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Operator
Welcome to the Acorda Therapeutics Third Quarter 2020 Financial and Business Update. (Operator Instructions) Please be advised that this call is being taped at the company's request.
I will now introduce your host for today's call, Tierney Saccavino, Executive Vice President, Corporate Communications at Acorda. Please go ahead.
Tierney Saccavino - EVP of Corporate Communications
Thank you. Good afternoon, everyone.
Before we begin, let me remind you that our presentation will contain forward-looking statements. Detailed disclosures can be found in our SEC filings, which are public, and we encourage you to refer to those filings.
I'll now pass the call over to our CEO, Ron Cohen. Ron?
Ron Cohen - Founder, CEO, President & Director
Thanks, Tierney, and welcome, everyone. INBRIJA sales increased by 24% in the third quarter over the second quarter to $5.8 million. We're particularly encouraged by this, especially given the impact of COVID-19. AMPYRA net revenue for the third quarter was $27.3 million that was a 5% increase over the second quarter, and AMPYRA revenue continues to be consistent with our internal projections. Physicians and patients maintain a high degree of brand loyalty, and Acorda continues to offer co-pay mitigation and a free 60-day trial to those patients who are eligible.
In addition, we received a $15 million milestone payment from Biogen related to sales of FAMPYRA outside the U.S. As a reminder, INBRIJA is inhaled levodopa. Levodopa is the gold standard therapy for improving symptoms of Parkinson's and INBRIJA has indicated to address the return of symptoms, also known as OFF periods, as needed.
The COVID-19 pandemic has had an impact on our business as people with Parkinson's and other at-risk populations, have reduced their physician visits and delayed routine care. We saw a recovery of new prescriptions from late April through July, then we actually saw a dip in new prescriptions in the late summer, followed by a resumed upward trajectory from late September to the present.
Physicians' offices and patients have been adapting to the pandemic over time, although much of the country has now been experiencing a second wave of infections. Notwithstanding these factors, we're seeing an encouraging momentum in INBRIJA's trajectory. And we believe that the initiatives that we've introduced during the year are having a positive impact.
INBRIJA net sales have increased 34% over the first quarter and the number of cartons ship increased 24% over the first quarter. We're also pleased that persistency remains high among patients who use INBRIJA at least every other day on average. With about 70% continuing on therapy at 12 months.
We also continued to make progress on patient access to INBRIJA. During the third quarter, access without medical exception reached 96% of all commercially insured patients. That was a 28% increase over the first quarter. And over 2,300 neurologists have prescribed INBRIJA, that's a 12% increase over the first quarter.
We also launched a telemedicine program during the quarter giving people with Parkinson's an important new option to consult with a physician if they're uncomfortable with an in-person visit. And the early response to this offering has been encouraging.
Moving to our third quarter 2020 financial performance. This slide outlines key financials for the third quarter and year-to-date, which you'll find addressed in detail in our press release. We ended the third quarter with cash, cash equivalents, investments and restricted cash of $101.3 million. Note that as we previously reported, in July, we received a $12.7 million tax refund under the CARES Act, which allowed us to carry back 2019 net operating losses to prior tax years, resulting in the refund. This amount is included in our quarter end cash balance.
Additionally, as I mentioned earlier, in the third quarter, we achieved a milestone payment of $15 million from Biogen. The payment was received in October, therefore, it is not included in our quarter end cash balance reported today, but it is recorded as a milestone revenue in our Q3 financials.
So in summary, our teams have adapted to the challenges imposed by COVID-19, and we've been seeing significant progress for INBRIJA across multiple fronts. Our top priorities are to accelerate INBRIJA's growth using all the strategies we've reviewed here and in previous calls, to support AMPYRA as it generates valuable cash and is still an important medication for the MS community and to optimize our cost structure and strengthen our balance sheet to drive long-term value for shareholders. The $15 million milestone payment we received from Biogen and AMPYRA's performance further strengthen our financial position.
One of our key initiatives is to monetize the excess capacity of our Chelsea manufacturing facility, which would offset expenses and reduce our cost of goods. We believe that this, in turn, would help to facilitate ex U.S. partnerships for INBRIJA. We are in active discussions now for both the manufacturing and ex U.S. partnering initiatives.
And now I'll open the line for your questions. Operator?
Operator
(Operator Instructions) Your first question conference from the line of Philip Nadeau from Cowen and Company.
Philip M. Nadeau - MD & Senior Research Analyst
First one on coverage. Ron, you mentioned the commercial lives covered, which was an impressive increase over the quarter. Where are you with Medicare lives covered? And do you have any sense as to how that could transition after January 1 when the new plans go into effect?
Ron Cohen - Founder, CEO, President & Director
Yes. Well, thanks, Phil. So far, we are maintaining 25% of covered lives that have access without medical exception. But there's been a, I think, pretty significant decrease in the numbers of Medicare lives that are blocked from access. So beginning of 2020, we were at about 38% blocked, and we're now at about 15%.
So what that means, obviously, is if a physician is willing to write the medical exception, and we do encourage them and educate them about that and so on, the patient can get the medication. So that has been real progress. We are bidding next year. So far, we're still at 25% of covered lives. But as I said, it's not we have improved the situation quite significantly. And I would say about half of the people who are getting INBRIJA are on Medicare.
Philip M. Nadeau - MD & Senior Research Analyst
Perfect. And then I guess the follow-up is in terms of visits to physicians offices, most of the neurology companies we cover report that the in-person visits of patients is way down. Some are suggesting it's about 60% of pre-COVID levels. But of course, no one's seeing the growth that you're seeing. So I guess how -- what are you seeing with the physicians office? Are patients not going in? And how are you overcoming that to grow INBRIJA like you did in the quarter?
Ron Cohen - Founder, CEO, President & Director
Yes. Let me just go back just for a second. There was something else, I had in my back of my mind to say, the other thing about the Medicare issue is, we haven't heard back on all of our responses to the RFPs yet, the request for proposals. So we expect over the next couple of months, we'll have clarity on what the situation looks like for 2021 and whether we'll be able to improve that 25% number. So we're not there yet. We're still waiting to get a lot of the information. Okay.
Philip M. Nadeau - MD & Senior Research Analyst
Got it. Okay.
Ron Cohen - Founder, CEO, President & Director
And then with regard to the visit to offices, the last good information we have, which is external surveys that were done, really goes back to the spring, late spring, early summer when there was about an 80% drop in -- certainly in neurology. There was about an 80% drop in physician visits. So that was pretty dramatic. We don't have any solid updates on that survey. So we're basing it on what our team is doing.
And what we're finding is it is quite variable across the country. There are certain places where visits have clearly increased beyond the 30% or 35% that those numbers would imply or 20% of that would imply. There are other places where they did open up, and then as COVID took off in those regions again, they started shutting down again. So it's all over the map. What I can tell you that what our team did early on was talk to all of their offices and a range to speak to the doctors and the staff by phone, by video, and in other ways, support them, most of those offices have adapted to telemedicine to a degree.
It's certainly not 100%. It's not replacing a 100% of the visits that they lost. But they've come up, I would say, significantly since March, April, May, for sure. How much they've come up? I think it depends on what part of the country you're talking about. We don't have a really solid handle on those numbers.
What we can say is that our trajectory of new prescriptions has gone up by and large, with the exception of the dip, I talked about in the late summer. That was August, early September. We're not sure whether that was COVID-related or vacation-related or something else. But it then resumed in September through October, and we're continuing to see an upward trajectory.
So all that tells us that the docs have adapted, they are seeing a lot more patients than they did before. It's almost certainly not back to normal in terms of volume, but it's enough that we're able, at least with INBRIJA, to see an upward trajectory.
Operator
(Operator Instructions) And there are no further questions at this time. Dr. Cohen, I turn the call back over to you.
Ron Cohen - Founder, CEO, President & Director
All right. Thank you, operator, and thank you, everyone. That concludes our call, and we look forward to updating you again next quarter. Have a great election day. Bye for now.
Operator
Ladies and gentlemen, this concludes today's conference call. Thank you for participating. You may now disconnect.