Viral Diseases of Public Health Importance in India: Current Priorities with Special Emphasis on Prevention

India faces problems with both communicable and non communicable diseases. The major non communicable diseases are cancer, cardiovascular disease and diabetes mellitus. This article focuses on communicable diseases (infectious diseases) especially viral infections of public health importance. The infections include bacterial, parasitic and viruses. It could be said that fungal infections by the nature of the spread are not of public health concern. The viral infections are transmitted by the respiratory route, water and food borne route, vectors and blood and blood products, sexual route and are of major concern. Efforts are aimed at early detection, prevention by use of vaccines and sentinel surveillance. For the success of public health programmes sentinel surveillance of diseases is mandatory. India has got several programme initiatives addressing the problem. The programs include IDSP, VBDCP and NACO. The approximate cumulative annual prevalence of infectious disease in India ranges from 100 to 200 million individuals affected in one year. India should aim to improve case detection by strengthening laboratory services with manpower training and nationwide quality control scheme, sentinel surveillance activity and prevention by improving the efficiency and scope of UIP. Also, creation of a single portal of infectious disease data handling hub to collect information from different sources will help avoid overlap and duplication of reporting

Development & standardization of an in-house IgM indirect ELISA for the detection of parvovirus B19 infections

Background & objectives: Parvovirus B19 infections occur worldwide; the infection is acquired early in childhood but could occur later. B19 is reported to cause infection in childhood febrile illnesses, and arthropathies in adults and children and in end-stage renal disease (ESRD) seen in adults. This study was designed to develop an in-house IgM indirect ELISA for serological screening among patients and controls, and to compare ELISA results with those of nested polymerase chain reaction (nPCR) assay. Methods: An in-house IgM indirect ELISA was standardized using peptide sequence of VP1/VP2 region of parvovirus B19. A total of 201 children and adult with febrile illnesses, 216 individuals with non-traumatic arthropathies, 201 cases of chronic anaemia associated with ESRD and 100 healthy controls were tested. Serum was separated from the blood and subsequently used for DNA extraction. The nested polymerase chain reaction (nPCR) for the detection of B19V DNA was performed using primers targeting the overlapping region of VP1/VP2 capsid protein genes. Results: A total of 618 samples were tested for parvovirus B19 by an in-house IgM indirect ELISA. Among these samples, six were positive by in-house ELISA. The inter-rater agreement between ELISA and PCR assays was calculated using kappa coefficient analysis. The value of κ was 0.77 and the strength of agreement was 'good' (P<0.001). Interpretation & conclusions: The in-house IgM indirect ELISA was found to be simple with high sensitivity and specificity when compared with nPCR and could be used as an alternative to expensive commercial kits in resource-poor settings

Novel Insights on Hantavirus Evolution: The Dichotomy in Evolutionary Pressures Acting on Different Hantavirus Segments

<div><p>Background</p><p>Hantaviruses are important emerging zoonotic pathogens. The current understanding of hantavirus evolution is complicated by the lack of consensus on co-divergence of hantaviruses with their animal hosts. In addition, hantaviruses have long-term associations with their reservoir hosts. Analyzing the relative abundance of dinucleotides may shed new light on hantavirus evolution. We studied the relative abundance of dinucleotides and the evolutionary pressures shaping different hantavirus segments.</p><p>Methods</p><p>A total of 118 sequences were analyzed; this includes 51 sequences of the S segment, 43 sequences of the M segment and 23 sequences of the L segment. The relative abundance of dinucleotides, effective codon number (ENC), codon usage biases were analyzed. Standard methods were used to investigate the relative roles of mutational pressure and translational selection on the three hantavirus segments.</p><p>Results</p><p>All three segments of hantaviruses are CpG depleted. Mutational pressure is the predominant evolutionary force leading to CpG depletion among hantaviruses. Interestingly, the S segment of hantaviruses is GpU depleted and in contrast to CpG depletion, the depletion of GpU dinucleotides from the S segment is driven by translational selection. Our findings also suggest that mutational pressure is the primary evolutionary pressure acting on the S and the M segments of hantaviruses. While translational selection plays a key role in shaping the evolution of the L segment. Our findings highlight how different evolutionary pressures may contribute disproportionally to the evolution of the three hantavirus segments. These findings provide new insights on the current understanding of hantavirus evolution.</p><p>Conclusions</p><p>There is a dichotomy among evolutionary pressures shaping a) the relative abundance of different dinucleotides in hantavirus genomes b) the evolution of the three hantavirus segments.</p></div

ENC-GC₃ plot.

<p>Correlation between GC₃ and the effective codon usage statistic (ENC) among (a) S segment, (b) M segment and (c) L segment. The red line represents the ENC expected values (ENC*) and the ENC values are shown in blue. ENC values for the L segment are significantly lower than that for the S segment (45.49±1.52 vs 50.11±2.52; P<0.0001) or the M segment (45.49±1.52 vs 47.93±3.11; P = 0.0003), suggesting that mutational pressure is the predominant evolutionary force acting on the S and M segments; while translational selection predominates in the evolution of the L segment.</p

Hantavirus genomes are depleted for CpG dinucleotides and underlying evolutionary pressure is specific to CpG (not GpC) dinucleotides.

<p>(a) Among the 3 segments of hantaviruses the CpG dinucleotide O/E ratios for the M segment were significantly lower than that for the S segment (0.22±0.04 vs 0.28±0.06; P<0.0001) and that for the L segment (0.22±0.04 vs 0.29±0.05; P<0.0001). The differences in CpG O/E ratios of the S segment and the L segment were not significant (0.28±0.06 vs 0.29±0.05; P = 0.18). (b) The CpG/GpC O/E ratios were significantly lower for the M segment of hantaviruses as compared to those for the S segment (0.22±0.04 vs 0.29±0.07; P<0.0001) and for the L segment (0.22±0.04 vs 0.28±0.04; P<0.0001); clearly demonstrating that CpG dinucleotides but not GpC dinucleotides are susceptible to the underlying evolutionary pressures.</p

GpU dinucleotide depletion in the S segment is linked to translational selection.

<p>The intracodon GpU O/E ratio for the S segment was significantly lower than that for the non-coding region of this segment (0.70±0.07 vs 0.95±0.14; P< 0.0001); clearly supporting translational selection as the major driver of GpU depletion in the S segment of hantaviruses.</p

Detection of parvovirus B19 in selected high-risk patient groups & their phylogenetic & selection analysis

Background & objectives: Human parvovirus B19V (B19V) is known to be associated with erythema infectiosum commonly in children, aplastic crisis, especially in persons with underlying haemolytic disorders, hydrops fetalis in pregnancies and arthritis. This cross-sectional study was aimed to determine the presence of B19V infection in childhood febrile illnesses, association of B19V with arthropathies and in adult patients with end-stage renal disease (ESRD) on dialysis. The genetic diversity among the sequences was also analysed. Methods: A nested polymerase chain reaction (nPCR) assay was used for B19V DNA targeting VP1/VP2 region and used for testing 618 patients and 100 healthy controls. Phylogenetic analysis on nucleotide and amino acid sequences was carried out to compare our sequences with other Indian strains and global strains. Results: Among 618 samples tested, seven (1.13%) were found positive. The phylogenetic analysis revealed that all the seven sequences belonged to genotype 1 and showed low genetic diversity. The clustering pattern of seven sequences was similar both by nucleotide and by predicted amino acid sequences. The fixed effects likelihood analysis showed no positive or negatively selected sites. Interpretation & conclusions: Seven samples (4 from non-traumatic arthropathies, 2 from patients with ESRD and 1 from febrile illness patient) were found positive by nPCR. When our seven sequences were compared with global strains, the closest neighbour was other Indian strains followed by the Tunisian strains

Relative abundance of dinucleotides in hantavirus genomes.

<p>(a) The mean ±standard deviation of dinucleotide O/E ratios for hantaviruses S segment is 1.0±0.25. The O/E ratios for most of the dinucleotides lie inside the confidence interval of 0.75–1.25 with the exceptions of CpG and GpU dinucleotides (underrepresented) and CpA dinucleotides (overrepresented). (b) The mean±standard deviation of dinucleotide O/E ratios for hantaviruses M segment is 1.0±0.25. CpG dinucleotides were underrepresented and CpA and UpG dinucleotides were overrepresented as the O/E ratios for these dinucleotides were located outside the confidence interval of 0.75–1.25. (c) The mean ±standard deviation of dinucleotide O/E ratios for hantaviruses L segment is 1.0±0.22. CpG and CpA dinucleotides were the most deviant dinucleotides as their O/E ratios were located outside the confidence interval of 0.78–1.22. (d) Comparison of the average dinucleotide O/E ratios for all three segments of hantaviruses. The depletion of CpG dinucleotides was common across all the three segments of hantaviruses.</p

Avoidance of GpU-containing codons in the S segment of hantaviruses.

<p>Box plots showing the RSCU values of synonymous GpU-containing codons. The RSCU values of GpU-containing codons are shown in yellow boxes. GpU-containing codons were avoided in the S segment of hantaviruses as evidenced by median RSCU values of less than one. The average RSCU values for GpT-containing codons in the S segment were lower as compared those in the M segment (0.91±0.32 vs 1.46±0.25; P<0.0001) or the L segment (0.91±0.32 vs 1.7±0.27; P<0.0001); this is a reflection of GpU dinucleotides depletion from the S segment.</p

CpG dinucleotide depletion in the M segment is linked to evolutionary lineage of host.

<p>(a) In M segment the CpG O/E ratios were significantly lower in insectivore borne viruses than that in rodent borne viruses (0.19±0.03 vs 0.22±0.03; P = 0.0077). The average CpG O/E ratios were lower in insectivore borne hantaviruses as compared to rodent borne hantaviruses for S segment (0.25±0.08 vs 0.29±0.06; P = 0.1344) and L segment (0.26±0.03 vs 0.30±0.05; P = 0.1481); however the difference was not statistically significant. (b) The GpU O/E ratios was not statistically different between insectivore borne and rodent borne hantaviruses in S segment (0.75±0.06 vs 0.72±0.06; P = 0.2289), M segment (0.97±0.02 vs 0.97±0.03;P = 0.9355) and L segment (0.89±0.05 vs 0.87±0.03).</p