Outbreaks and sporadic cases of japanese encephalitis in the state of Odisha, India: Outcome of 7 years of laboratory surveillance

Acute encephalitis syndrome (AES) is a major public health challenge in India. We report here the epidemiology of sporadics and outbreaks of Japanese Encephalitis (JE) in Odisha state during 2012-2018. A total of 4235 AES cases (sporadics - 3394, outbreak cases - 841) recorded including 42 outbreaks; majority (n = 18) of which were during 2016. Overall JE virus (JEV) positivity was 11.78% (outbreak cases - 24.5%, sporadic cases - 8.6%). Age ≤15 years were largely affected during outbreaks, while 16-60 years population was dominant among sporadics. The major outbreak (2016) involved 336 patients from a tribal dominated district, spread over 173 villages. JEV seropositivity was high (43.45%) with 28.57% mortality. Epidemiological linkage with pig rearing was documented through JEV neutralizing antibodies in 50% of pig serum samples. Although the postvaccination period (2017-18) showed increase in AES case reporting but low JE proportion. Ongoing surveillance and preparedness of the health system would be of importance, especially in tribal-dominated districts.

Bluetongue virus: Past, present, and future scope

Bluetongue (BT), once considered a disease of sheep confined to the southern African region, has spread all over the world. BT is a viral disease caused by the bluetongue virus (BTV). BT is regarded as an economically important disease in ruminants of compulsory notification to OIE. BTV is transmitted by the bite of Culicoides species. Research over the years has led to a better understanding of the disease, the nature of the virus life cycle between ruminants and Culicoides species, and its distribution in different geographical regions. Advances have also been made in understanding the molecular structure and function of the virus, the biology of the Culicoides species, its ability to transmit the disease, and the persistence of the virus inside the Culicoides and the mammalian hosts. Global climate change has enabled the colonization of new habitats and the spread of the virus into additional species of the Culicoides vector. This review highlights some of the current findings on the status of BT in the world based on the latest research on disease aspects, virus-host-vector interactions, and the different diagnostic approaches and control strategies available for BTV.

A comparison of SARS-CoV-2 rapid antigen testing with realtime RT-PCR among symptomatic and asymptomatic individuals

BACKGROUND

Identification of SARS-CoV-2 positive patients with rapid and cost-effective test methods is the key for isolating infected individuals, interrupting the transmission chain, and thus, containment of the CoVID-19 disease. In this regard, Rapid Antigen Test (RAT) plays an important role at point of care testing but the low sensitivity attributing towards escape of positive cases is reported as a major disadvantage of RAT which led us to evaluate a RAT kit among symptomatic and asymptomatic individuals suspected of CoVID-19.

METHODS

We analyzed 329 parallel nasopharyngeal swabs for RAT (Zydus Cadila, India) at the point of collection in a hospital-based facility and RealTime RT-PCR in the laboratory. The performance parameters were analyzed by evaluating the specificity, sensitivity, Negative Predictive Value (NPV), Positive Predictive Value (PPV), and Kappa coefficient.

RESULTS

The sensitivity and specificity were found to be 75.17% and 98.89% respectively. Positive Predictive value was 98.25% and the negative predictive value was 82.79%. The accuracy between the two techniques was found to be 88.14% with a kappa coefficient of 0.756 (SE: 0.036 and CI at 95%: 0.686 to 0.826) with a good strength of agreement (0.61-0.80) between the two testing techniques. Among the false-negative cases, 22 (59.5%) were asymptomatic having the Cycle Threshold (Ct) range 27 to 32.9 including 12 cases with a history of close contact with the known positive cases (i.e. household contact). The remaining 15 cases (40.5%) were symptomatic having low to moderate Ct values.

CONCLUSION

It is observed from the results that the false negative result for symptomatic individuals is a matter of concern as it was noted in 4 cases of our study subjects who required hospitalisation later. Also the positives among asymptomatic contacts are important from epidemiological point of view for isolation and curtailing the infection from spreading in a community. These results support the fact that RAT showing sensitivity below 80% can be used for mass screening purposes with provision for additional testing in case of false negative with symptomatic individuals. Also false-negative results should be interpreted cautiously considering the epidemiological link as well as the clinical condition of the patients.

A spectrum of viral diseases in Odisha state, eastern India: An evidence-based analysis from 2010-2017

Introduction

Emerging and re-emerging viral diseases are a major threat to public health. Proper laboratory surveillance plays an important role in estimating the disease burden that helps in taking preventive measures for controlling seasonal diseases. This study focuses on the prevalence of different viral diseases in the state of Odisha, India, from 2010-2017.

Material and Methods

A total of 43,397 patients with clinical suspicion of viral diseases were screened for different viral etiology during 2010-2017. The laboratory diagnosis was conducted by serology (ELISA) and RealTime RT-PCR for 24 different viruses, i.e., Dengue, Chikungunya, Japanese Encephalitis, Hepatitis A Virus, Hepatitis E Virus, Hepatitis B Virus, Hepatitis C Virus, Rotavirus, Herpes Simplex Virus-1 and Herpes Simplex Virus-2, Epstein -Barr Virus & Cytomegalo Virus, and respiratory viruses. Patients were enrolled from sporadic hospital admissions and outbreaks under different categories as per clinical diagnosis like fever with rash, diarrhoea, encephalitis, jaundice, respiratory illness, and fever of unknown etiology.

Results

The majority of patients belonged to exanthematous group, i.e., fever with rash (32.24%). The number of males were more in all categories except fever with rash, where females (53.34%) were more. Children <16 years of age were found to be the predominant age group for suspected viral diarrhoea (85.26%), encephalitis (76.96%), fever of unknown origin (40.16%), and respiratory infections (27.23%).

Conclusion

Odisha being one of the coastal states in the country, reports many viral illnesses due to its typical geographical location. Initially, it was thought to be the only vector-borne disease that posed a threat to the state, but subsequently, other viral illnesses were also diagnosed and reported. This is the first report of laboratory confirmation and distribution of different viral diseases in the state of Odisha and neighboring regions, which will support public health management.

Dynamicity and persistence of severe acute respiratory syndrome coronavirus-2 antibody response after double dose and the third dose with BBV-152 and AZD1222 vaccines: A prospective, longitudinal cohort study

Introduction

Vaccines are available worldwide to combat coronavirus disease-19 (COVID-19). However, the long-term kinetics of the vaccine-induced antibodies against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have not been sufficiently evaluated. This study was performed to investigate the persistence and dynamicity of BBV-152 (Covaxin)- and AZD1222 (Covishield)-induced immunoglobulin-G (IgG) antibodies over the year and neutralizing antibodies’ status after 1-month of booster dose.

Materials and methods

This 52-week longitudinal cohort study documented antibody persistence and neutralizing antibodies status among 304 healthcare workers (HCWs) from six hospitals and research facilities in Odisha, enrolled during January 2021 and continued till March 2022. IgG antibodies against spike receptor-binding domain (RBD) of SARS-CoV-2 were quantified in an automated chemiluminescence immune assay-based (CLIA) platform and a surrogate virus neutralization test (sVNT) was performed by enzyme-linked immunosorbent assay (ELISA).

Results

Among these 304 HCWs vaccinated with double doses, 154 HCWs (50.66%) were Covaxin recipients and the remaining 150 (49.34%) were Covishield recipients. During the follow-ups for seven times, a total of 114 participants were identified as vaccine breakthrough cases. In 190 non-infected HCWs, the median antibody titer was significantly waned from DD2 to DD10, both for Covaxin (231.8 vs. 42.7 AU/ml) and Covishield (1,884.6 vs. 369.2 AU/ml). No statistically significant differences in antibody titers were observed based on age, gender, comorbidities, and blood groups. The median inhibition activity of sVNT increased from 23.8 to 91.3% for Covaxin booster recipients and from 41.2 to 96.0% for Covishield booster recipients. Among 146 booster dose recipients, 48 were breakthrough cases after booster and all were contracted by the omicron variant.

Conclusion

This year-long follow-up study found a 7- and 5-fold antibody waning in Covaxin and Covishield recipients, respectively, without any breakthrough infection history. However, individuals with booster breakthrough had mild symptoms and did not require hospital admission. The data also indicate the possible escape of omicron variants despite the presence of vaccine-induced neutralizing antibodies.

Viral characteristics and clinical presentation in dengue co-infection- Findings from a facility based observational study in Odisha, India

Background:

Dengue has affected many countries globally. Two-fifths part of the world is at risk, which can be affected by dengue disease. In India, the dengue incidence has increased in the recent past and emerged as an important health problem in many states including Odisha. Dengue disease presents with atypical clinical symptoms when associated with other co-infections.

Materials and Methods:

A facility-based longitudinal study was carried out over a period of 1 year to determine the dengue co-infection and its outcome. The suspected cases were clinically assessed following a standard case report format and serological investigations including serotyping were carried out.

Results:

33.6% samples were dengue positive of which 78.5% were positive for NS1 Ag, 26.6% positive for dengue IgM and 5.1% to both. Among the dengue positive cases, 60.9% were male and mean age was 31.52 (±17.03) years. High occurrence of cases was during May to November with maximum in August. Among the 975 dengue positives, 57 (5.8%) were found to have co-infection. Chikungunya was the most common co-infection in 71.9%, followed by herpes simplex (HSV) (7%) and other diseases. Fever was the most common presenting symptom (98.2%), followed by myalgia (91.2%), retro orbital pain (91.2%), pain abdomen (12.3%), rash/lesion (8.8%), burning micturition (5.3%), petechiae (1.7%) and pruritus (1.7%) among the co-infected cases.

Conclusions:

All the four dengue serotypes were found to be circulating with DEN 2 as the most predominant one. About 5.8% of dengue cases have co-infection (mainly with Chikungunya) and clinically present with atypical signs and symptoms.

Breakthrough SARS-CoV-2 infections among BBV-152 (COVAXIN®) and AZD1222 (COVISHIELDTM ) recipients: Report from the eastern state of India

In this study, we attempted to record the breakthrough cases reported through passive and voluntary reporting at various healthcare facilities from different districts of Odisha, their clinical presentation, requirement of hospitalization postinfection, and antibody titer against spike antigen. Nasopharyngeal swab and serum samples alongwith demographic, clinical presentation and requirement of hospitalization postinfection were collected from vaccinated individuals through passive and voluntary reporting to various healthcare facilities of Odisha state to detect the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) virus infection and quantitative estimation of antibody titers. A total of 274 samples were found to be positive after 14 days of receiving complete doses of the vaccines. More than 83.2% of the individuals were found to be symptomatic with 9.9% of those required hospitalization. The seropositivity in individuals receiving Covishield (96.7%) was significantly higher than in Covaxin (77.1%). Hospitalized patients were having less median antibody titers than individuals in home isolation. The median age for breakthrough infection among the referred cases was 47.0 years (interquartile range [IQR]: 28.0) with a significantly older age group among Covishield recipients. The median spike receptor binding domain IgG titer values for Covaxin and Covishield recipients were 213.5 AU/ml (IQR: 537.5) and 647.5 AU/ml (IQR: 1645.1), respectively. The results reported here highlight the need for systematic data capture for the breakthrough infections to monitor the emergence of any vaccine escape variants and to plan the next steps in the coronavirus disease‐19 (COVID‐19) vaccine development by understanding the link between clinical protection and measured immunity against SARS‐CoV‐2 infection.

Sequence analysis of Indian SARS-CoV-2 isolates shows a stronger interaction of mutant receptor-binding domain with ACE2

OBJECTIVE

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected the whole world, including Odisha, a state in eastern India. Many people have migrated to the state from different countries as well as other states during this SARS-CoV-2 pandemic. The aim of this study was to analyse the receptor-binding domain (RBD) sequence of the spike protein from isolates collected from throat swab samples of COVID-19-positive patients and further to assess the RBD affinity for angiotensin-converting enzyme 2 (ACE2) of different species, including humans.

METHODS

Whole-genome sequencing for 35 clinical SARS-CoV-2 isolates from COVID-19-positive patients was performed by ARTIC amplicon-based sequencing. Sequence analysis and phylogenetic analysis were performed for the spike region and the RBD region of all isolates. The interaction between the RBD and ACE2 of five different species was also analysed.

RESULTS

The spike region of 32 isolates showed one or multiple alterations in nucleotide bases in comparison with the Wuhan reference strain. One of the identified mutations, at position 1204 (Ref A, RMRC 22 C), in the RBD coding region of the spike protein showed stronger binding affinity for human ACE2. Furthermore, RBDs of all the Indian isolates showed binding affinity for ACE2 of different species.

CONCLUSION

As mutant RBD showed stronger interaction with human ACE2, it could potentially result in higher infectivity. The binding affinity of the RBDs for ACE2 of all five species studied suggests that the virus can infect a wide variety of animals, which could also act as natural reservoir for SARS-CoV-2.

COVID-19 in children in Odisha state, India: a retrospective review

We retrospectively analysed the swab samples tested for COVID-19 from 7 March 2020 to 17 August 2021 at the Indian Council of Medical Research-Regional Medical Research Centre, Bhubaneswar, Odisha. 553 763 nasopharyngeal swabs were collected from individuals suspected with COVID-19 in Odisha state. 75 190 (13.6%) samples were positive by reverse transcription-PCR. There were 5988 (8%) cases in children and young people under 18 years old. Odisha reported 996 153 COVID-19 cases which resulted in 6985 deaths in adults and 36 in children and young people under 18 years old.

Pooled testing for COVID-19 diagnosis by real-time RT-PCR: A multi-site comparative evaluation of 5- & 10-sample pooling

BACKGROUND & OBJECTIVES

Public health and diagnostic laboratories are facing huge sample loads for COVID-19 diagnosis by real-time reverse transcription-polymerase chain reaction (RT-PCR). High sensitivity of optimized real-time RT-PCR assays makes pooled testing a potentially efficient strategy for resource utilization when positivity rates for particular regions or groups of individuals are low. We report here a comparative analysis of pooled testing for 5- and 10-sample pools by real-time RT-PCR across 10 COVID-19 testing laboratories in India.

METHODS

Ten virus research and diagnostic laboratories (VRDLs) testing for COVID-19 by real-time RT-PCR participated in this evaluation. At each laboratory, 100 nasopharyngeal swab samples including 10 positive samples were used to create 5- and 10-sample pools with one positive sample in each pool. RNA extraction and real-time RT-PCR for SARS-CoV-2-specific E gene target were performed for individual positive samples as well as pooled samples. Concordance between individual sample testing and testing in the 5- or 10-sample pools was calculated, and the variation across sites and by sample cycle threshold (Ct) values was analyzed.

RESULTS

A total of 110 each of 5- and 10-sample pools were evaluated. Concordance between the 5-sample pool and individual sample testing was 100 per cent in the Ct value ≤30 cycles and 95.5 per cent for Ctvalues ≤33 cycles. Overall concordance between the 5-sample pooled and individual sample testing was 88 per cent while that between 10-sample pool and individual sample testing was 66 per cent. Although the concordance rates for both the 5- and 10-sample pooled testing varied across laboratories, yet for samples with Ct values ≤33 cycles, the concordance was ≥90 per cent across all laboratories for the 5-sample pools.

INTERPRETATION & CONCLUSIONS

Results from this multi-site assessment suggest that pooling five samples for SARS-CoV-2 detection by real-time RT-PCR may be an acceptable strategy without much loss of sensitivity even for low viral loads, while with 10-sample pools, there may be considerably higher numbers of false negatives. However, testing laboratories should perform validations with the specific RNA extraction and RT-PCR kits in use at their centres before initiating pooled testing.

Epidemiological and clinical profile of Influenza A(H1N1) pdm09 in Odisha, eastern India

Epidemic of flu is highly contagious and it spreads through air. In 2009 H1N1 influenza virus emerged after reassortment of North American TRIG and Eurasia Avian like virus of swine and started epidemic in Mexico. The first cases were reported from Hyderabad city on 16th May 2009 in India that spread rapidly within a short span of time. During this period large population of Odisha situated at the eastern side of India was also affected and incidences of H1N1 cases were recorded through state Government surveillance system. In this study real time RT-PCR based diagnosis was conducted for the throat swabs collected from suspected H1N1 cases in Odisha during 2009–2017. A total of 2872 throat swabs were received from 23 different Government and private hospitals and 21.1% positivity was confirmed. The disease affected mostly 46–60 years age group, males (50.6%) being more affected. The clinical features had shown that fever with cough (89.6%) was the most common symptom followed by shortness of breath (72.7%). Post monsoon was the peak season in which most of the cases were reported. Neurological signs, pregnancy, diabetes and hypertension were found to be risk factors for H1N1. The case fatality rate (CFR) was 15%.

Molecular and phylogenetic analysis of the dengue strains circulating in Odisha, India

Dengue has emerged as a major public health challenge in terms of both changing clinical pattern and epidemiological features. The state of Odisha reported first dengue epidemic in the year 2010 and this continued each year in epidemic form during post monsoon period gradually becoming an endemic phenomenon. Present study depicts the changing epidemiological and clinical pattern of dengue with reference to its serotypes and genotypes. The study included 5320 suspected dengue cases from different health facilities of the state during 2010-2017. Dengue NS1 antigen and IgM antibody was done through ELISA. Serotyping was done through RTPCR by amplifying a part of core-pre-membrane gene (CprM) followed by sequencing and phylogenetic analysis. Dengue IgM antibody in 17.7% cases and NS1 antigen in 53.20% cases was detected. Dengue serotype 2 (DEN-2) was the only serotype detected in 2010 and 2011 where as all four serotypes 1, 2, 3, 4 were detected in 2012-2017, DEN-2 being dominant but in 2017 DEN-3 was found to be dominant. Phylogenetic analysis revealed genotype IV of DEN-2 and genotype III of DEN-1 and DEN-3 circulating in this region. In 6 cases involvement of DEN-2 in clinically evident encephalitis cases is an important observation in this region and needs public health attention. High prevalence of dengue was observed without any previous reported outbreaks in the state with increased number of cases from 2010 to 2012 affecting both urban and rural areas. High incidence in 2012 was due to co-circulation of more than one serotype which continued in the following years. Severity in some cases was associated with mixed infection but in most cases it was mild indicating the endemic nature of the virus in most parts of Odisha.

Comparison of bluetongue virus detection and quantitation methods in south India

INTRODUCTION

Bluetongue (BT), a vector-borne viral disease, primarily affects sheep. Of the 26 serotypes of BTV identified so far, 22 are reported to be circulating in India. Due to an increase in vector population and delays in disease diagnosis, the BT control program heavily relies on rapid and confirmatory diagnosis. Polymerase chain reaction (PCR)-based real-time detection assays may be an ideal method to detect the BTV genome in animal blood at an early stage of infection.

METHODOLOGY

In this study, a SYBR green-based real-time RT-PCR assay was evaluated, validated, and compared with conventional RT-PCR. The specificity and sensitivity of an assay using BTV-2 RNA extracted from tenfold serially diluted (starting from 1.0 TCID50/mL) cell culture virus was also evaluated.

RESULTS

While conventional RT-PCR could detect 3.16 × 10(2) TCID50 of virus/mL, the real-time PCR test had a detection limit of 3.16 × 10(-4) TCID50/mL. Melting curve analysis indicated the absence of non-specific amplification (R(2) = 0.987). Out of the 32 infected blood samples examined, 24 tested positive for BTV RNA. Seven that were found negative through conventional PCR tested positive through real-time PCR.

CONCLUSIONS

These results showed that the SYBR green-based real-time PCR assay is rapid, sensitive, and equally specific in the diagnosis of BT in BTV-affected animals.

Proteomic analysis of Mecistocirrus digitatus and Haemonchus contortus intestinal protein extracts and subsequent efficacy testing in a vaccine trial

BACKGROUND

Gastrointestinal nematode infections, such as Haemonchus contortus and Mecistocirrus digitatus, are ranked in the top twenty diseases affecting small-holder farmers' livestock, yet research into M. digitatus, which infects cattle and buffalo in Asia is limited. Intestine-derived native protein vaccines are effective against Haemonchus, yet the protective efficacy of intestine-derived M. digitatus proteins has yet to be determined.

METHODOLOGY/PRINCIPAL FINDINGS

A simplified protein extraction protocol (A) is described and compared to an established method (B) for protein extraction from H. contortus. Proteomic analysis of the H. contortus and M. digitatus protein extracts identified putative vaccine antigens including aminopeptidases (H11), zinc metallopeptidases, glutamate dehydrogenase, and apical gut membrane polyproteins. A vaccine trial compared the ability of the M. digitatus extract and two different H. contortus extracts to protect sheep against H. contortus challenge. Both Haemonchus fractions (A and B) were highly effective, reducing cumulative Faecal Egg Counts (FEC) by 99.19% and 99.89% and total worm burdens by 87.28% and 93.64% respectively, compared to the unvaccinated controls. There was no effect on H. contortus worm burdens following vaccination with the M. digitatus extract and the 28.2% reduction in cumulative FEC was not statistically significant. However, FEC were consistently lower in the M. digitatus extract vaccinates compared to the un-vaccinated controls from 25 days post-infection.

CONCLUSIONS/SIGNIFICANCE

Similar, antigenically cross-reactive proteins are found in H. contortus and M. digitatus; this is the first step towards developing a multivalent native vaccine against Haemonchus species and M. digitatus. The simplified protein extraction method could form the basis for a locally produced vaccine against H. contortus and, possibly M. digitatus, in regions where effective cold chains for vaccine distribution are limited. The application of such a vaccine in these regions would reduce the need for anthelmintic treatment and the resultant selection for anthelmintic resistant parasites.

Development and validation of real-time PCR for rapid detection of Mecistocirrus digitatus

Hematophagous activity of Mecistocirrus digitatus, which causes substantial blood and weight loss in large ruminants, is an emerging challenge due to the economic loss it brings to the livestock industry. Infected animals are treated with anthelmintic drugs, based on the identification of helminth species and the severity of infection; however, traditional methods such as microscopic identification and the counting of eggs for diagnosis and determination of level of infection are laborious, cumbersome and unreliable. To facilitate the detection of this parasite, a SYBR green-based real-time PCR was standardized and validated for the detection of M. digitatus infection in cattle and buffaloes. Oligonucleotides were designed to amplify partial Internal Transcribed Spacer (ITS)-1 sequence of M. digitatus. The specificity of the primers was confirmed by non-amplification of DNA extracted from other commonly occurring gastrointestinal nematodes in ruminants. Plasmids were ligated with partial ITS-1 sequence of M. digitatus, serially diluted (hundred fold) and used as standards in the real-time PCR assay. The quantification cycle (Cq) values were plotted against the standard DNA concentration to produce a standard curve. The assay was sensitive enough to detect one plasmid containing the M. digitatus DNA. Clinical application of this assay was validated by testing the DNA extracted from the faeces of naturally infected cattle (n = 40) and buffaloes (n = 25). The results were compared with our standard curve to calculate the quantity of M. digitatus in each faecal sample. The Cq value of the assay depicted a strong linear relationship with faecal DNA content, with a regression coefficient of 0.984 and efficiency of 99%. This assay has noteworthy advantages over the conventional methods of diagnosis because it is more specific, sensitive and reliable.

Hepatitis E virus: the current scenario

Hepatitis E infection, caused by the hepatitis E virus (HEV), is a common cause of acute hepatitis in developing countries with poor sanitation and hygiene. The virus is classified into four genotypes (1-4) with one serotype. Genotypes 1 and 2 exclusively infect humans, whereas genotypes 3 and 4 also infect other animals, particularly pigs. In endemic areas, large outbreaks of acute hepatitis caused by viruses of genotype 1 or 2 frequently occur due to fecal-oral transmission, usually through contamination of drinking water. With a high attack rate in young adults (aged 15-45 years), the disease is particularly severe among pregnant women (20-30% mortality). HEV appears to be a zoonotic disease, with transmission from pigs, wild boars, and deer, or foodborne. Chronic infections are rare, except in immunosuppressed persons, such as organ transplant recipients. A subunit vaccine has been shown to be effective in preventing the clinical disease, but is not yet commercially available. Our understanding of HEV has undergone major changes in recent years and in this article we review the currently available information with regard to the molecular biology, pathobiology, and epidemiology of HEV infection. We also review the current therapeutic interventions and strategies being used to control HEV infection, with emphasis on possible approaches that could be used to develop an effective vaccine against HEV.