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Does altering the DOM with JavaScript/jQuery mess with accessibility?

I'm trying to figure out if altering the DOM of a website will present any accessibility problems. I am placing all of the jQuery in a $(document).ready() function. Will this cause any accessibility issues with the altered elements?
We don't have access to the theme template HTML files, only CSS and JS files. So for example I'm adding a div into our theme using$('[element name]').before('<div>[div content here]</div>') will this content be as accessible as the rest of the DOM as long as I include all the appropriate aria attributes etc.?

In theory, you shouldn't rely on JavaScript to produce the whole HTML code of your site, it's basically a bad practice.
However, it's exactly how big frameworks like angular and react work.
Given that 99% of browsers support JavaScript, it's in fact no longer a problem nowadays.
The true answer is in fact both yes and no, it depends. It depends on the actual HTML code injected.
The key point is that, you must have the same care with generated code as with the code directly written in HTML by hand, i.e. be careful on headings, form labels, alt texts, ARIA attributes if you need them, etc. all the time and in particular each time you add/remove something in the DOM. Additionally, you must pay attention to where the focus is or might be and a few other things.
It's often overlooked precisely because some people assume that it's anyway not accessible, what isn't true.
In order to be accessible, a site with dynamic contents must be accessible at any moment. If it isn't always the case, then you will lose users in need of accessibility at some point. In practice the loss of accessibility often happens at the most critical moment: checkout or paiement, maybe not because of your fault if the paiement site isn't accessible.

You might even improve accessibility by manipulating the DOM via JavaScript (JS). So no, per se, manipulating the DOM does not pose accessibility issues.
If you cannot control the HTML, and the theme is badly accessible, all you can do to improve that is using JavaScript. Think adding role attributes to generic <div> elements. Also, CSS-only solutions seem appealing, but are often not exposing the appropriate state via ARIA-attributes to assistive technology, which needs to be corrected via JS.
Whether your manipulations produce problems or improve accessibility, therefore depends strongly on your implementation.
Here are some examples.
Adding or Removing Content
When adding content, like in your example, it depends on where that content is added in the document, and at which moment.
If it’s being added on DOM Ready, there should be no issue (One exception might be live regions added after the DOM loaded). But if it’s being added at arbitrary moments, it’s problematic.
The Web Content Accessibility Guidelines (WCAG) refer to this as a Change of Context, which must not happen on focus, on input and on user request
See A change of content is not always a change of context. Changes in content, such as an expanding outline, dynamic menu, or a tab control do not necessarily change the context, unless they also change one of the above (e.g., focus).
If it’s being added after DOM Ready, it should happen on user request, or must be a status message and carry the appropriate role to be announced.
For example, in a Disclosure pattern, the aria-expanded of the trigger indicates that new content will become accessible right after the trigger on pressing it. It might just be added to the DOM, depending on the implementation.
Lazy Loading Content
Another, very valid use case would be content that’s added asynchronously. This is tricky to get right, but basically aria-busy can render this more accessible.

Using new window instead of web-workers

Since I've tried out webworkers for the first time I'm struggling to find a real use case for them. Communication with them isn't as easy as just passing objects or references, they don't have a window object so I can't use JQuery and the increased complexity of building an interface is not worth the load saved on the main thread. So all the options I'm left with are basically working through large arrays to gain a performance advantage.
Today I thought about opening a new window by window.open() and use the newly created window object to do some task and pass the result back to the main window. I should even be able to access the DOM of the main window by accessing the window.openervariable in the new window.
My questions are:
Is that really going to give me a performance advantage?
Are there any caveats about this idea besides more complicated debugging?
Can I access the DOM of the main window from the new window using the window.opener variable and take the load of creating new DOM elements from the main thread?

Is that really going to give me a performance advantage?
No, as long as you can access window.opener or access objects from one tab to another, that means they share same instance of javascript interpreter, and javascript interpreter is single-threaded.
There is literally no (practical) way around this. You either have separate thread, or share same objects.
Are there any caveats about this idea besides more complicated debugging?
Main caveat: it does not work. Also caveat: separate window is probably not something suitable for production.
Can I access the DOM of the main window from the new window using the window.opener variable and take the load of creating new DOM elements from the main thread?
You can, but you should probably use correct document instance for calling document.createElement.
So all the options I'm left with are basically working through large arrays to gain a performance advantage.
That's exactly what workers are for, unless you are processing large amount of raw data, they are probably not a solution to your problem.
If you have performance drops when creating DOM nodes, you're most likely doing something wrong. Remember that:
createDocumentFragment exists for creating self contained element groups before appending them.
innerHTML causes DOM to rebalance tree in which you cahnged the HTML
new Text or document.createTextNode can be used to fill in text without innerHTML
If your page is scrollable table of many items, only those on screen need to be rendered.
You should also profile your code using developper tools to see where is the performance bottleneck. WebWorker is for data processing (eg. resizing images before upload), not for DOM manipulation.
Final note: it's the end of 2019, "I can't use jQuery" shouldn't be a problem any more. We now have document.querySelector and CSS animations, which were main uses of jQuery in the past.

make single-page web app perform faster

I have a single-page web app (actually, its PhoneGap).
It has a lot of different 'pages' or screens - about 30 now.
The issue is if each page has loaded some content (complex element lists, sometimes hundreds of items long), the app starts to bog down and become very slow, as all the html is present, even if hidden.
I was thinking that if between pages changes i store the HTML for the content in a variable, to be called and put back in the DOM when a user wants to go back to that page, will this make other pages faster than leaving everything in the DOM? So basically I only have 1 full page in the html at a time.
Just wanted to ask before i spent time doing it! any other links for fast web apps would be appreciated too

You may need to remove the useless DOMs to release the memory.
Actually, when you realize your page (or App) is going slower and slower, you should pay attention on the memory.
Remove all useless DOMs would be a smart choice on your case. Next time, you need to show it again, you can re-initialize it.
Sometimes, you may also need to remove useless js objects, unbind events, etc.

Notify screen reader a page changed [duplicate]

Imagine you have a simple, single-page application - regardless of whether it was written using Backbone, Angular, Ember or anything else.
How can you tell a screen reader that we've changed 'page' when a route is followed?
In a classic application, when I navigate from /index.html to /about.html the screen reader obviously detects the page change, and re-reads as you'd expect.
In my Backbone application though, when I follow a route I cannot work out how to trigger a 're-read'. I've tried triggering a focus event which I'd seen somewhere, but that doesn't seem to work.
Note: I'm currently testing with NVDA/Chrome.

Overall, you should not need to trigger a 're-read', and depending on your UI that might not be a good thing anyway.
My experience has been with angular.js (as an accessibility person rather than the developer), and our overall approach was to manage the focus rather than trigger a re-read. (We do extensive accessibility testing.)
The key thing from a UI point of view (primarily for screen reader users) is that selecting a link (e.g. about.html) should take you somewhere.
In this case the appropriate place to put the focus would be the top of the content area of the about 'page', hopefully an <h1>.
In order for that to work the target element should be focusable via a script, so probably needs tabindex unless it is a link or form control:
<h1 id="test" tabindex="-1">
The -1 means it is not in the default tab order, but is focusable via a script. See more at WAI-ARIA authoring practices.
Then at the end of the function that loads the new content, including the tabindex attribute, add something like:
$('#test').attr('tabindex', '-1').css('outline', 'none');
$('#test').focus();
When adding tabindex dynamically it is best to do so in a line before the focus() function otherwise it may not work (I remember that from testing with JAWS).
To test this I would use either:
NVDA & Firefox, Windows
Jaws & IE, Windows
It is also good to test with VoiceOver on Safari/OSX, but that works differently and may not hit the same issues as a windows based screen reader.
You will hit a lot of issues with Chrome/NVDA as that is not supported very well, and end-users are very unlikely to use that. IE is ok with NVDA, but Firefox is best.
Overall, it is worth getting to know the WAI-ARIA authoring practices, particularly Using ARIA in HTML. Even though you are using a JS app, the browser (and therefore screen reader) is interpreting the resulting HTML so that advice is still relevant.
Lastly, if you are updating page content without the user pressing space/enter to activate something, you might find that JAWS/NVDA do not know about the new content as their 'virtual buffer' has not updated. In that case, you might need to add a JS shim to make them update, but only do that if you run into problems in testing, it should not be a global patch.

Taking the answer from #AlastairC, and the comments below it. I've taken this a bit further now and am going with this as my solution going forward:
My go-forward solution
I found that just reading out the first heading wasn't really that useful. Especially if the last page you were on was a loading sequence. You can hear that there something new has been focused, but it's certainly not clear that this forms the part of a whole now page.
Add some useful, descriptive text to the page
As such I now have a single paragraph at the top of my page layout template. This includes a screen-reader friendly message, along with a very rough overview of what the page.
<p class="screenreader-summary" tabindex="-1">
The <strong>Dashboard</strong> page is now on-screen.
It contains several widgets for summarizing your data.
</p>
Note that the tabindex value allows us to focus this element with JavaScript. You might not want to use a p element for this, you can use anything you like really.
Hide it off-screen (optional, only required if it would break your design/readability)
This is then coupled with CSS to move this element off-screen:
.screenreader-summary {
position: absolute;
left:-10000px;
top:auto;
width:1px;
height:1px;
overflow:hidden;
outline: none; /* Important, don't show an outline on-focus */
}
Focus this element, when a new page is shown on-screen
Finally, in the JavaScript code that shows your page on screen (e.g. in MarionetteJS using onShow or the show event):
$yourViewEl.find('.screenreader-summary').focus();
The result
I'm a sighted person, so take what I say with a pinch of salt - however I found that reading out a short description is so much more useful.

For angular the url changes, If someone REALLY needs to reread everything, (like me because of requirements), what did the trick for us was this:
$(window).on('hashchange', function () {
location.reload();
});
and we just added extra code to handle pages like "success" were no reloads are supposed to happen.
this simulates the actual page loading, and screen readers will read it normally like a page change.
kind of defeats the purpose of angular in a way, but this will help people like me who already have the application, and want a quick fix.

How much content being replaced with an AJAX call is too much?

I run into a common problem when trying to do AJAX development. Where possible, I like to try and just update data in an existing layout, and not the layout itself. For example, take the div below:
<div id="content-5">Here is some content</div>
I would get the updated value for content-5 from the server and just replace the contents of content-5 with the value. This makes a lot of sense for simple data replacements where the value is always going to be displayed in its pure form.
Sometimes the content is more complicated, and I have to actually get more than just raw data... maybe there is some logic to determine how a value is displayed and perhaps the style needs to be different depending on the data inside. In that case, I generally produce the HTML on the server side and inject the HTML into the element instead of just raw data.
Example: A status field from the controller comes back as "complete", but from the design doc, "complete" is supposed to show the user the text "Available" and it needs to be styled in a way different from other statuses.
Doing this in Javascript would require some in-depth view knowledge that the template layer probably already handles. The end result would be the same (code snippet below), but the difference is that there could possibly be some code duplication and a far more complicated Javascript layer.
<div id="content-5"><span class="success">Available</span></div>
Without fail, the requirement comes up that the system will need to handle "new" contents as well. The easiest solution to implement is to just get all of the content's at the same time so that I do not need to handle the extra complexity of injecting a new element instead of just replacing existing content.
So, I create a new template, wrap the contents in another element with an ID, and bulk replace all of the content divs at the same time any time there is a change.
<div id="allContent">
<div id="content-1">Some content A</div>
<div id="content-2">Some content B</div>
<div id="content-3">Some content C</div>
<div id="content-4">Some content D</div>
<div id="content-5">Some content E</div>
</div>
At some point, I have to wonder: Where is the line? At some point it feels like I'll eventually just be replacing the whole page with an AJAX request. Would this really be a problem?
I realize this may be pretty subjective, but what are some good strategies for determining to which level you should be replacing content with AJAX? Replacing just the data seems to be my preferred method when possible as it makes the AJAX controllers very simple. Replacing larger chunks of HTML from a template seems to be the easiest for handling more complicating layout and design issues and also feels like it could be more easily maintained. Are there other options I have not considered?
I expect there will be some discussion about manipulating the DOM programatically, but I personally really dislike this. The code ends up looking pretty horrible and really starts to integrate too much layout and design into the JS layer for my liking. Since I generally work with template libraries of some sort (whether raw PHP, PHP templates like Smarty or JSP in Java) it seems to make more sense to leave as much visual design there as possible.
EDIT
Based on the first few answers, it seems like this is being read as trying to keep the user on the same page but navigating around around the site or otherwise changing the page in a radical way with each update. The question is more about how to determine where the layout work for AJAX calls should happen and whether or not it is an acceptable practice to change large chunks of code with an AJAX request, knowing that replacement code may look nearly identical to what had been there before.

I think the most important requirement is the refresh requirement. If after several AJAX updates I hit refresh, the page I was just looking at should be the page that arrives. If the page reverts to a previous state for any reason then the URL is wrong. If for any reason your AJAX data is going to make the URL in the browser invalid then you should not be using AJAX to fetch that data.
There are exceptions, of course for data the is even newer than the last AJAX request. But that's obviously not what I'm talking about. A live chat screen could receive an update between the last AJAX request and the refresh. No big deal. I'm talking about the logical content and the URL describing it should always be in sync.

Complete personal opinion ex nihil, my rule of thumb is to change no more than 1 "panel" unit or 33% of the page whichever is less.
The basis for this is that the user should be able to clearly recognise the previous page state is related to the new state - how would you feel if you were suddenly teleported into the building to your right? Be gentle with your poor user.
There are also serious technical questions about the benefits of moving and inserting basically a page worth of data, which I think is a bit of an AJAX anti-pattern. What benefit does AJAX provide if you're going to do that?
Your specific question seems dependant on the supposition that the response coming back from your AJAX request isn't "just" data. This feels wrong to me from a separation of concerns point of view: I would expect a page to have all the layout information it requires already, the AJAX response itself to provide nothing more than dumb data/markup, and the JS event handler which created the request to sew the two together, MVC style. In that respect I think, yes, you're doing too much.
(by panel, I mean one logical design element - a menu, a ribbon, an item metadata panel, etc..)
edit: now that I think about it, I think SO's user profile page breaks my rule of thumb with those tab clicks

Depending on whether you want people to be able to to link to / bookmark etc the current page, you might want to navigate the user's browser.
This isn't a concern for some apps like GMail etc, and they won't ever refresh the page.
For myself, I tend to think it's a good practice to navigate the browser when navigating to a logically different place. eg. a person's profile vs. a list of their messages.
Sorry if this is vague, it's rather subjective :-)

A good guideline for something like this is to ask yourself, "Is this dynamic application 'content', or is it content-content?" Your use case sounds like application content that will change with each user. This is probably the best place for Ajax, but with everything, it's always nice not to just have one hammer. You don't want to do too much on one page. For instance, if one part breaks, the entire thing might, thereby frustrating the user.
Anywhere you're looking at actual page content or anything where the information is static, I strongly suggest avoiding the use of JavaScript, as it runs the risk of being invisible to search engines. Make sure anything linking to information like this is crawlable. The first step towards this is dynamic generation on the server side rather than browser side.

If you're using Smarty templates to produce a page, just fragment a template into various meaningful sections - news.tpl, email.tpl, weather.tpl - and have a master.tpl producing the structure of the page and calling child templates.
Then, if you're for example using an AJAX call triggered by a timeout to refresh the news, you can just call the server, cram the necessary data into news.tpl, and return the results into the news div you set up with master.tpl. This way your news layout is always following the pattern of news.tpl. (If you used JavaScript to manipulate formatting bits or set up event handling on document load, you'll need to attach that post-processing to fire after the AJAX call.)
You haven't really gotten specific about the types of things you're trying to replace here, and my initial reaction is that, if a single event is triggering multiple sections of the page to update at once, that's a sign that maybe you should be coallating those sections into a single display.
How much formatting gets done on the server end versus how much gets done on the client end with JavaScript? I'd say server-side formatting if possible, that way you have code that reflects discussions you've made about display layout and logic. Client-side formatting can be used for more interface-based issues - sorting rows in a table and alternating row colors with :odd and :even selectors, showing and hiding divs to create a "tabbed display" without hitting the server since the data won't change just from selecting a new tab, that sort of thing.
Finally, AJAX is one-way. If your web page is a view on a database, this isn't as much of a problem, but using AJAX manipulation to take the place of normal navigation is a terrible idea.

If you were habitually replacing the entire contents of a page using AJAX calls, I would agree that you have a problem. However, it appears to me that you are attempting to carefully think through the implications of your design and attempting, where possible, to avoid what annakata has called this "AJAX anti-pattern."
My rule is a bit simpler: as long as a substantial amount of context (e.g. menu on the left, header, various controls, page title, etc.) remains on a page, I am Ok with replacing almost anything with an AJAX call. That being said, I've never struggled with a page that has as much AJAX-generated code as you are.
I do have one question though: isn't it possible to encode state so that you can just replace some of the Divs in your example rather than all of them? If not, have you thought about doing so?