Rodger Main

Bio: Rodger Main is an academic researcher from Iowa State University. The author has contributed to research in topics: Porcine epidemic diarrhea virus & Porcine reproductive and respiratory syndrome virus. The author has an hindex of 24, co-authored 103 publications receiving 2284 citations. Previous affiliations of Rodger Main include Kansas State University & United States Department of Agriculture.

Isolation and Characterization of Porcine Epidemic Diarrhea Viruses Associated with the 2013 Disease Outbreak among Swine in the United States

Abstract: Porcine epidemic diarrhea virus (PEDV) was detected in May 2013 for the first time in U.S. swine and has since caused significant economic loss. Obtaining a U.S. PEDV isolate that can grow efficiently in cell culture is critical for investigating pathogenesis and developing diagnostic assays and for vaccine development. An additional objective was to determine which gene(s) of PEDV is most suitable for studying the genetic relatedness of the virus. Here we describe two PEDV isolates (ISU13-19338E and ISU13-22038) successfully obtained from the small intestines of piglets from sow farms in Indiana and Iowa, respectively. The two isolates have been serially propagated in cell culture for over 30 passages and were characterized for the first 10 passages. Virus production in cell culture was confirmed by PEDV-specific real-time reverse-transcription PCR (RT-PCR), immunofluorescence assays, and electron microscopy. The infectious titers of the viruses during the first 10 passages ranged from 6 × 102 to 2 × 105 50% tissue culture infective doses (TCID50)/ml. In addition, the full-length genome sequences of six viruses (ISU13-19338E homogenate, P3, and P9; ISU13-22038 homogenate, P3, and P9) were determined. Genetically, the two PEDV isolates were relatively stable during the first 10 passages in cell culture. Sequences were also compared to those of 4 additional U.S. PEDV strains and 23 non-U.S. strains. All U.S. PEDV strains were genetically closely related to each other (≥99.7% nucleotide identity) and were most genetically similar to Chinese strains reported in 2011 to 2012. Phylogenetic analyses using different genes of PEDV suggested that the full-length spike gene or the S1 portion is appropriate for sequencing to study the genetic relatedness of these viruses.

Role of Transportation in Spread of Porcine Epidemic Diarrhea Virus Infection, United States

Abstract: After porcine epidemic diarrhea virus (PEDV) was detected in the United States in 2013, we tested environmental samples from trailers in which pigs had been transported. PEDV was found in 5.2% of trailers not contaminated at arrival, , suggesting that the transport process is a source of transmission if adequate hygiene measures are not implemented.

Increasing weaning age improves pig performance in a multisite production system.

Abstract: Two trials were conducted to determine the effects of weaning age on pig performance in a multisite production system. The second trial also evaluated the effects of modifying the nursery feeding program according to weaning age. In Trial 1 (2,272 pigs), treatments included weaning litters at 12, 15, 18, or 21 d of age. In Trial 2 (3,456 pigs), litters were weaned at 15, 16, 18, 19, 21, or 22 d of age and categorized into three treatments (15.5, 18.5, or 21.5 d of age). In Trial 2, pigs in each age group were fed one of two nursery feeding programs. Nursery feeding programs varied in both diet formulation and in the quantity of diets fed containing increased levels of whey and spray-dried animal plasma. Each trial was conducted as a randomized complete block design with four blocks of nursery and finishing sites. All weaning-age treatments were weaned from a 7,300-sow farm on the same day into the same nursery. Each block remained intact as pigs moved from nursery to finishing site. Increasing weaning age (12, 15, 18, or 21 d in Trials 1; and 15.5, 18.5, or 21.5 d in Trial 2) increased (linear, P < 0.001) ADG (299, 368, 409, 474 +/- 7 g/d; 435, 482, 525 +/- 13 g/d) and tended to decrease (linear, P < 0.09) mortality (5.25, 2.82, 2.11, 0.54 +/- 0.76%; 2.17, 1.56, 1.30 +/- 0.36%) in the initial 42 d after weaning. Finishing ADG (722, 728, 736, 768 +/- 11 g/d; 783, 790, 805 +/- 11 g/d) also improved (linear, P < 0.01) with increasing weaning age. Overall, increasing weaning age increased (linear, P < 0.001) wean-to-finish ADG (580, 616, 637, 687 +/- 8 g/d; 676, 697, 722 +/- 6 g/d), weight sold per pig weaned (94.1, 100.5, 104.4, 113.1 +/- 1.3 kg; 107.6, 111.6, 116.2 +/- 1.1 kg), and decreased (linear, P < 0.03) mortality rate (9.4, 7.9, 6.8, 3.6 +/- 0.95%; 3.9, 3.4, 2.5 +/- 0.5%). Altering the nursery feeding program did not affect wean-to-finish growth performance. In this multisite production system, increasing weaning age from 12 to 21.5 d of age increased weight sold per pig weaned by 1.80 +/- 0.12 kg for each day increase in weaning age. These studies suggest increasing weaning age up to 21.5 d can be an effective management strategy to improve wean-to-finish growth performance in multisite pig production.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Integrative Genomics Viewer

Abstract: Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Structure, Function, and Evolution of Coronavirus Spike Proteins.

Abstract: The coronavirus spike protein is a multifunctional molecular machine that mediates coronavirus entry into host cells. It first binds to a receptor on the host cell surface through its S1 subunit and then fuses viral and host membranes through its S2 subunit. Two domains in S1 from different coronaviruses recognize a variety of host receptors, leading to viral attachment. The spike protein exists in two structurally distinct conformations, prefusion and postfusion. The transition from prefusion to postfusion conformation of the spike protein must be triggered, leading to membrane fusion. This article reviews current knowledge about the structures and functions of coronavirus spike proteins, illustrating how the two S1 domains recognize different receptors and how the spike proteins are regulated to undergo conformational transitions. I further discuss the evolution of these two critical functions of coronavirus spike proteins, receptor recognition and membrane fusion, in the context of the corresponding fu...

Porcine epidemic diarrhea virus: An emerging and re-emerging epizootic swine virus

Abstract: The enteric disease of swine recognized in the early 1970s in Europe was initially described as “epidemic viral diarrhea” and is now termed “porcine epidemic diarrhea (PED)”. The coronavirus referred to as PED virus (PEDV) was determined to be the etiologic agent of this disease in the late 1970s. Since then the disease has been reported in Europe and Asia, but the most severe outbreaks have occurred predominantly in Asian swine-producing countries. Most recently, PED first emerged in early 2013 in the United States that caused high morbidity and mortality associated with PED, remarkably affecting US pig production, and spread further to Canada and Mexico. Soon thereafter, large-scale PED epidemics recurred through the pork industry in South Korea, Japan, and Taiwan. These recent outbreaks and global re-emergence of PED require urgent attention and deeper understanding of PEDV biology and pathogenic mechanisms. This paper highlights the current knowledge of molecular epidemiology, diagnosis, and pathogenesis of PEDV, as well as prevention and control measures against PEDV infection. More information about the virus and the disease is still necessary for the development of effective vaccines and control strategies. It is hoped that this review will stimulate further basic and applied studies and encourage collaboration among producers, researchers, and swine veterinarians to provide answers that improve our understanding of PEDV and PED in an effort to eliminate this economically significant viral disease, which emerged or re-emerged worldwide.