Disposable graphene-oxide screen-printed electrode integrated with portable device for detection of SARS-CoV-2 in clinical samples

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis is the need of the hour, as cases are persistently increasing, and new variants are constantly emerging. The ever-changing nature of the virus leading to multiple variants, has brought an imminent need for early, accurate and rapid detection methods. Herein, we have reported the design and fabrication of Screen-Printed Electrodes (SPEs) with graphene oxide (GO) as working electrode and modified with specific antibodies for SARS-CoV-2 Receptor Binding Domain (RBD). Flexibility of design, and portable nature has made SPEs the superior choice for electrochemical analysis. The developed immunosensor can detect RBD as low as 0.83 fM with long-term storage capacity. The fabricated SPEs immunosensor was tested using a miniaturized portable device and potentiostat on 100 patient nasopharyngeal samples and corroborated with RT-PCR data, displayed 94 % sensitivity. Additionally, the in-house developed polyclonal antibodies detected RBD antigen of the mutated Omicron variant of SARS-CoV-2 successfully. We have not observed any cross-reactivity/binding of the fabricated immunosensor with MERS (cross-reactive antigen) and Influenza A H1N1 (antigen sharing common symptoms). Hence, the developed SPEs sensor may be applied for bedside point-of-care diagnosis of SARS-CoV-2 using miniaturized portable device, in clinical samples.

Pan-India influenza-like illness (ILI) and Severe acute respiratory infection (SARI) surveillance: epidemiological, clinical and genomic analysis

Background

Over time, COVID-19 testing has significantly declined across the world. However, it is critical to monitor the virus through surveillance. In late 2020, WHO released interim guidance advising the use of the existing Global Influenza Surveillance and Response System (GISRS) for the integrated surveillance of influenza and SARS-CoV-2.

Methods

In July 2021, we initiated a pan-India integrated surveillance for influenza and SARS-CoV-2 through the geographically representative network of Virus Research and Diagnostic Laboratories (VRDLs) across 26 hospital and laboratory sites and 70 community sites. A total of 34,260 cases of influenza-like illness (ILI) and Severe acute respiratory infection (SARI) were enrolled from 4 July 2021 to 31 October 2022.

Findings

Influenza A(H3) and B/Victoria dominated during 2021 monsoon season while A(H1N1)pdm09 dominated during 2022 monsoon season. The SARS-CoV-2 "variants of concern" (VoC) Delta and Omicron predominated in 2021 and 2022, respectively. Increased proportion of SARI was seen in extremes of age: 90% cases in < 1 year; 68% in 1 to 5 years and 61% in ≥ 8  years age group. Approximately 40.7% of enrolled cases only partially fulfilled WHO ILI and SARI case definitions. Influenza- and SARS-CoV-2-infected comorbid patients had higher risks of hospitalization, ICU admission, and oxygen requirement.

Interpretation

The results depicted the varying strains and transmission dynamics of influenza and SARS-CoV-2 viruses over time, thus emphasizing the need to continue and expand surveillance across countries for improved decision making. The study also describes important information related to clinical outcomes of ILI and SARI patients and highlights the need to review existing WHO ILI and SARI case definitions.

Gold nanoparticle conjugate-based lateral flow immunoassay (LFIA) for rapid detection of RBD antigen of SARS-CoV-2 in clinical samples using a smartphone-based application

The coronavirus disease 2019 (COVID-19) pandemic has emphasized the need for development of a rapid diagnostic device for the effective treatment and its mitigation. Lateral flow immunoassay (LFIA) belongs to a class of diagnostic devices, which has the benefit of providing quick results, easy to handle, low cost, and on-site applicable. So far, several LFIA has been developed for the detection of infectious severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), however, only a few of them are antigen (Ag)-based. Here, we describe an antibody (Ab)-labeled gold nanoparticles (AuNPs)-based LFIA (AuNPs-LFIA) for the detection of Receptor-Binding Domain (RBD) of SARS-CoV-2. For this, RBD Ab of SARS-CoV-2 was conjugated with the AuNPs, which served as a detecting probe. The fabricated LFIA strip was optimized for different parameters such as membrane pore size, blocking conditions, Ab coating concentration, and conjugate incubation. The optimized LFIA strips were validated in spiked buffer samples and the optimal limit of detection was found to be 1 ng/ml, which was confirmed by a smartphone-based application. Moreover, the developed AuNPs-LFIA strips effectively detected RBD Ag in 100 clinical samples with 94.3% sensitivity and 90.9% specificity in clinical samples when compared with the gold standard (RT-PCR). The fabricated LFIAs are reported to have storage stability of up to 21 days at 4°C and room temperature (RT). Hence, the developed LFIA can be used as a portable, cost-effective diagnostic device for rapid detection of SARS-CoV-2.

Delta variant SARS-CoV-2 infections in pediatric cases during the second wave in India

BACKGROUND

During October 2020, Delta variant was detected for the first time in India and rampantly spread across the globe. It also led to second wave of pandemic in India which affected millions of people. However, there is limited information pertaining to the SARS-CoV-2 strain infecting the children in India.

METHODS

Here, we assessed the SARS-CoV-2 lineages circulating in the pediatric population of India during the second wave of the pandemic. Clinical and demographic details linked with the nasopharyngeal/oropharyngeal swabs (NPS/OPS) collected from SARS-CoV-2 cases (n = 583) aged 0-18 year and tested positive by real-time RT-PCR were retrieved from March to June 2021.

RESULTS

Symptoms were reported among 37.2% of patients and 14.8% reported to be hospitalized. The E gene CT value had significant statistical difference at the point of sample collection when compared to that observed in the sequencing laboratory. Out of these 512 sequences 372 were VOCs, 51 were VOIs. Most common lineages observed were Delta, followed by Kappa, Alpha and B.1.36, seen in 65.82%, 9.96%, 6.83% and 4.68%, respectively in the study population.

CONCLUSION

Overall, it was observed that Delta strain was the leading cause of SARS-CoV-2 infection in Indian children during the second wave of the pandemic. We emphasize on the need of continuous genomic surveillance in SARS-CoV-2 infection even amongst children.

Zika a Vector Borne Disease Detected in Newer States of India Amidst the COVID-19 Pandemic

Background

During the second wave of the COVID-19 pandemic, outbreaks of Zika were reported from Kerala, Uttar Pradesh, and Maharashtra, India in 2021. The Dengue and Chikungunya negative samples were retrospectively screened to determine the presence of the Zika virus from different geographical regions of India.

Methods

During May to October 2021, the clinical samples of 1475 patients, across 13 states and a union territory of India were screened and re-tested for Dengue, Chikungunya and Zika by CDC Trioplex Real time RT-PCR. The Zika rRTPCR positive samples were further screened with anti-Zika IgM and Plaque Reduction Neutralization Test. Next generation sequencing was used for further molecular characterization.

Results

The positivity was observed for Zika (67), Dengue (121), and Chikungunya (10) amongst screened cases. The co-infections of Dengue/Chikungunya, Dengue/Zika, and Dengue/Chikungunya/Zika were also observed. All Zika cases were symptomatic with fever (84%) and rash (78%) as major presenting symptoms. Of them, four patients had respiratory distress, one presented with seizures, and one with suspected microcephaly at birth. The Asian Lineage of Zika and all four serotypes of Dengue were found in circulation.

Conclusion

Our study indicates the spread of the Zika virus to several states of India and an urgent need to strengthen its surveillance.

Evaluation of Fluoride Contamination Using GIS in Thirukkazhukundram Block, Tamil Nadu, India

The presence of fluoride in the groundwater in the Thirukkazhukundram Block in south India is now becoming an increasingly alarming issue. With the semi-arid climatic conditions, charnockite and gneiss rocks form the basement, contributing to the geology of the study area. The pre-monsoon (August 2016) and post-monsoon (February 2017) fluoride concentrations have an average output of 1.3 mg.L-1 and 0.72 mg.L-1 respectively. As of date, only in Neikuppi, the fluoride contamination is found to be 2 mg.L-1 in pre-monsoon which is beyond the accepted limit as per the WHO standards. Other 29 locations taken up for study have fluoride value fluctuation from 1 mg.L-1 to 2 mg.L-1 in the pre-monsoon and from 0 to 1.5 mg.L-1 in the post-monsoon. The main factor responsible for this fluoride contamination lies in the study area’s hydro-geological condition which must be attended to immediately to prevent a public health problem in the future.

GIS-Based Surface Runoff Modeling Using Empirical Technique For A River Basin In South India

Precipitation is the primary source of fresh water in the world. Surface runoff will happen when the amount of rainfall is greater than the soil’s infiltration capacity. In most water resource applications, runoff is the most important hydrological variable. Aside from these rainfall characteristics, there are a number of catchment-specific elements that have a direct impact on runoff amount and volume. This research focuses on estimating surface runoff over the lower Vellar basin, a river basin in the southern part of India, by integrating Soil Conservation Service-Curve Number (SCS-CN) method with GIS. This technique is one of the most common methods used by hydrologists for estimating surface runoff. Curve Number (CN) is an index established by the Natural Resource Conservation Service (NRCS) to denote the potential for stormwater runoff. The nature of the watershed is explored first by creating land use and land cover pattern followed by the preparation of slope, drainage, and location maps. The area taken for this study is the lower Vellar basin situated in the Cuddalore District of Tamil Nadu, India. The curve number is analyzed using the rainfall data of 15 years (2001-2015) and the runoff is being calculated. The watershed pattern of the study area is also explored being analyzed and executed. Preservation of the runoff water is also discussed.

Groundwater Recharge Planning Using Field Survey for Talupula Mandal in Anantapur District, Andhra Pradesh, India

Groundwater is essential to the sustainability of India’s environment, economy, and living conditions because it isn’t just the primary source of domestic supply of water in rural areas, but it is also the major and most productive origin of the water. The increased demand for groundwater as a result of reduced rainfall has put a strain on groundwater resources in areas where groundwater is the primary supply of water. The main aim of this study is to identify and explore the groundwater potential zones in Talupula Mandal of 280.3 km2 in Ananthapur district in Andhra Pradesh, India with semi-arid climatic conditions. Based on the field survey approach, groundwater availability is found out in the villages. Schlumberger Vertical Electrical Sounding (VES) survey technique was used to discover the resistivity and thickness of the unmistakable layers. It was carried out in 18 randomly selected sites where groundwater plays an important role in agricultural and domestic use. The thickness and resistivity of first- and second-layer crack sites of the various layers were separated from ground data using IPI2WIN programming. Using software, graphs were plotted and groundwater potential zones were identified for recharging the groundwater. Based on the results, different models of recharge structures for the study area are identified and recommended. Hence the management of groundwater paves the way for sustainable groundwater levels.

Rugose atypical Vibrio cholerae O1 El Tor responsible for 2009 cholera outbreak in India

Vibrio cholerae causes cholera outbreaks in endemic regions where the water quality and sanitation facilities remain poor. Apart from biotype and serotype changes, V. cholerae undergoes phase variation, which results in the generation of two morphologically different variants termed smooth and rugose. In this study, 12 rugose (R-VC) and 6 smooth (S-VC) V. cholerae O1 Ogawa isolates were identified in a cholera outbreak that occurred in Hyderabad, India. Antimicrobial susceptibility results showed that all the isolates were resistant to ampicillin, furazolidone and nalidixic acid. In addition, R-VC isolates were resistant to ciprofloxacin (92 %), streptomycin (92 %), erythromycin (83 %), trimethoprim-sulfamethoxazole (75 %) and tetracycline (75 %). Based on the ctxB gene analysis, all the isolates were identified as El Tor variant with mutation in two positions of ctxB, similar to the classical biotype. The R-VC isolates specifically showed excessive biofilm formation and were comparatively less motile. In addition, the majority of these isolates (~83 %) displayed random mutations in the hapR gene, which encodes haemagglutinin protease regulatory protein. In the PFGE analysis, R-VC and S-VC were placed in distinct clusters but remained clonally related. In the ribotyping analysis, all the R-VC isolates exhibited R-III pattern, which is a prevailing type among the current El Tor isolates. A hapR deletion mutant generated using an S-VC isolate expressed rugose phenotype. To our knowledge, this is the first report on the association of rugose V. cholerae O1 in a large cholera outbreak with extended antimicrobial resistance and random mutations in the haemagglutinin protease regulatory protein encoding gene (hapR).

Putative Virulence Genes and Biofilm Production Among Typical Enteroaggregative Escherichia coli Isolates from Diarrhoeic Children in Kashmir and Andhra Pradesh

Fifty-eight typical EAEC isolates from children with diarrhoea were examined for HEp-2 cell adherence assay, presence of dispersin (aap), yersiniabactin (irp2), plasmid encoded toxins (pet), Shigella enterotoxin1 (set1A) and cryptic open reading frame (shf) putative virulence genes by polymerase chain reaction as well as for biofilm production. All the isolates showed aggregative adherence pattern on HEp-2 cells. All but five isolates (91.3 %) carried aap gene. While irp2, pet, set1A and shf genes were detected in 68.9, 5.1, 39.6, and 60.3 % isolates, respectively. Thirty-three (64.7 %) isolates out of 51 tested were found to produce biofilm which was found to be significantly associated only with set1A virulence gene (P = 0.025). Highest amount of biofilm was produced by a strain that possessed all the genes studied. Out of 14 isolates in which the most frequent gene combination (aap, irp2 and shf) was observed, only six produced biofilm. It is concluded that there is significant heterogeneity in putative virulence genes of EAEC isolates from diarrhoeic children and biofilm formation is associated with multiple genes.

Evaluation of a rapid dipstick test for identifying cholera cases during the outbreak

BACKGROUND & OBJECTIVES

Intermittent cholera outbreaks are major problem in many of the states of India. It is essential to identify cholera at the earliest for timely mobilization of public health responses and to abort the outbreaks. The present study was a part of a diarrhoeal outbreak investigation in Secunderabad, India, during May 2009 where the usefulness of Crystal VC rapid dipstick kit was assessed for detecting the aetiologic agent of the outbreak.

METHODS

Stool specimens were collected from 15 hospitalized patients with acute watery diarrhoea and analyzed for detection of cholera vibrios using Crystal VC rapid dipstick kit and the usefulness of the kit was determined by comparative analysis of the same set of specimens using both microbiological and real-time PCR (RT-PCR) based assays.

RESULTS

Detection of Vibrio cholerae O1 from 10 of 15 specimens was recorded using dipstick assay. Microbiological methods detected V. cholerae O1 positivity among 11 specimens. However, RT-PCR based assay showed all 15 specimens positive for the presence of V. cholerae O1. In addition, the same assay showed that the pathogen load in the dipstick as well as RT-PCR positive specimens ranged from 10 6 colony forming units (cfu)/ml or more.

INTERPRETATION & CONCLUSIONS

Crystal VC kit had the potential to identify cholera cases in 10 min in field conditions without having good laboratory support. Therefore, dipstick kit may be considered as cholera detecting tool in diarrhoeal outbreak investigations. Specimens from clinically typical cholera cases, if negative by dipstick, should be reanalyzed by culture based methods.

Unresolving pericarditis: suspect filariasis in the tropics

Filariasis, a mosquito-borne disease, is wide spread in India. While laboratory diagnosis has been conventionally done by demonstrating microfilaria in peripheral blood smears, occasionally they are reported in various body fluids including pericardial fluid. We report the case of 33-year-old man with severe dyspnoea and chest pain, referred from a private nursing home with a provisional diagnosis of unresolving pericarditis. Pericardial tap revealed massive pericardial effusion with actively motile microfilariae. No microfilariae (Mf) were seen in the peripheral blood. Haemorrhagic effusion resolved completely with DEC. Though relatively uncommon, tropical diseases must always be considered in the etiological diagnosis of pericardial effusion.

Molecular characterisation of Cryptosporidium: an emerging parasite

PURPOSE

The aim of the present study was to determine the prevalence of Crytposporidium in local population and to understand its epidemiology by molecular methods.

METHODS

Faecal samples from 681 children and 804 adults, admitted to tertiary care hospitals in twin cities of Hyderabad and Secunderabad with complaints of diarrhoea; and six calves with diarrhoea, were screened for Cryptosporidium oocysts by microscopy and enzyme linked immunosorbent assay (ELISA). Polymerase chain reaction restriction fragment length polymorphism (PCR RFLP) based identification of Cryptosporidium species in positive specimens was done to elucidate epidemiology of Cryptosporidium.

RESULTS

Cryptosporidium was found in 52 (7.6%) children and 7(0.9%) adults and 1(16.6%) calf with diarrhoea. The prevalence of Cryptosporidium in children below five years of age was 8.2% and 14.3% in children in the age group of six months to one year. Of the 42 samples genotyped 29 (69%) were C. hominis and 8 (19%) were C. parvum and 5 (11.9%) were mixed infection with the two species.

CONCLUSIONS

Children in the age group of six months to one year were found to be the most vulnerable. The occurrence of C. parvum, in nearly one third of cases in the present series indicates that the zoonotic transmission is of considerable significance in the epidemiology of Cryptosporidiosis in the study area.

Cryptosporidiosis in a tertiary care hospital in Andhra Pradesh

Enteric protozoal parasitic infection has become an important cause of morbidity in children and adults. In the developing countries the association of Cryptosporidium with acute and persistent diarrhoea has been striking. Stool samples from 1002 patients (800 adults and 202 children) suffering from diarrhoea or other gastrointestinal symptoms were examined for the presence of Cryptosporidium parvum oocysts by modified Ziehl Neelsen stained smears. C. parvum was detected in 2.99% of children and 0.12% adults. Other parasites detected were E. histolytica (6.18%), G. lamblia (1.49%), A. lumbricoides (1.49%), hookworm (1.39%), Strongyloides stercoralis (0.39%), and Taenia (0.09%).

Interferon resistance is independent from copy numbers in benign HPV-induced lesions

Interferons (IFNs) are successfully used in treatment of different human papillomavirus (HPV)-related diseases, such as condyloma acuminatum. Unresponsiveness can be seen in a number of patients which is related to a differential expression of early (E7) and late (L1) viral genes, according to our preliminary studies rather than to impaired IFN-signalling. The molecular basis for this differential expression might imply differential viral replication (copy numbers) in responder vs. nonresponder patients. PCR analysis revealed that the two groups did not differ significantly in HPV copy numbers before treatment. In contrast E7 and L1 levels significantly differed in responders versus nonresponders, regardless of copy numbers. Also, the IFN-mediated antiproliferative effect was mostly influenced by other factors rather than just the copy number. Our data imply that the unresponsiveness of certain patients to IFN treatment may relate to differential viral gene transcription rather than different copy numbers of infecting HIVs.