Could not load file or assembly 'Microsoft.Web.Infrastructure,

It turns out after doing a Reference Cleaning, it removed Microsoft.Web.Infrastructure, but not from the packages.config file. After trying to add it again using the Package Manager Console, Visual Studio says that it is already installed which is false because it was removed.

I then removed the line of code in the packages.config file

<package id="Microsoft.Web.Infrastructure" version="1.0.0.0" targetFramework="net45" />

and ran the command again

PM> Install-Package Microsoft.Web.Infrastructure

After this, now it works fine.

Install AspNetMVC3ToolsUpdateSetup downloaded from here would solve this problem without adding reference

You will need to include the dll with your project and add a reference to it as well.

Here is a link to a similar issue already on Stack: MVC3 Deployment Dependency Problems

Despite the number of answers I'll add another one which IMHO makes the things a bit clearer.

As Rob and wrightmail already mentioned Microsoft.Web.Infrastructure is a NuGet package (link not needed, you have it in NuGet Package Manager).

Apparently, it was referenced by your project and suddenly disappeared. A number of reason may exists but the important thing is that despite you may have enabled Automatic Package Restore in Visual Studio by:

• Manage NuGet packages for solution (context menu in Solution Explorer),
• Allow NuGet to download missing packages (settings),
• Automatically check for missing packages during build in Visual Studio (settings),

certain packages may require a manual reinstall. I am not aware what confuses NuGet, maybe manually removing a reference, but here is the solution I usually apply in such cases. The following PM Console helps restoring a package while preserving the original version (not updating to possibly existing new one):

Update-Package Microsoft.Web.Infrastructure -Reinstall

Version preservation may be required if you do not want to accidentally overwrite an existing package with its newer version which possibly removes "old" functionality you may have used in your project.

And, as a proof, despite a bit lengthy one, that the version does not change, here's the output when the command is executed:

PM> Update-Package Microsoft.Web.Infrastructure -Reinstall
Attempting to gather dependencies information for multiple packages with respect to project 'Samples.NuGet\DemoApp\DemoApp', targeting '.NETFramework,Version=v4.5.2'
Attempting to resolve dependencies for multiple packages
Resolving actions install multiple packages
...
Package removal starts here...
...
Removed package 'Microsoft.AspNet.Web.Optimization 1.1.3' from 'packages.config'
Successfully uninstalled 'Microsoft.AspNet.Web.Optimization 1.1.3' from DemoApp
Removed package 'WebGrease 1.5.2' from 'packages.config'
Executing script file 'D:\Projects\DemoApp\packages\WebGrease.1.5.2\tools\uninstall.ps1'
Successfully uninstalled 'WebGrease 1.5.2' from DemoApp
...
More package removals here. Omitted for brevity...
...
Removed package 'Microsoft.Web.Infrastructure 1.0.0.0' from 'packages.config'
Successfully uninstalled 'Microsoft.Web.Infrastructure 1.0.0.0' from DemoApp
...
More package removals here. Omitted for brevity...
...
Removed package 'Antlr 3.4.1.9004' from 'packages.config'
Successfully uninstalled 'Antlr 3.4.1.9004' from MvcLenseApp
Package 'Antlr.3.4.1.9004' already exists in folder 'D:\Projects\Lense.Mvc5\packages'
--- Install packages (in reverse order) ---
Package 'Antlr.3.4.1.9004' already exists in folder 'D:\Projects\DemoApp\packages'
Added package 'Antlr.3.4.1.9004' to 'packages.config'
Successfully installed 'Antlr 3.4.1.9004' to DemoApp
...
More package installs here. Omitted for brevity...
...
Package 'Microsoft.Web.Infrastructure.1.0.0' already exists in folder 'D:\Projects\Lense.Mvc5\packages'
Added package 'Microsoft.Web.Infrastructure.1.0.0' to 'packages.config'
Successfully installed 'Microsoft.Web.Infrastructure 1.0.0' to MvcLenseApp
...
More package installs here. Omitted for brevity...
...
Package 'WebGrease.1.5.2' already exists in folder 'D:\Projects\DemoApp\packages'
Added package 'WebGrease.1.5.2' to 'packages.config'
Executing script file 'D:\Projects\DemoApp\packages\WebGrease.1.5.2\tools\install.ps1'
Successfully installed 'WebGrease 1.5.2' to DemoApp
Package 'Microsoft.AspNet.Web.Optimization.1.1.3' already exists in folder 'D:\Projects\DemoApp\packages'
Added package 'Microsoft.AspNet.Web.Optimization.1.1.3' to 'packages.config'
...
End of package re-install. 
...
Successfully installed 'Microsoft.AspNet.Web.Optimization 1.1.3' to DemoApp
PM> 

Of course if you wish to reinstall all packages you may need to get familiar with update/install commands in NuGet here and here.