. Persistence of faecal RNA might impose challenge in infection control and the disease may spread to household contacts if discharged. Perineal cleaning and hygiene may be advised at the time of vaginal delivery.

Upsurge of chikungunya cases in Uttar Pradesh, India.

BACKGROUND & OBJECTIVES: Chikungunya (CHIK) re-emerged in India in 2006 after a gap of three decades. In Uttar Pradesh (UP), <100 confirmed cases per million were reported during this outbreak. Based on an upsurge of CHIK cases at UP, this retrospective study was conducted to investigate clinical and serological profile of CHIK cases in UP. METHODS: A retrospective study was done on all clinically suspected CHIK cases that had been tested by ELISA for anti-CHIK virus IgM antibodies from September 2012 to December 2017. Based on clinical features, a subset of patients had earlier been tested serologically for dengue and Japanese encephalitis (JE). RESULTS: Of the 3240 cases enrolled, 771 (23.8%) were seropositive. Patients had a range of clinical manifestations with seropositivity highest in those exhibiting arthralgia with fever (40%), followed by fever of unknown origin (FUO) (22%), encephalitis (13%) and fever with rash (12%). Cases (total, seropositive) increased over 20-fold in 2016 (1389, 412) and 2017 (1619, 341), compared to 2012-2015. Nearly a third of dengue serology-positive cases and a fifth of JE serology-positive cases were co-positive for CHIKV. INTERPRETATION & CONCLUSIONS: Archival data from 2006-2011 and data from this study (2012-2017) indicated that UP experienced first CHIK outbreak in the decade in 2016, as part of a large-scale upsurge across northern India. CHIK should be considered as a differential diagnosis in patients presenting with fever of unknown origin or fever with rash or acute encephalitis, in addition to classical arthralgia.

Aetiology of acute encephalitis syndrome in Uttar Pradesh, India from 2014 to 2016.

BACKGROUND & OBJECTIVES: It is imperative to know the aetiology of acute encephalitis syndrome (AES) for patient management and policy making. The present study was carried out to determine the prevalence of common aetiological agents of AES in Uttar Pradesh (UP) state of India. METHODS: Serum and/or CSF samples were collected from AES patients admitted at Gandhi Memorial and Associated Hospital, King George's Medical University, Lucknow, a tertiary care centre, UP during 2014-16. Cerebrospinal fluid (CSF) and serum samples from cases were tested for IgM antibodies against Japanese encephalitis virus (anti-JEV), and dengue virus (anti-DENV) by ELISA; and for enterovirus, herpes simplex virus (HSV) and varicella zoster virus (VZV) by real-time PCR. Serum samples of cases having sufficient CSF volume, were also tested for anti-scrub typhus IgM antibodies and for Neisseria meningitides, Streptococcus pneumoniae and Haemophilus influenzae. RESULTS: JEV and DENV (8% each) were the most common identified aetiology from the 4092 enrolled patients. Enterovirus, HSV and VZV, each were detected in <1% AES cases. Co-positivity occurred in 48 cases. Scrub typhus (31.8%) was the most common aetiology detected. Haemophilus influenzae and S. pneumoniae were detected in 0.97 and 0.94% cases, respectively, however, N. meningitides was not detected in any of the cases. About 40% of the JEV/DENV positive AES cases were adults. The gap between the total number of AES cases and those with JEV/ DENV infection increased during monsoon and post-monsoon seasons. INTERPRETATION & CONCLUSION: Scrub typhus, JEV and DENV are the main aetiological agents of AES in UP. DENV and JEV can no longer be considered paediatric diseases. The prevalence of non-JEV/DENV aetiology of AES increases in the monsoon and post-monsoon seasons.

Genotype 3b of human parvovirus B19 detected from hospitalized children with solid malignancies in a North Indian tertiary care hospital.

Human parvovirus B19 (B19V) infection is known to cause serious consequences in immuno-compromized individuals. The present cross sectional study was designed to estimate the prevalence and genotype distribution of B19V in children receiving chemotherapy for solid malignancies at a tertiary care hospital in North India during October 2013 to May 2015. Serum samples from all the patients were tested for anti-B19V IgM and IgG antibodies and for B19V-DNA as soon as received. Samples testing positive for B19V-DNA were subjected to viral load estimation and to genotype determination by sequencing. Total 96 children were enrolled of which 9 (9.3%), 32 (33.3%), and 25 (26%) tested positive for anti-B19V IgM, anti-B19V IgG, and B19V-DNA, respectively. The viral load of B19V-DNA positive children ranged from 5.5 × 10(2) to 3.5 × 10(12) copies/ml. Accordingly children were divided into three groups: group I, with acute infection (n = 25); group II, previously exposed (n = 27), and group III, negative for B19V infection or with inappropriate antibody response (n = 44). B19V positivity was significantly associated (P-value < 0.0001) with a history of blood transfusion in the past 6 months, severe anemia (hemoglobin levels <6 gm%) and thrombocytopenia (platelets <150,000/cu.mm.). Sequence analysis of 21 of 25 DNA positive samples showed that all of them were Genotype 3b that clustered into three groups. All the sequences within each cluster were identical. The nucleotide identity of the sequences suggests a nosocomial outbreak of B19V during the study period. Children on chemotherapy for solid tumors should be routinely screened for B19V infection by both serology and PCR. J. Med. Virol. 88:1922-1929, 2016. © 2016 Wiley Periodicals, Inc.

Prevalence and genotypic characterization of human parvovirus B19 in children with hemato-oncological disorders in North India.

Human parvovirus B19 (B19V) has been associated with chronic anemia in immuno-compromised patients. In the present study, the prevalence and genotype distribution of B19V in children from North India, suffering with hemato-oncological disorders is reported. Children with aplastic anemia/leukemia/chronic hematological disorders, and healthy blood donors were enrolled in the study. Blood samples from cases and blood donors were analyzed for anti-B19V IgM and anti-B19V IgG antibodies by ELISA and for B19V-DNA by PCR. B19V-DNA positive samples were studied further for determination of viral load in samples and for B19V-DNA sequence (VP1/VP2 overlapping region) analysis. Total 238 cases (103 leukemia, 77 aplastic anemia and 58 chronic hematological disorders) and 350 blood donors were enrolled in the study. Anti-B19V IgM was positive in 16 (6.7%) cases, B19V-DNA was detected in 13 (5.5%) cases and anti-B19V IgG was positive in 127 (53.4%) cases. Total 223 (63.5%) blood donors were positive for anti-B19V IgG, however, anti-B19V IgM and B19V-DNA was not detected in any blood donor. The prevalence of anti-B19V IgG was significantly higher in children > 10 years of age. Viral load of B19V decreased with appearance of specific antibodies. Phylogenetic analysis of the VP1/VP2 overlapping region revealed that genotype 1 predominated in these patients (11/13, 84.6%), followed by genotype 3 (2/13, 15.4%). No genotype 2 was detected. All the genotype 1strains were sub-typed as 1a, except four strains, which matched neither 1a nor 1b and formed a separate cluster. Both the genotype 3 strains were sub-typed as 3b.