Publications

Pathogen surveillance and epidemiology in endangered peninsular bighorn sheep (Ovis canadensis nelsoni)

Published in Conservation Science and Practice, 2022

Abstract

Peninsular bighorn sheep (Ovis canadensis nelsoni) are found exclusively in Southern California and Baja Mexico. They are federally endangered due to multiple threats, including introduced infectious disease. From 1981 to 2017, we conducted surveillance for 16 pathogens and estimated population sizes, adult survival, and lamb survival. We used mixed effects regression models to assess disease patterns at the individual and population levels. Pathogen infection/exposure prevalence varied both spatially and temporally. Our findings indicate that the primary predictor of individual pathogen infection/exposure was the region in which an animal was captured, implying that transmission is driven by local ecological or behavioral factors. Higher Mycoplasma ovipneumoniae seropositivity was associated with lower lamb survival, consistent with lambs having high rates of pneumonia-associated mortality, which may be slowing population recovery. There was no association between M. ovipneumoniae and adult survival. Adult survival was positively associated with population size and parainfluenza-3 virus seroprevalence in the same year, and orf virus seroprevalence in the previous year. Peninsular bighorn sheep are recovering from small population sizes in a habitat of environmental extremes, compounded by infectious disease. Our research can help inform future pathogen surveillance and population monitoring for the long-term conservation of this population.

Recommended citation: Sanchez, J. N., Munk, B. A., Colby, J., Torres, S. G., Gonzales, B. J., DeForge, J. R., ... & Johnson, C. K. (2022). Pathogen surveillance and epidemiology in endangered peninsular bighorn sheep (Ovis canadensis nelsoni). Conservation Science and Practice, 4(11), e12820. https://conbio.onlinelibrary.wiley.com/doi/full/10.1111/csp2.12820

Predicting the potential for zoonotic transmission and host associations for novel viruses

Published in Communications Biology, 2022

Abstract

Host-virus associations have co-evolved under ecological and evolutionary selection pressures that shape cross-species transmission and spillover to humans. Observed virus-host associations provide relevant context for newly discovered wildlife viruses to assess knowledge gaps in host-range and estimate pathways for potential human infection. Using models to predict virus-host networks, we predicted the likelihood of humans as hosts for 513 newly discovered viruses detected by large-scale wildlife surveillance at high-risk animal-human interfaces in Africa, Asia, and Latin America. Predictions indicated that novel coronaviruses are likely to infect a greater number of host species than viruses from other families. Our models further characterize novel viruses through prioritization scores and directly inform surveillance targets to identify host ranges for newly discovered viruses.

Recommended citation: Pandit, P. S., Anthony, S. J., Goldstein, T., Olival, K. J., Doyle, M. M., Gardner, N. R., ... & Johnson, C. K. (2022). Predicting the potential for zoonotic transmission and host associations for novel viruses. Communications biology, 5(1), 844. https://www.nature.com/articles/s42003-022-03797-9

Evaluation of Minimally Invasive Sampling Methods for Detecting Avipoxvirus: Hummingbirds as a Case Example

Published in Frontiers in Veterinary Science, 2022

Abstract

Avian pox is a common avian virus that in its cutaneous form can cause characteristic lesions on a bird’s dermal surfaces. Detection of avian pox in free-ranging birds historically relies on observations of visual lesions or histopathology, which can underestimate avian pox prevalence. We compared traditional visual observation methods for avian pox with these molecular methods that utilize minimally invasive samples in an ecologically important group of birds, hummingbirds. Specifically, avian pox prevalence in several species of hummingbirds were examined across multiple locations using three different methods: 1) visual inspection of hummingbirds for pox-like lesions from a long-term banding data set, 2) qPCR assay of samples from hummingbird carcasses from wildlife rehabilitation centers, and 3) qPCR assay of samples from live-caught hummingbirds. A stark difference in prevalences among these three methods was identified, with an avian pox prevalence of 1.5% from banding data, 20.4% from hummingbird carcasses, and 32.5% from live-caught hummingbirds in California. This difference in detection rates underlines the necessity of a molecular method to survey for avian pox, and this study establishes one such method that could be applied to other wild bird species. Across all three methods, Anna’s Hummingbirds harbored a significantly higher avian pox prevalence than other species examined, as did males compared with females and birds caught in Southern California compared with Northern California. After hatch-year hummingbirds also harbored higher avian pox prevalences than hatch-year hummingbirds in the California banding data set and the carcass data set. This is the first study to estimate the prevalence of avian pox in hummingbirds and address the ecology of this hummingbird-specific strain of avian pox virus, providing vital information to inform future studies on this charismatic and ecologically important group of birds.

Recommended citation: Galvin, A., Pandit, P., English, S., Quock, R., Bandivadekar, R., Colwell, R., Robinson, B., Ernest, H., Brown, M., Sehgal, R., and Tell, L., 2022. Evaluation of minimally invasive sampling methods for detecting avipoxvirus: Hummingbirds as a case example. Frontiers in Veterinary Science.

Predicting the potential for zoonotic transmission and host associations for novel viruses

Published in Communications Biology, 2022

Abstract

Host-virus associations have co-evolved under ecological and evolutionary selection pressures that shape cross-species transmission and spillover to humans. Observed virus-host associations provide relevant context for newly discovered wildlife viruses to assess knowledge gaps in host range and estimate pathways for potential human infection. Using models to predict virus-host networks, we predicted the likelihood of humans as host for 513 newly discovered viruses detected by large scale wildlife surveillance at high-risk animal-human interfaces in Africa, Asia, and Latin America. Predictions indicated that novel coronaviruses are likely to infect a greater number of host species than viruses from other families. Our models further characterize novel viruses through prioritization scores and directly inform surveillance targets to identify host ranges for newly discovered viruses.

Recommended citation: Pandit, Pranav, Simon Anthony, Tracey Goldstein, Kevin Olival, Megan Doyle, Nicole Gardner, Brian Bird et al. 2022. Predicting the potential for zoonotic transmission and host associations for novel viruses. Accepted in Communications Biololgy. https://www.researchsquare.com/article/rs-846253/v1

Evolutionary trajectory of SARS-CoV-2 and emerging variants

Published in Virology journal, 2021

Abstract

The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.

Recommended citation: Singh, J., Pandit, P., McArthur, A.G., Banerjee, A. and Mossman, K., 2021. Evolutionary trajectory of SARS-CoV-2 and emerging variants. Virology journal, 18(1), pp.1-21. https://link.springer.com/article/10.1186/s12985-021-01633-w

Dairy management practices associated with multi-drug resistant fecal commensals and Salmonella in cull cows: a machine learning approach.

Published in PeerJ, 2021

Abstract

Background

Recommended citation: Pandit PS, Williams DR, Rossitto P, Adaska JM, Pereira R, Lehenbauer TW, Byrne BA, Li X, Atwill ER, Aly SS. 2021. Dairy management practices associated with multi-drug resistant fecal commensals and Salmonella in cull cows: a machine learning approach. PeerJ 9:e11732 https://doi.org/10.7717/peerj.11732 https://peerj.com/articles/11732/

Early detection of wildlife morbidity and mortality through an event-based surveillance system.

Published in Proceedings of the Royal Society B, 2021

Abstract

The ability to rapidly detect and respond to wildlife morbidity and mortality events is critical for reducing threats to wildlife populations. Surveillance systems that use pre-diagnostic clinical data can contribute to the early detection of wildlife morbidities caused by a multitude of threats, including disease and anthropogenic disturbances. Here, we demonstrate proof of concept for use of a wildlife disease surveillance system, the ‘Wildlife Morbidity and Mortality Event Alert System’, that integrates pre-diagnostic clinical data in near real-time from a network of wildlife rehabilitation organizations, for early and enhanced detection of unusual wildlife morbidity and mortality events. The system classifies clinical pre-diagnostic data into relevant clinical classifications based on a natural language processing algorithm, generating alerts when more than the expected number of cases is recorded across the rehabilitation network. We demonstrated the effectiveness and efficiency of the system in alerting to events associated with both common and emerging diseases. Tapping into this readily available unconventional general surveillance data stream offers added value to existing wildlife disease surveillance programmes through a relatively efficient, low-cost strategy for the early detection of threats.

Recommended citation: Kelly, T.R., Pandit, P.S., Carion, N., Dombrowski, D.F., Rogers, K.H., McMillin, S.C., Clifford, D.L., Riberi, A., Ziccardi, M.H., Donnelly-Greenan, E.L. and Johnson, C.K., 2021. Early detection of wildlife morbidity and mortality through an event-based surveillance system. Proceedings of the Royal Society B, 288(1954), p.20210974. https://royalsocietypublishing.org/doi/10.1098/rspb.2021.0974

Retrospective study on admission trends of Californian hummingbirds found in urban habitats (1991–2016).

Published in PeerJ, 2021

Abstract

Background

Hummingbirds are frequently presented to California wildlife rehabilitation centers for medical care, accounting for approximately 5% of overall admissions. Age, sex, and reason for admission could impact hummingbird survivability, therefore identification of these factors could help maximize rehabilitation efforts.

Recommended citation: Pandit PS, Bandivadekar RR, Johnson CK, Mikoni N, Mah M, Purdin G, Ibarra E, Tom D, Daugherty A, Lipman MW, Woo K. Retrospective study on admission trends of Californian hummingbirds found in urban habitats (1991–2016). PeerJ. 2021 Apr 13;9:e11131. https://peerj.com/articles/11131/

Vulnerabilities for Exposure to Emerging Infectious Disease at Urban Settlements in Nepal

Published in EcoHealth, 2020

Abstract

In Nepal, rapid urbanization and rural-to-urban migration especially due to internal civil conflict have catalyzed the development of temporary settlements, often along rivers on undeveloped land. This study conducted surveillance for viruses in small mammals and assessed potential risks for virus transmission to people in urban settlements along rivers in Kathmandu, Nepal. We collected samples from 411 small mammals (100 rodents and 311 shrews) at four riverside settlement sites and detected six viruses from four virus families including Thottapalayam virus; a strain of murine coronavirus; two new paramyxoviruses; and two new rhabdoviruses. Additionally, we conducted surveys of 264 residents to characterize animal–human contact. Forty-eight percent of individuals reported contact with wildlife, primarily with rodents and shrews (91%). Our findings confirm that rodents and shrews should be considered a health threat for residents of temporary settlements, and that assessment of disease transmission risk coupled with targeted surveillance for emerging pathogens could lead to improved disease control and health security for urban populations. Additionally, interventions focused on disease prevention should consider the unique urban ecology and social dynamics in temporary settlements, along with the importance of community engagement for identifying solutions that address specific multi-dimensional challenges that life on the urban river margins presents.

Recommended citation: Wolking, D., Karmacharya, D., Bista, M., Shrestha, R., Pandit, P., Sharma, A., Manandhar, S., Shrestha, B., Bajracharya, S., Bhatta, T. and Dulal, S., 2020. Vulnerabilities for Exposure to Emerging Infectious Disease at Urban Settlements in Nepal. EcoHealth, 17(3), pp.345-358. https://link.springer.com/article/10.1007/s10393-020-01499-4

Global shifts in mammalian population trends reveal key predictors of virus spillover risk

Published in Proceedings of the Royal Society B, 2020

Abstract

Emerging infectious diseases in humans are frequently caused by pathogens originating from animal hosts, and zoonotic disease outbreaks present a major challenge to global health. To investigate drivers of virus spillover, we evaluated the number of viruses mammalian species have shared with humans. We discovered that the number of zoonotic viruses detected in mammalian species scales positively with global species abundance, suggesting that virus transmission risk has been highest from animal species that have increased in abundance and even expanded their range by adapting to human-dominated landscapes. Domesticated species, primates and bats were identified as having more zoonotic viruses than other species. Among threatened wildlife species, those with population reductions owing to exploitation and loss of habitat shared more viruses with humans. Exploitation of wildlife through hunting and trade facilitates close contact between wildlife and humans, and our findings provide further evidence that exploitation, as well as anthropogenic activities that have caused losses in wildlife habitat quality, have increased opportunities for animal–human interactions and facilitated zoonotic disease transmission. Our study provides new evidence for assessing spillover risk from mammalian species and highlights convergent processes whereby the causes of wildlife population declines have facilitated the transmission of animal viruses to humans.

Recommended citation: Johnson, C.K., Hitchens, P.L., Pandit, P.S., Rushmore, J., Evans, T.S., Young, C.C. and Doyle, M.M., 2020. Global shifts in mammalian population trends reveal key predictors of virus spillover risk. Proceedings of the Royal Society B, 287(1924), p.20192736. https://royalsocietypublishing.org/doi/full/10.1098/rspb.2019.2736

Predicting wildlife reservoirs and global vulnerability to zoonotic Flaviviruses

Published in Nature Communications, Accepted, In Press, 2018

Abstract

Flaviviruses continue to cause globally relevant epidemics and have emerged or re-emerged in regions that were previously unaffected. Factors determining emergence of flaviviruses and continuing circulation in sylvatic cycles are incompletely understood. Here we identify potential sylvatic reservoirs of flaviviruses and characterize the macro-ecological traits common to known wildlife hosts to predict the risk of sylvatic flavivirus transmission among wildlife and identify regions that could be vulnerable to outbreaks. We evaluate variability in wildlife hosts for zoonotic flaviviruses and find that flaviviruses group together in distinct clusters with similar hosts. Models incorporating ecological and climatic variables as well as life history traits shared by flaviviruses predict new host species with similar host characteristics. The combination of vector distribution data with models for flavivirus hosts allows for prediction of global vulnerability to flaviviruses and provides potential targets for disease surveillance in animals and humans.

Recommended citation: Pranav Pandit, Megan Doyle, Katrina Smart, Cristin Young, Gaylen Drape, and Christine Johnson. "Predicting wildlife reservoirs and global vulnerability to zoonotic Flaviviruses" Nature Communications, 9.

Use of RFID technology to characterize feeder visitations and contact network of hummingbirds in urban habitats

Published in PLOS ONE, 2018

Recommended citation: Ruta Bandivadekar, Pranav Pandit, Rahel Sollmann, Michael Thomas, Scott Logan, Jennifer Brown, A.P. Klimley, Lisa Tell. "Use of RFID technology to characterize feeder visitations and contact network of hummingbirds in urban habitats" PLOS ONE, 13, no.12, (2018), e0208057. https://doi.org/10.1371/journal.pone.0208057 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0208057

Spread of Coxiella burnetii between dairy cattle herds in an enzootic region: modelling contributions of airborne transmission and trade

Published in Veterinary Research, 2016

Abstract

Q fever, a worldwide zoonotic disease caused by Coxiella burnetii, is a looming concern for livestock and public health. Epidemiological features of inter-herd transmission of C. burnetii in cattle herds by wind and trade of cows are poorly understood. We present a novel dynamic spatial model describing the inter-herd regional spread of C. burnetii in dairy cattle herds, quantifying the ability of airborne transmission and animal trade in C. burnetii propagation in an enzootic region. Among all the new herd infections, 92% were attributed to airborne transmission and the rest to cattle trade. Infections acquired following airborne transmission were shown to cause relatively small and ephemeral intra-herd outbreaks. On the contrary, disease-free herds purchasing an infectious cow experienced significantly higher intra-herd prevalence. The results also indicated that, for short duration, both transmission routes were independent from each other without any synergistic effect. The model outputs applied to the Finistère department in western France showed satisfactory sensitivity (0.71) and specificity (0.80) in predicting herd infection statuses at the end of one year in a neighbourhood of 3 km around expected incident herds, when compared with data. The model developed here thus provides important insights into the spread of C. burnetii between dairy cattle herds and paves the way for implementation and assessment of control strategies.

Recommended citation: Pranav Pandit, Thierry Hoch, Pauline Ezanno, François Beaudeau, and Elisabeta Vergu. "Spread of Coxiella burnetii between dairy cattle herds in an enzootic region: modelling contributions of airborne transmission and trade." Veterinary Research. 47, no. 1 (2016): 1 https://veterinaryresearch.biomedcentral.com/articles/10.1186/s13567-016-0330-4

Modeling highly pathogenic avian influenza transmission in wild birds and poultry in West Bengal, India.

Published in Scientific Reports volume 3, 2013

Abstract

Wild birds are suspected to have played a role in highly pathogenic avian influenza (HPAI) H5N1 outbreaks in West Bengal. Cluster analysis showed that H5N1 was introduced in West Bengal at least 3 times between 2008 and 2010. We simulated the introduction of H5N1 by wild birds and their contact with poultry through a stochastic continuous-time mathematical model. Results showed that reducing contact between wild birds and domestic poultry, and increasing the culling rate of infected domestic poultry communities will reduce the probability of outbreaks. Poultry communities that shared habitat with wild birds or those indistricts with previous outbreaks were more likely to suffer an outbreak. These results indicate that wild birds can introduce HPAI to domestic poultry and that limiting their contact at shared habitats together with swift culling of infected domestic poultry can greatly reduce the likelihood of HPAI outbreaks.
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Recommended citation: Pranav Pandit, David Bunn, Satish Pande, and Sharif Aly. "Modeling highly pathogenic avian influenza transmission in wild birds and poultry in West Bengal, India." Scientific reports 3 (2013). https://www.nature.com/articles/srep02175

Avian collision threat assessment at ‘Bhambarwadi Wind Farm Plateau’in northern Western Ghats, India.

Published in Journal of Threatened Taxa, 2013

Abstract

To address the shortage of power in India, wind energy is increasingly harnessed as an alternate and renewable energy source. There is a rapid increase in the number of wind farms at suitable sites all over the country. Some of the key sites with optimal wind velocities are the plateaus on the Western Ghats - a global hotspot of biological diversity. The rocky plateaus on the Western Ghats are terrestrial habitat islands facing extreme micro-environmental conditions; however, scanty information is available on the ecology of these plateaus. We undertook a two-year study to assess the impact of wind farms on birds. We also documented the avian diversity at Bhambarwadi Plateau, northern Western Ghats, India. To the best of our knowledge this is the first such study in India. We recorded 89 avian species on the plateau, 27 of which flew in the risk area swept by the rotor blades, and hence are potentially at risk of collision. The collision index (the number of bird collisions with wind turbines over a period of one year assuming that the birds do not take any avoidance measure) for these species were estimated. We also identified species at risk from collision with transformers and wind-masts, and at risk from electrocution. Reduction in avian activity in the study area was evident with progress of wind farm erection. Despite the small footprint of an individual wind turbine, the associated infrastructure development causes wider habitat modification and destruction resulting in a displacement effect. Therefore, wind farm erections in strategic locations such as biodiversity hotspots should be subject to prior site based strategic environmental assessments (SEA) as well as environmental impact assessment (EIA) studies.
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Recommended citation: Pande, Satish, Anand Padhye, Aditya Ponkshe, Pranav Pandit, Amit Pawashe, Shivkumar Pednekar, Rohan Pandit, and Pramod Deshpande. "Avian collision threat assessment at ‘Bhambarwadi Wind Farm Plateau’in northern Western Ghats, India." Journal of Threatened Taxa 5, no. 1 (2013): 3504-3515. http://threatenedtaxa.org/index.php/JoTT/article/view/1419/2594

Tick infestation on wild snakes in northern part of Western Ghats of India.

Published in Journal of Medical Entomology, 2011

Recommended citation: Pranav Pandit, Ruta Bandivdekar, Geevarghese Geevarghese, Satish Pande, and Omkar Mandke. "Tick infestation on wild snakes in northern part of Western Ghats of India." Journal of Medical Entomology 48, no. 3 (2011): 504-507. https://academic.oup.com/jme/article/48/3/504/882162

Behavioural and virological studies on a rescued Oriental white-backed vulture Gyps bengalensis from western Maharashtra, India.

Published in Journal of Threatened Taxa , 2011

Abstract

An exhausted Indian White-backed Vulture Gyps bengalensis was rescued in Maharashtra State, India. Examination revealed that it was not injured but was emaciated due to starvation. The vulture was fed in captivity by the Forest Department. To rule out the possibility of viral infections, cloacal, tracheal and serum samples were collected from the vulture. They were negative for Avian Influenza (AI) viruses, Newcastle Disease Virus (NDV), Infectious Bursal Disease Virus by virus isolation. We observed neck drooping behavior by vulture when approached by humans. The vulture flew away but after two days, was found dead 60km away, due to electrocution. Our report suggests that electrocution may also be an explanation for the decreasing numbers of vultures in India.

Recommended citation: Pande, Satish, Pandit Pranav, Ponkshe Aditya, Mone Ram, Pawar Shailesh, and Mishra Akhilesh. "Behavioural and virological studies on a rescued Oriental white-backed vulture Gyps bengalensis from western Maharashtra, India." Journal of Threatened Taxa 3, no. 1 (2011): 1490-1492. http://threatenedtaxa.org/index.php/JoTT/article/view/1202/2174

Avian influenza surveillance in wild migratory, resident, domestic birds and in poultry in Maharashtra and Manipur, India, during avian migratory season 2006–2007.

Published in Current Science, 2009

Abstract

India reported outbreaks of Highly Pathogenic Avian Influenza (HPAI) H5N1 in poultry in the states of Maharashtra, Gujarat and Madhya Pradesh (February–April 2006); Manipur (July 2007); West Bengal (January 2008) and Tripura (April 2008). The role of migratory birds in the transmission of the HPAI H5N1 remains a subject of debate. Avian Influenza (AI) surveillance in wild migratory, wild resident, domestic birds and poultry was undertaken by National Institute of Virology (NIV) jointly with Ela Foundation, Pune, India during 2006–07. A total of 1968 faecal specimens (1369 droppings from wild migratory and wild resident birds; 474 droppings from poultry and 125 cloacal swabs from chickens and ducks) were collected. These samples representing 10 avian families of wild migratory birds, four families of wild resident birds totalling 36 species, were from eight districts of Maharashtra covering 20 water bodies and two districts of Manipur. The samples were screened for AI viruses by reverse transcriptase polymerase chain reaction (RT-PCR), real-time PCR and were processed for virus isolation in embryonated chicken eggs and cell culture. Two samples from wild ducks were positive for viruses other than AI, newcastle disease virus (NDV) and infectious bursal disease virus (IBDV). During the study period no sample was positive for Influenza A viruses, Influenza A (H5N1) or any other strain of HPAI by RT-PCR and virus isolation. In view of the recent HPAI H5N1 outbreaks in poultry in India, continued and more widespread AI surveillance is necessary to elucidate the role of wild migratory, resident, domestic birds and poultry in the transmission of AI viruses.

Recommended citation: Pawar, Shailesh., Satish Pande, Aniruddha Jamgaonkar, S. S. Koratkar, Bishwajoy Pal, Satish Raut, Madhuri Nanaware., Koninika Ray, Alok Chakrabarti, Sadhana Kode, Vishal Thite, Madhukar Khude, Satish Randive, Atanu Basu, Amit Pawashe, Aditya Ponkshe, Pranav Pandit and Pramod Deshpande "Avian influenza surveillance in wild migratory, resident, domestic birds and in poultry in Maharashtra and Manipur, India, during avian migratory season 2006–2007." Curr. Sci 97 (2009): 550-554 http://www.jstor.org/stable/24111884