Spatiotemporal genotype replacement of H5N8 avian influenza viruses contributed to H5N1 emergence in 2021/2022 panzootic.

Since 2020, clade 2.3.4.4b highly pathogenic avian influenza H5N8 and H5N1 viruses have swept through continents, posing serious threats to the world. Through comprehensive analyses of epidemiological, genetic, and bird migration data, we found that the dominant genotype replacement of the H5N8 viruses in 2020 contributed to the H5N1 outbreak in the 2021/2022 wave. The 2020 outbreak of the H5N8 G1 genotype instead of the G0 genotype produced reassortment opportunities and led to the emergence of a new H5N1 virus with G1's HA and MP genes. Despite extensive reassortments in the 2021/2022 wave, the H5N1 virus retained the HA and MP genes, causing a significant outbreak in Europe and North America. Furtherly, through the wild bird migration flyways investigation, we found that the temporal-spatial coincidence between the outbreak of the H5N8 G1 virus and the bird autumn migration may have expanded the H5 viral spread, which may be one of the main drivers of the emergence of the 2020-2022 H5 panzootic.IMPORTANCESince 2020, highly pathogenic avian influenza (HPAI) H5 subtype variants of clade 2.3.4.4b have spread across continents, posing unprecedented threats globally. However, the factors promoting the genesis and spread of H5 HPAI viruses remain unclear. Here, we found that the spatiotemporal genotype replacement of H5N8 HPAI viruses contributed to the emergence of the H5N1 variant that caused the 2021/2022 panzootic, and the viral evolution in poultry of Egypt and surrounding area and autumn bird migration from the Russia-Kazakhstan region to Europe are important drivers of the emergence of the 2020-2022 H5 panzootic. These findings provide important targets for early warning and could help control the current and future HPAI epidemics.

A 10-m annual grazing intensity dataset in 2015-2021 for the largest temperate meadow steppe in China.

Mapping grazing intensity (GI) using satellites is crucial for developing adaptive utilization strategies according to grassland conditions. Here we developed a monitoring framework based on a paired sampling strategy and the classification probability of random forest algorithm to produce annual grazing probability (GP) and GI maps at 10-m spatial resolution from 2015 to 2021 for the largest temperate meadow in China (Hulun Buir grasslands), by harmonized Landsat 7/8 and Sentinel-2 images. The GP maps used values of 0-1 to present detailed grazing gradient information. To match widely used grazing gradients, annual GI maps with ungrazed, moderately grazed, and heavily grazed levels were generated from the GP dataset with a decision tree. The GI maps for 2015-2021 had an overall accuracy of more than 0.97 having significant correlations with the statistical data at city (r = 0.51) and county (r = 0.75) scales. They also effectively captured the GI gradients at site scale (r = 0.94). Our study proposed a monitoring approach and presented annual 10-m grazing information maps for sustainable grassland management.

The 10-m crop type maps in Northeast China during 2017-2019.

Northeast China is the leading grain production region in China where one-fifth of the national grain is produced; however, consistent and reliable crop maps are still unavailable, impeding crop management decisions for regional and national food security. Here, we produced annual 10-m crop maps of the major crops (maize, soybean, and rice) in Northeast China from 2017 to 2019, by using (1) a hierarchical mapping strategy (cropland mapping followed by crop classification), (2) agro-climate zone-specific random forest classifiers, (3) interpolated and smoothed 10-day Sentinel-2 time series data, and (4) optimized features from spectral, temporal, and texture characteristics of the land surface. The resultant maps have high overall accuracies (OA) spanning from 0.81 to 0.86 based on abundant ground truth data. The satellite estimates agreed well with the statistical data for most of the municipalities (R2 ≥ 0.83, p < 0.01). This is the first effort on regional annual crop mapping in China at the 10-m resolution, which permits assessing the performance of the soybean rejuvenation plan and crop rotation practice in China.

Large increases of paddy rice area, gross primary production, and grain production in Northeast China during 2000-2017.

China is the largest rice producer and consumer in the world. Accurate estimations of paddy rice planting area and rice grain production is important for feeding the increasing population in China. However, Southern China had substantial losses in paddy rice area over the last three decades in those regions where paddy rice has traditionally been produced. Several studies have shown increased paddy rice area in Northeast China. Here we document the annual dynamics of paddy rice area, gross primary production (GPP), and grain production in Northeast China (Heilongjiang, Jilin and Liaoning provinces) during 2000-2017 using agricultural statistical data, satellite images, and model simulations. Annual maps derived from satellite images show that paddy rice area in Northeast China has increased by 3.68 million ha from 2000 to 2017, which is more than the total combined paddy rice area of North Korea, South Korea, and Japan. Approximately 82% of paddy rice pixels had an increase in annual GPP during 2000-2017. The expansion of paddy rice area slowed down substantially since 2015. Annual GPP from those paddy rice fields cultivated continuously over the 18 years were moderately higher than that from other paddy rice fields, which suggested that improved management practices could increase grain production in the region. There was a strong linear relationship between annual GPP and annual rice grain production in Northeast China by province and year, which illustrates the potential of using satellite-based data-driven model to track and assess grain production of paddy rice in the region. Northeast China is clearly an emerging rice production base and plays an increasing role in crop production and food security in China. However, many challenges for the further expansion and sustainable cultivation of paddy rice in Northeast China remain.

Fingerprint of rice paddies in spatial-temporal dynamics of atmospheric methane concentration in monsoon Asia.

Agriculture (e.g., rice paddies) has been considered one of the main emission sources responsible for the sudden rise of atmospheric methane concentration (XCH4) since 2007, but remains debated. Here we use satellite-based rice paddy and XCH4 data to investigate the spatial-temporal relationships between rice paddy area, rice plant growth, and XCH4 in monsoon Asia, which accounts for ~87% of the global rice area. We find strong spatial consistencies between rice paddy area and XCH4 and seasonal consistencies between rice plant growth and XCH4. Our results also show a decreasing trend in rice paddy area in monsoon Asia since 2007, which suggests that the change in rice paddy area could not be one of the major drivers for the renewed XCH4 growth, thus other sources and sinks should be further investigated. Our findings highlight the importance of satellite-based paddy rice datasets in understanding the spatial-temporal dynamics of XCH4 in monsoon Asia.

High resolution paddy rice maps in cloud-prone Bangladesh and Northeast India using Sentinel-1 data.

Knowledge of where, when, and how much paddy rice is planted is crucial information for understating of regional food security, freshwater use, climate change, and transmission of avian influenza virus. We developed seasonal paddy rice maps at high resolution (10 m) for Bangladesh and Northeast India, typical cloud-prone regions in South Asia, using cloud-free Synthetic Aperture Radar (SAR) images from Sentinel-1 satellite, the Random Forest classifier, and the Google Earth Engine (GEE) cloud computing platform. The maps were provided for all the three distinct rice growing seasons of the region: Boro, Aus and Aman. The paddy rice maps were evaluated against the independent validation samples, and compared with the existing products from the International Rice Research Institute (IRRI) and the analysis of Moderate Resolution Imaging Spectroradiometer (MODIS) data. The generated paddy rice maps were spatially consistent with the compared maps and had a satisfactory accuracy over 90%. This study showed the potential of Sentinel-1 data and GEE on large scale paddy rice mapping in cloud-prone regions like tropical Asia.

Dynamics of the 2004 avian influenza H5N1 outbreak in Thailand: The role of duck farming, sequential model fitting and control.

The Highly Pathogenic Avian Influenza (HPAI) subtype H5N1 virus persists in many countries and has been circulating in poultry, wild birds. In addition, the virus has emerged in other species and frequent zoonotic spillover events indicate that there remains a significant risk to human health. It is crucial to understand the dynamics of the disease in the poultry industry to develop a more comprehensive knowledge of the risks of transmission and to establish a better distribution of resources when implementing control. In this paper, we develop a set of mathematical models that simulate the spread of HPAI H5N1 in the poultry industry in Thailand, utilising data from the 2004 epidemic. The model that incorporates the intensity of duck farming when assessing transmision risk provides the best fit to the spatiotemporal characteristics of the observed outbreak, implying that intensive duck farming drives transmission of HPAI in Thailand. We also extend our models using a sequential model fitting approach to explore the ability of the models to be used in "real time" during novel disease outbreaks. We conclude that, whilst predictions of epidemic size are estimated poorly in the early stages of disease outbreaks, the model can infer the preferred control policy that should be deployed to minimise the impact of the disease.

Divergent trends of open-surface water body area in the contiguous United States from 1984 to 2016.

The contiguous United States (CONUS), especially the West, faces challenges of increasing water stress and uncertain impacts of climate change. The historical information of surface water body distribution, variation, and multidecadal trends documented in remote-sensing images can aid in water-resource planning and management, yet is not well explored. Here, we detected open-surface water bodies in all Landsat 5, 7, and 8 images (∼370,000 images, >200 TB) of the CONUS and generated 30-meter annual water body frequency maps for 1984-2016. We analyzed the interannual variations and trends of year-long water body area, examined the impacts of climatic and anthropogenic drivers on water body area dynamics, and explored the relationships between water body area and land water storage (LWS). Generally, the western half of the United States is prone to water stress, with small water body area and large interannual variability. During 1984-2016, water-poor regions of the Southwest and Northwest had decreasing trends in water body area, while water-rich regions of the Southeast and far north Great Plains had increasing trends. These divergent trends, mainly driven by climate, enlarged water-resource gaps and are likely to continue according to climate projections. Water body area change is a good indicator of LWS dynamics in 58% of the CONUS. Following the 2012 prolonged drought, LWS in California and the southern Great Plains had a larger decrease than surface water body area, likely caused by massive groundwater withdrawals. Our findings provide valuable information for surface water-resource planning and management across the CONUS.

Exacerbated grassland degradation and desertification in Central Asia during 2000-2014.

Grassland degradation and desertification is a complex process, including both state conversion (e.g., grasslands to deserts) and gradual within-state change (e.g., greenness dynamics). Existing studies hardly separated the two components and analyzed it as a whole based on time series vegetation index data, which cannot provide a clear and comprehensive picture for grassland degradation and desertification. Here we propose an integrated assessment strategy, by considering both state conversion and within-state change of grasslands, to investigate grassland degradation and desertification process in Central Asia. First, annual maps of grasslands and sparsely vegetated land were generated to track the state conversions between them. The results showed increasing grasslands were converted to sparsely vegetated lands from 2000 to 2014, with the desertification region concentrating in the latitude range of 43-48° N. A frequency analysis of grassland vs. sparsely vegetated land classification in the last 15 yr allowed a recognition of persistent desert zone (PDZ), persistent grassland zone (PGZ), and transitional zone (TZ). The TZ was identified in southern Kazakhstan as one hotspot that was unstable and vulnerable to desertification. Furthermore, the trend analysis of Enhanced Vegetation Index during thermal growing season (EVITGS ) was investigated in individual zones using linear regression and Mann-Kendall approaches. An overall degradation across the area was found; moreover, the second desertification hotspot was identified in northern Kazakhstan with significant decreasing in EVITGS , which was located in PGZ. Finally, attribution analyses of grassland degradation and desertification were conducted by considering precipitation, temperature, and three different drought indices. We found persistent droughts were the main factor for grassland degradation and desertification in Central Asia. Considering both state conversion and gradual within-state change processes, this study provided reference information for identification of desertification hotspots to support further grassland degradation and desertification treatment, and the method could be useful to be extended to other regions.

Temporal consistency between gross primary production and solar-induced chlorophyll fluorescence in the ten most populous megacity areas over years.

The gross primary production (GPP) of vegetation in urban areas plays an important role in the study of urban ecology. It is difficult however, to accurately estimate GPP in urban areas, mostly due to the complexity of impervious land surfaces, buildings, vegetation, and management. Recently, we used the Vegetation Photosynthesis Model (VPM), climate data, and satellite images to estimate the GPP of terrestrial ecosystems including urban areas. Here, we report VPM-based GPP (GPPvpm) estimates for the world's ten most populous megacities during 2000-2014. The seasonal dynamics of GPPvpm during 2007-2014 in the ten megacities track well that of the solar-induced chlorophyll fluorescence (SIF) data from GOME-2 at 0.5° × 0.5° resolution. Annual GPPvpm during 2000-2014 also shows substantial variation among the ten megacities, and year-to-year trends show increases, no change, and decreases. Urban expansion and vegetation collectively impact GPP variations in these megacities. The results of this study demonstrate the potential of a satellite-based vegetation photosynthesis model for diagnostic studies of GPP and the terrestrial carbon cycle in urban areas.

A global moderate resolution dataset of gross primary production of vegetation for 2000-2016.

Accurate estimation of the gross primary production (GPP) of terrestrial vegetation is vital for understanding the global carbon cycle and predicting future climate change. Multiple GPP products are currently available based on different methods, but their performances vary substantially when validated against GPP estimates from eddy covariance data. This paper provides a new GPP dataset at moderate spatial (500 m) and temporal (8-day) resolutions over the entire globe for 2000-2016. This GPP dataset is based on an improved light use efficiency theory and is driven by satellite data from MODIS and climate data from NCEP Reanalysis II. It also employs a state-of-the-art vegetation index (VI) gap-filling and smoothing algorithm and a separate treatment for C3/C4 photosynthesis pathways. All these improvements aim to solve several critical problems existing in current GPP products. With a satisfactory performance when validated against in situ GPP estimates, this dataset offers an alternative GPP estimate for regional to global carbon cycle studies.

Spatiotemporal patterns of paddy rice croplands in China and India from 2000 to 2015.

Due to rapid population growth and urbanization, paddy rice agriculture is experiencing substantial changes in the spatiotemporal pattern of planting areas in the two most populous countries-China and India-where food security is always the primary concern. However, there is no spatially explicit and continuous rice-planting information in either country. This knowledge gap clearly hinders our ability to understand the effects of spatial paddy rice area dynamics on the environment, such as food and water security, climate change, and zoonotic infectious disease transmission. To resolve this problem, we first generated annual maps of paddy rice planting areas for both countries from 2000 to 2015, which are derived from time series Moderate Resolution Imaging Spectroradiometer (MODIS) data and the phenology- and pixel-based rice mapping platform (RICE-MODIS), and analyzed the spatiotemporal pattern of paddy rice dynamics in the two countries. We found that China experienced a general decrease in paddy rice planting area with a rate of 0.72 million (m) ha/yr from 2000 to 2015, while a significant increase at a rate of 0.27mha/yr for the same time period happened in India. The spatial pattern of paddy rice agriculture in China shifted northeastward significantly, due to simultaneous expansions in paddy rice planting areas in northeastern China and contractions in southern China. India showed an expansion of paddy rice areas across the entire country, particularly in the northwestern region of the Indo-Gangetic Plain located in north India and the central and south plateau of India. In general, there has been a northwesterly shift in the spatial pattern of paddy rice agriculture in India. These changes in the spatiotemporal patterns of paddy rice planting area have raised new concerns on how the shift may affect national food security and environmental issues relevant to water, climate, and biodiversity.

Could Changes in the Agricultural Landscape of Northeastern China Have Influenced the Long-Distance Transmission of Highly Pathogenic Avian Influenza H5Nx Viruses?

In the last few years, several reassortant subtypes of highly pathogenic avian influenza viruses (HPAI H5Nx) have emerged in East Asia. These new viruses, mostly of subtype H5N1, H5N2, H5N6, and H5N8 belonging to clade 2.3.4.4, have been found in several Asian countries and have caused outbreaks in poultry in China, South Korea, and Vietnam. HPAI H5Nx also have spread over considerable distances with the introduction of viruses belonging to the same 2.3.4.4 clade in the U.S. (2014-2015) and in Europe (2014-2015 and 2016-2017). In this paper, we examine the emergence and spread of these new viruses in Asia in relation to published datasets on HPAI H5Nx distribution, movement of migratory waterfowl, avian influenza risk models, and land-use change analyses. More specifically, we show that between 2000 and 2015, vast areas of northeast China have been newly planted with rice paddy fields (3.21 million ha in Heilongjiang, Jilin, and Liaoning) in areas connected to other parts of Asia through migratory pathways of wild waterfowl. We hypothesize that recent land use changes in northeast China have affected the spatial distribution of wild waterfowl, their stopover areas, and the wild-domestic interface, thereby altering transmission dynamics of avian influenza viruses across flyways. Detailed studies of the habitat use by wild migratory birds, of the extent of the wild-domestic interface, and of the circulation of avian influenza viruses in those new planted areas may help to shed more light on this hypothesis, and on the possible impact of those changes on the long-distance patterns of avian influenza transmission.

Mapping paddy rice planting area in northeastern Asia with Landsat 8 images, phenology-based algorithm and Google Earth Engine.

Area and spatial distribution information of paddy rice are important for understanding of food security, water use, greenhouse gas emission, and disease transmission. Due to climatic warming and increasing food demand, paddy rice has been expanding rapidly in high latitude areas in the last decade, particularly in northeastern (NE) Asia. Current knowledge about paddy rice fields in these cold regions is limited. The phenology- and pixel-based paddy rice mapping (PPPM) algorithm, which identifies the flooding signals in the rice transplanting phase, has been effectively applied in tropical areas, but has not been tested at large scale of cold regions yet. Despite the effects from more snow/ice, paddy rice mapping in high latitude areas is assumed to be more encouraging due to less clouds, lower cropping intensity, and more observations from Landsat sidelaps. Moreover, the enhanced temporal and geographic coverage from Landsat 8 provides an opportunity to acquire phenology information and map paddy rice. This study evaluated the potential of Landsat 8 images on annual paddy rice mapping in NE Asia which was dominated by single cropping system, including Japan, North Korea, South Korea, and NE China. The cloud computing approach was used to process all the available Landsat 8 imagery in 2014 (143 path/rows, ~3290 scenes) with the Google Earth Engine (GEE) platform. The results indicated that the Landsat 8, GEE, and improved PPPM algorithm can effectively support the yearly mapping of paddy rice in NE Asia. The resultant paddy rice map has a high accuracy with the producer (user) accuracy of 73% (92%), based on the validation using very high resolution images and intensive field photos. Geographic characteristics of paddy rice distribution were analyzed from aspects of country, elevation, latitude, and climate. The resultant 30-m paddy rice map is expected to provide unprecedented details about the area, spatial distribution, and landscape pattern of paddy rice fields in NE Asia, which will contribute to food security assessment, water resource management, estimation of greenhouse gas emissions, and disease control.

Mapping paddy rice planting area in rice-wetland coexistent areas through analysis of Landsat 8 OLI and MODIS images.

Accurate and up-to-date information on the spatial distribution of paddy rice fields is necessary for the studies of trace gas emissions, water source management, and food security. The phenology-based paddy rice mapping algorithm, which identifies the unique flooding stage of paddy rice, has been widely used. However, identification and mapping of paddy rice in rice-wetland coexistent areas is still a challenging task. In this study, we found that the flooding/transplanting periods of paddy rice and natural wetlands were different. The natural wetlands flood earlier and have a shorter duration than paddy rice in the Panjin Plain, a temperate region in China. We used this asynchronous flooding stage to extract the paddy rice planting area from the rice-wetland coexistent area. MODIS Land Surface Temperature (LST) data was used to derive the temperature-defined plant growing season. Landsat 8 OLI imagery was used to detect the flooding signal and then paddy rice was extracted using the difference in flooding stages between paddy rice and natural wetlands. The resultant paddy rice map was evaluated with in-situ ground-truth data and Google Earth images. The estimated overall accuracy and Kappa coefficient were 95% and 0.90, respectively. The spatial pattern of OLI-derived paddy rice map agrees well with the paddy rice layer from the National Land Cover Dataset from 2010 (NLCD-2010). The differences between RiceLandsat and RiceNLCD are in the range of ±20% for most 1-km grid cell. The results of this study demonstrate the potential of the phenology-based paddy rice mapping algorithm, via integrating MODIS and Landsat 8 OLI images, to map paddy rice fields in complex landscapes of paddy rice and natural wetland in the temperate region.

Semi-natural areas of Tarim Basin in northwest China: Linkage to desertification.

Semi-natural lands are not intensively managed lands, which have ecological significance in protecting artificial oasis and preventing desertification in arid regions. The significant shrinkage and degradation of semi-natural lands in the land-use intensification process have caused severe desertification. However, there is a knowledge gap regarding the spatio-temporal pattern and detailed classification of semi-natural lands and its quantitative relationship with desertification. Taking the Tarim Basin as an example, we proposed a comprehensive classification system to identify semi-natural lands for 1990, 2000, and 2010, respectively, using multi-source datasets at large scales. Spatio-temporal changes of semi-natural lands were then characterized by map comparisons at decade intervals. Finally, statistical relationships between semi-natural lands and desertification were explored based on 241 watersheds. The area of semi-natural lands in Tarim Basin was 10.77×104km2 in 2010, and desert-vegetation type, native-oasis type, artificial-oasis type, saline type and wetland type accounted for 59.59%, 14.65%, 11.25%, 9.63% and 4.88% of the total area, respectively. A rapid loss of semi-natural lands (9769.05km2) was demonstrated from 1990 to 2010. In the fragile watersheds, the semi-natural lands were mainly converted to desert; while in the watersheds with advanced oasis agriculture, artificial-oasis type reclaimed to arable land was the major change. The occurrence of desertification was closely related to the type, area proportion and combination patterns of semi-natural lands. Desertification was prone to occur in regions abundant in desert-vegetation type and saline type, while less serious desertification was observed in regions with high proportion of artificial-oasis type and wetland type. Policy intervention and reasonable water resource allocation were encouraged to prevent the substantial loss of semi-natural lands, especially for the water-limiting watersheds and periods.

Mapping forests in monsoon Asia with ALOS PALSAR 50-m mosaic images and MODIS imagery in 2010.

Extensive forest changes have occurred in monsoon Asia, substantially affecting climate, carbon cycle and biodiversity. Accurate forest cover maps at fine spatial resolutions are required to qualify and quantify these effects. In this study, an algorithm was developed to map forests in 2010, with the use of structure and biomass information from the Advanced Land Observation System (ALOS) Phased Array L-band Synthetic Aperture Radar (PALSAR) mosaic dataset and the phenological information from MODerate Resolution Imaging Spectroradiometer (MOD13Q1 and MOD09A1) products. Our forest map (PALSARMOD50 m F/NF) was assessed through randomly selected ground truth samples from high spatial resolution images and had an overall accuracy of 95%. Total area of forests in monsoon Asia in 2010 was estimated to be ~6.3 × 10(6 )km(2). The distribution of evergreen and deciduous forests agreed reasonably well with the median Normalized Difference Vegetation Index (NDVI) in winter. PALSARMOD50 m F/NF map showed good spatial and areal agreements with selected forest maps generated by the Japan Aerospace Exploration Agency (JAXA F/NF), European Space Agency (ESA F/NF), Boston University (MCD12Q1 F/NF), Food and Agricultural Organization (FAO FRA), and University of Maryland (Landsat forests), but relatively large differences and uncertainties in tropical forests and evergreen and deciduous forests.

Mapping paddy rice planting area in wheat-rice double-cropped areas through integration of Landsat-8 OLI, MODIS, and PALSAR images.

As farmland systems vary over space and time (season and year), accurate and updated maps of paddy rice are needed for studies of food security and environmental problems. We selected a wheat-rice double-cropped area from fragmented landscapes along the rural-urban complex (Jiangsu Province, China) and explored the potential utility of integrating time series optical images (Landsat-8, MODIS) and radar images (PALSAR) in mapping paddy rice planting areas. We first identified several main types of non-cropland land cover and then identified paddy rice fields by selecting pixels that were inundated only during paddy rice flooding periods. These key temporal windows were determined based on MODIS Land Surface Temperature and vegetation indices. The resultant paddy rice map was evaluated using regions of interest (ROIs) drawn from multiple high-resolution images, Google Earth, and in-situ cropland photos. The estimated overall accuracy and Kappa coefficient were 89.8% and 0.79, respectively. In comparison with the National Land Cover Data (China) from 2010, the resultant map better detected changes in the paddy rice fields and revealed more details about their distribution. These results demonstrate the efficacy of using images from multiple sources to generate paddy rice maps for two-crop rotation systems.